U.S. patent application number 16/145859 was filed with the patent office on 2019-04-04 for non-human animals comprising a humanized ttr locus and methods of use.
The applicant listed for this patent is Regeneron Pharmaceuticals, Inc.. Invention is credited to Meghan Drummond-Samuelson, David Frendewey, Jeffery Haines, Suzanne Hartford, Andrew J. Murphy, Brian Zambrowicz.
Application Number | 20190098879 16/145859 |
Document ID | / |
Family ID | 63858215 |
Filed Date | 2019-04-04 |
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United States Patent
Application |
20190098879 |
Kind Code |
A1 |
Drummond-Samuelson; Meghan ;
et al. |
April 4, 2019 |
Non-Human Animals Comprising A Humanized TTR Locus And Methods Of
Use
Abstract
Non-human animal genomes, non-human animal cells, and non-human
animals comprising a humanized TTR locus and methods of using such
non-human animal genomes, non-human animal cells, and non-human
animals are provided. Non-human animal cells or non-human animals
comprising a humanized TTR locus express a human transthyretin
protein or a chimeric transthyretin protein, fragments of which are
from human transthyretin. Methods are provided for using such
non-human animals comprising a humanized TTR locus to assess in
vivo efficacy of human-TTR-targeting reagents such as nuclease
agents designed to target human TTR. Methods are also provided for
making such non-human animals comprising a humanized TTR locus.
Inventors: |
Drummond-Samuelson; Meghan;
(Katonah, NY) ; Haines; Jeffery; (New York,
NY) ; Hartford; Suzanne; (Putnam Valley, NY) ;
Frendewey; David; (New York, NY) ; Zambrowicz;
Brian; (Sleepy Hollow, NY) ; Murphy; Andrew J.;
(Croton-on-Hudson, NY) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Regeneron Pharmaceuticals, Inc. |
Tarrytown |
NY |
US |
|
|
Family ID: |
63858215 |
Appl. No.: |
16/145859 |
Filed: |
September 28, 2018 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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62720292 |
Aug 21, 2018 |
|
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|
62679142 |
Jun 1, 2018 |
|
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62565980 |
Sep 29, 2017 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12N 2310/20 20170501;
A01K 2217/058 20130101; C12N 2710/10041 20130101; A01K 2207/15
20130101; A01K 2227/105 20130101; A01K 2267/0306 20130101; A61K
48/0041 20130101; A01K 2217/072 20130101; C07K 14/47 20130101; C12N
15/113 20130101; A01K 67/0275 20130101; C12N 15/86 20130101; A01K
67/0278 20130101; C07K 2319/02 20130101 |
International
Class: |
A01K 67/027 20060101
A01K067/027; C12N 15/86 20060101 C12N015/86 |
Claims
1. A non-human animal comprising in its genome a genetically
modified endogenous Ttr locus comprising a human TTR sequence
comprising both TTR coding sequence and non-coding sequence.
2. The non-human animal of claim 1, wherein a region of the
endogenous Ttr locus comprising both Ttr coding sequence and
non-coding sequence has been deleted and replaced with a
corresponding human TTR sequence comprising both TTR coding
sequence and non-coding sequence.
3. The non-human animal of claim 1, wherein the genetically
modified endogenous Ttr locus comprises the endogenous Ttr
promoter, wherein the human TTR sequence is operably linked to the
endogenous Ttr promoter.
4. The non-human animal of claim 1, wherein at least one intron and
at least one exon of the endogenous Ttr locus have been deleted and
replaced with the corresponding human TTR sequence.
5. The non-human animal of claim 1, wherein the entire Ttr coding
sequence of the endogenous Ttr locus has been deleted and replaced
with the corresponding human TTR sequence.
6. The non-human animal of claim 5, wherein the region of the
endogenous Ttr locus from the Ttr start codon to the Ttr stop codon
has been deleted and replaced with the corresponding human TTR
sequence.
7. The non-human animal of claim 1, wherein the genetically
modified endogenous Ttr locus comprises a human TTR 3' untranslated
region.
8. The non-human animal of claim 1, wherein the endogenous Ttr 5'
untranslated region has not been deleted and replaced with the
corresponding human TTR sequence.
9. The non-human animal of claim 1, wherein the region of the
endogenous Ttr locus from the Ttr start codon to the Ttr stop codon
has been deleted and replaced with a human TTR sequence comprising
the corresponding human TTR sequence and a human TTR 3'
untranslated region, and wherein the endogenous Ttr 5' untranslated
region has not been deleted and replaced with the corresponding
human TTR sequence, and wherein the endogenous Ttr promoter has not
been deleted and replaced with the corresponding human TTR
sequence.
10. The non-human animal of claim 9, wherein: (i) the human TTR
sequence at the genetically modified endogenous Ttr locus comprises
a sequence at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical
to the sequence set forth in SEQ ID NO: 18; or (ii) the genetically
modified endogenous Ttr locus encodes a protein comprising a
sequence at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical
to the sequence set forth in SEQ ID NO: 1; (iii) the genetically
modified endogenous Ttr locus comprises a coding sequence
comprising a sequence at least 90%, 95%, 96%, 97%, 98%, 99%, or
100% identical to the sequence set forth in SEQ ID NO: 90; or (iv)
the genetically modified endogenous Ttr locus comprises a sequence
at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the
sequence set forth in SEQ ID NO: 14 or 15.
11. The non-human animal of claim 1, wherein the genetically
modified endogenous Ttr locus encodes a transthyretin precursor
protein comprising a signal peptide, and the region of the
endogenous Ttr locus encoding the signal peptide has not been
deleted and replaced with the corresponding human TTR sequence.
12. The non-human animal of claim 11, wherein the first exon of the
endogenous Ttr locus has not been deleted and replaced with the
corresponding human TTR sequence.
13. The non-human animal of claim 12, wherein the first exon and
first intron of the endogenous Ttr locus have not been deleted and
replaced with the corresponding human TTR sequence.
14. The non-human animal of claim 11, wherein the region of the
endogenous Ttr locus from the start of the second Ttr exon to the
Ttr stop codon has been deleted and replaced with the corresponding
human TTR sequence.
15. The non-human animal of claim 11, wherein the genetically
modified endogenous Ttr locus comprises a human TTR 3' untranslated
region.
16. The non-human animal of claim 11, wherein the region of the
endogenous Ttr locus from the second Ttr exon to the Ttr stop codon
has been deleted and replaced with a human TTR sequence comprising
the corresponding human TTR sequence and a human TTR 3'
untranslated region, and wherein the endogenous Ttr 5' untranslated
region has not been deleted and replaced with the corresponding
human TTR sequence, and wherein the endogenous Ttr promoter has not
been deleted and replaced with the corresponding human TTR
sequence.
17. The non-human animal of claim 16, wherein: (i) the human TTR
sequence at the genetically modified endogenous Ttr locus comprises
a sequence at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical
to the sequence set forth in SEQ ID NO: 19; or (ii) the genetically
modified endogenous Ttr locus encodes a protein comprising a
sequence at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical
to the sequence set forth in SEQ ID NO: 2; (iii) the genetically
modified endogenous Ttr locus comprises a coding sequence
comprising a sequence at least 90%, 95%, 96%, 97%, 98%, 99%, or
100% identical to the sequence set forth in SEQ ID NO: 91; or (iv)
the genetically modified endogenous Ttr locus comprises a sequence
at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the
sequence set forth in SEQ ID NO: 16 or 17.
18. The non-human animal of claim 1, wherein the genetically
modified endogenous Ttr locus does not comprise a selection
cassette or a reporter gene.
19. The non-human animal of claim 1, wherein the non-human animal
is homozygous for the genetically modified endogenous Ttr
locus.
20. The non-human animal of claim 1, wherein the non-human animal
is a mammal.
21. The non-human animal of claim 20, wherein the non-human animal
is a rat or mouse.
22. The non-human animal of claim 21, wherein the non-human animal
is a mouse.
23. A method of assessing the activity of a human-TTR-targeting
reagent in vivo, comprising: (a) administering the
human-TTR-targeting reagent to the non-human animal of claim 1; and
(b) assessing the activity of the human-TTR-targeting reagent in
the non-human animal.
24.-40. (canceled)
41. A method of optimizing the activity of a human-TTR-targeting
reagent in vivo, comprising: (I) performing the method of claim 23a
first time in a first non-human animal comprising in its genome a
genetically modified endogenous Ttr locus comprising a human TTR
sequence comprising both TTR coding sequence and non-coding
sequence; (II) changing a variable and performing the method of
step (I) a second time with the changed variable in a second
non-human animal comprising in its genome the genetically modified
endogenous Ttr locus comprising the human TTR sequence comprising
both TTR coding sequence and non-coding sequence; and (III)
comparing the activity of the human-TTR-targeting reagent in step
(I) with the activity of the human-TTR-targeting reagent in step
(II), and selecting the method resulting in the higher
activity.
42.-51. (canceled)
52. A method of making the non-human animal of claim 1, comprising:
(a) introducing into a non-human animal embryonic stem (ES) cell:
(i) a nuclease agent that targets a target sequence in the
endogenous Ttr locus; and (ii) a targeting vector comprising a
nucleic acid insert comprising the human TTR sequence flanked by a
5' homology arm corresponding to a 5' target sequence in the
endogenous Ttr locus and a 3' homology arm corresponding to a 3'
target sequence in the endogenous Ttr locus, wherein the targeting
vector recombines with the endogenous Ttr locus to produce a
genetically modified non-human ES cell comprising in its genome the
genetically modified endogenous Ttr locus comprising the human TTR
sequence; (b) introducing the genetically modified non-human ES
cell into a non-human animal host embryo; and (c) gestating the
non-human animal host embryo in a surrogate mother, wherein the
surrogate mother produces an F0 progeny genetically modified
non-human animal comprising in its genome the genetically modified
endogenous Ttr locus comprising the human TTR sequence.
53.-57. (canceled)
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of U.S. Application No.
62/565,980 filed Sep. 29, 2017, U.S. Application No. 62/679,142
filed Jun. 1, 2018, and U.S. Application No. 62/720,292 filed Aug.
21, 2018, each of which is herein incorporated by reference in its
entirety for all purposes.
REFERENCE TO A SEQUENCE LISTING SUBMITTED AS A TEXT FILE VIA EFS
WEB
[0002] The Sequence Listing written in file 519829SEQLIST.txt is
139 kilobytes, was created on Sep. 28, 2018, and is hereby
incorporated by reference.
BACKGROUND
[0003] Transthyretin (TTR) is a protein found in the serum and
cerebrospinal fluid that carries thyroid hormone and
retinol-binding protein to retinol. The liver secretes TTR into the
blood, while the choroid plexus secretes it into the cerebrospinal
fluid. TTR is also produced in the retinal pigmented epithelium and
secreted into the vitreous. Misfolded and aggregated TTR
accumulates in multiple tissues and organs in the amyloid diseases
senile systemic amyloidosis (SSA), familial amyloid polyneuropathy
(FAP), and familial amyloid cardiomyopathy (FAC).
[0004] One promising therapeutic approach for the TTR amyloidosis
diseases is to reduce the TTR load in the patient. However, there
remains a need for suitable non-human animals providing the true
human target or a close approximation of the true human target of
human-TTR-targeting reagents at the endogenous Ttr locus, thereby
enabling testing of the efficacy and mode of action of such agents
in live animals as well as pharmacokinetic and pharmacodynamics
studies in a setting where the humanized protein and humanized gene
are the only version of TTR present.
SUMMARY
[0005] Non-human animals comprising a humanized TTR locus are
provided, as well as methods of using such non-human animals.
Non-human animal genomes or cells comprising a humanized TTR locus
are also provided.
[0006] In one aspect, provided are non-human animal genomes,
non-human animal cells, or non-human animals comprising a humanized
TTR locus. Such a non-human animal genome, non-human animal cell,
or non-human animal can comprise in its genome a genetically
modified endogenous Ttr locus comprising a human TTR sequence
comprising both TTR coding sequence and non-coding sequence. Some
such non-human animal genomes, non-human animal cells, or non-human
animals can comprise a genetically modified endogenous Ttr locus,
wherein a region of the endogenous Ttr locus comprising both Ttr
coding sequence and non-coding sequence has been deleted and
replaced with a corresponding human TTR sequence comprising both
TTR coding sequence and non-coding sequence. Optionally, the
genetically modified endogenous Ttr locus comprises the endogenous
Ttr promoter. Optionally, the human TTR sequence is operably linked
to the endogenous Ttr promoter. Optionally, at least one intron and
at least one exon of the endogenous Ttr locus have been deleted and
replaced with the corresponding human TTR sequence.
[0007] In some such non-human animal genomes, non-human animal
cells, or non-human animals, the entire Ttr coding sequence of the
endogenous Ttr locus has been deleted and replaced with the
corresponding human TTR sequence. Optionally, the region of the
endogenous Ttr locus from the Ttr start codon to the Ttr stop codon
has been deleted and replaced with the corresponding human TTR
sequence.
[0008] In some such non-human animal genomes, non-human animal
cells, or non-human animals, the genetically modified endogenous
Ttr locus comprises a human TTR 3' untranslated region. In some
such non-human animals, the endogenous Ttr 5' untranslated region
has not been deleted and replaced with the corresponding human TTR
sequence.
[0009] In some such non-human animal genomes, non-human animal
cells, or non-human animals, the region of the endogenous Ttr locus
from the Ttr start codon to the Ttr stop codon has been deleted and
replaced with a human TTR sequence comprising the corresponding
human TTR sequence and a human TTR 3' untranslated region, and the
endogenous Ttr 5' untranslated region has not been deleted and
replaced with the corresponding human TTR sequence, and the
endogenous Ttr promoter has not been deleted and replaced with the
corresponding human TTR sequence. Optionally, the human TTR
sequence at the genetically modified endogenous Ttr locus
comprises, consists essentially of, or consists of a sequence at
least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the
sequence set forth in SEQ ID NO: 18. Optionally, the genetically
modified endogenous Ttr locus encodes a protein comprising,
consisting essentially of, or consisting of a sequence at least
90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the sequence set
forth in SEQ ID NO: 1. Optionally, the genetically modified
endogenous Ttr locus comprises a coding sequence comprising,
consisting essentially of, or consisting of a sequence at least
90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the sequence set
forth in SEQ ID NO: 90. Optionally, the genetically modified
endogenous Ttr locus comprises, consists essentially of, or
consists of a sequence at least 90%, 95%, 96%, 97%, 98%, 99%, or
100% identical to the sequence set forth in SEQ ID NO: 14 or
15.
[0010] In some such non-human animal genomes, non-human animal
cells, or non-human animals, the genetically modified endogenous
Ttr locus encodes a transthyretin precursor protein comprising a
signal peptide, and the region of the endogenous Ttr locus encoding
the signal peptide has not been deleted and replaced with the
corresponding human TTR sequence. Optionally, the first exon of the
endogenous Ttr locus has not been deleted and replaced with the
corresponding human TTR sequence. Optionally, the first exon and
first intron of the endogenous Ttr locus have not been deleted and
replaced with the corresponding human TTR sequence. Optionally, the
region of the endogenous Ttr locus from the start of the second Ttr
exon to the Ttr stop codon has been deleted and replaced with the
corresponding human TTR sequence. Optionally, the genetically
modified endogenous Ttr locus comprises a human TTR 3' untranslated
region.
[0011] In some such non-human animal genomes, non-human animal
cells, or non-human animals, the region of the endogenous Ttr locus
from the second Ttr exon to the Ttr stop codon has been deleted and
replaced with a human TTR sequence comprising the corresponding
human TTR sequence and a human TTR 3' untranslated region, and the
endogenous Ttr 5' untranslated region has not been deleted and
replaced with the corresponding human TTR sequence, and the
endogenous Ttr promoter has not been deleted and replaced with the
corresponding human TTR sequence. Optionally, the human TTR
sequence at the genetically modified endogenous Ttr locus
comprises, consists essentially of, or consists of a sequence at
least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the
sequence set forth in SEQ ID NO: 19. Optionally, the genetically
modified endogenous Ttr locus encodes a protein comprising,
consisting essentially of, or consisting of a sequence at least
90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the sequence set
forth in SEQ ID NO: 2. Optionally, the genetically modified
endogenous Ttr locus comprises a coding sequence comprising,
consisting essentially of, or consisting of a sequence at least
90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the sequence set
forth in SEQ ID NO: 91. Optionally, the genetically modified
endogenous Ttr locus comprises, consists essentially of, or
consists of a sequence at least 90%, 95%, 96%, 97%, 98%, 99%, or
100% identical to the sequence set forth in SEQ ID NO: 16 or
17.
[0012] In some such non-human animal genomes, non-human animal
cells, or non-human animals, the genetically modified endogenous
Ttr locus does not comprise a selection cassette or a reporter
gene. In some such non-human animal genomes, non-human animal
cells, or non-human animals, the genetically modified endogenous
Ttr locus does comprise a selection cassette or a reporter gene. In
some such non-human animal genomes, non-human animal cells, or
non-human animals, the non-human animal genome, non-human animal
cell, or non-human animal is homozygous for the genetically
modified endogenous Ttr locus. In some such non-human animal
genomes, non-human animal cells, or non-human animals, the
non-human animal genome, non-human animal cell, or non-human animal
is heterozygous for the genetically modified endogenous Ttr
locus.
[0013] In some such non-human animal genomes, non-human animal
cells, or non-human animals, the non-human animal is a mammal.
Optionally, the mammal is a rodent. Optionally, the rodent is a rat
or mouse. Optionally, the non-human animal is a mouse.
[0014] In another aspect, provided are methods of using the
non-human animals comprising a humanized TTR locus to assess the
activity of human-TTR-targeting reagents in vivo. Such methods can
comprise: (a) administering the human-TTR-targeting reagent to any
of the above non-human animals; and (b) assessing the activity of
the human-TTR-targeting reagent in the non-human animal.
[0015] In some such methods, the administering comprises
adeno-associated virus (AAV)-mediated delivery, lipid nanoparticle
(LNP)-mediated delivery, or hydrodynamic delivery (HDD).
Optionally, the administering comprises LNP-mediated delivery, and
optionally the LNP dose is between about 0.1 mg/kg and about 2
mg/kg. Optionally, the administering comprises AAV8-mediated
delivery.
[0016] In some such methods, step (b) comprises isolating a liver
from the non-human animal and assessing activity of the
human-TTR-targeting reagent in the liver. Optionally, step (b)
further comprises assessing activity of the human-TTR-targeting
reagent in an organ or tissue other than the liver.
[0017] In some such methods, the human-TTR-targeting reagent is a
genome-editing agent, and the assessing comprises assessing
modification of the genetically modified Ttr locus. Optionally, the
assessing comprises measuring the frequency of insertions or
deletions within the genetically modified Ttr locus. In some such
methods, the assessing comprises measuring expression of a Ttr
messenger RNA encoded by the genetically modified Ttr locus. In
some such methods, the assessing comprises measuring expression of
a TTR protein encoded by the genetically modified Ttr locus.
Optionally, measuring expression of the TTR protein comprises
measuring serum levels of the TTR protein in the non-human animal.
Optionally, the activity is assessed in the liver of the non-human
animal.
[0018] In some such methods, the human-TTR-targeting reagent
comprises a nuclease agent designed to target a region of a human
TTR gene. Optionally, the nuclease agent comprises a Cas protein
and a guide RNA designed to target a guide RNA target sequence in
the human TTR gene. Optionally, the Cas protein is a Cas9 protein.
Optionally, the human-TTR-targeting reagent further comprises an
exogenous donor nucleic acid, wherein the exogenous donor nucleic
acid is designed to recombine with the human TTR gene. Optionally,
the exogenous donor nucleic acid is a single-stranded
oligodeoxynucleotide (ssODN).
[0019] In another aspect, provided are methods of optimizing the
activity of a human-TTR-targeting reagent in vivo. Such methods can
comprise: (I) performing any of the above methods of assessing the
activity of human-TTR-targeting reagents in vivo a first time in a
first non-human animal comprising in its genome a genetically
modified endogenous Ttr locus comprising a human TTR sequence
comprising both TTR coding sequence and non-coding sequence; (II)
changing a variable and performing the method of step (I) a second
time with the changed variable in a second non-human animal
comprising in its genome the genetically modified endogenous Ttr
locus comprising the human TTR sequence comprising both TTR coding
sequence and non-coding sequence; and (III) comparing the activity
of the human-TTR-targeting reagent in step (I) with the activity of
the human-TTR-targeting reagent in step (II), and selecting the
method resulting in the higher activity. Optionally, step (III) can
comprise selecting the method resulting in the higher efficacy,
higher precision, higher consistency, or higher specificity.
[0020] Optionally, the changed variable in step (II) is the
delivery method of introducing the human-TTR-targeting reagent into
the non-human animal. Optionally, the administering comprises
LNP-mediated delivery, and the changed variable in step (II) is the
LNP formulation. Optionally, the changed variable in step (II) is
the route of administration of introducing the human-TTR-targeting
reagent into the non-human animal. Optionally, the changed variable
in step (II) is the concentration or amount of the
human-TTR-targeting reagent introduced into the non-human animal.
Optionally, the changed variable in step (II) is the form of the
human-TTR-targeting reagent introduced into the non-human animal.
Optionally, the changed variable in step (II) is the
human-TTR-targeting reagent introduced into the non-human
animal.
[0021] In some such methods, the human-TTR-targeting reagent
comprises a Cas protein (e.g., a Cas9 protein) and a guide RNA
designed to target a guide RNA target sequence in the human TTR
gene. Optionally, the changed variable in step (II) is the guide
RNA sequence or the guide RNA target sequence. Optionally, the Cas
protein and the guide RNA are each administered in the form of RNA,
and the changed variable in step (II) is the ratio of Cas mRNA to
guide RNA. Optionally, the changed variable in step (II) is guide
RNA modifications.
[0022] In another aspect, provided are methods of making the
non-human animals comprising a humanized TTR locus. Some such
methods comprise: (a) introducing into a non-human animal embryonic
stem (ES) cell: (i) a nuclease agent that targets a target sequence
in the endogenous Ttr locus; and (ii) a targeting vector comprising
a nucleic acid insert comprising the human TTR sequence flanked by
a 5' homology arm corresponding to a 5' target sequence in the
endogenous Ttr locus and a 3' homology arm corresponding to a 3'
target sequence in the endogenous Ttr locus, wherein the targeting
vector recombines with the endogenous Ttr locus to produce a
genetically modified non-human ES cell comprising in its genome the
genetically modified endogenous Ttr locus comprising the human TTR
sequence; (b) introducing the genetically modified non-human ES
cell into a non-human animal host embryo; and (c) gestating the
non-human animal host embryo in a surrogate mother, wherein the
surrogate mother produces an F0 progeny genetically modified
non-human animal comprising in its genome the genetically modified
endogenous Ttr locus comprising the human TTR sequence.
[0023] In some such methods, the nuclease agent comprises a Cas
protein (e.g., a Cas9 protein) and a guide RNA. In some such
methods, the targeting vector is a large targeting vector at least
10 kb in length or in which the sum total of the 5' and 3' homology
arms is at least 10 kb in length. In some such methods, the
non-human animal is a mouse or a rat. In some such methods, the
non-human animal is a mouse.
BRIEF DESCRIPTION OF THE FIGURES
[0024] FIG. 1A shows an alignment of human and mouse transthyretin
(TTR) precursor proteins (SEQ ID NOS: 1 and 6, respectively). The
signal peptide, T4 binding domain, phase 0 exon/intron boundaries,
and phase 1/2 exon/intron boundaries are denoted.
[0025] FIG. 1B shows an alignment of human and mouse transthyretin
(TTR) coding sequences (SEQ ID NOS: 90 and 92, respectively).
[0026] FIG. 2 shows schematics (not drawn to scale) of the
wild-type murine Ttr locus, a first version of a humanized mouse
Ttr locus, and a second version of a humanized mouse Ttr locus.
Exons, introns, 5' untranslated regions (UTRs), 3' UTRs, start
codons (ATG), stop codons (TGA), and loxP scars from selection
cassettes are denoted. White boxes indicate murine sequence; black
boxes indicate human sequence.
[0027] FIG. 3 shows a schematic (not drawn to scale) of the
targeting to create the first version of the humanized mouse Ttr
locus. The wild type mouse Ttr locus, the F0 allele of the
humanized mouse Ttr locus with the self-deleting neomycin (SDC-Neo)
selection cassette (MAID 7576), and the F1 allele of the humanized
mouse Ttr locus with the loxP scar from removal of the SDC-Neo
selection cassette (MAID 7577) are shown. White boxes indicate
murine sequence; black boxes indicate human sequence.
[0028] FIG. 4 shows a schematic (not drawn to scale) of the
targeting to create the second version of the humanized mouse Ttr
locus. The wild type mouse Ttr locus, the F0 allele of the
humanized mouse Ttr locus with the SDC-Neo selection cassette, and
the F1 allele of the humanized mouse Ttr locus with the loxP scar
from removal of the SDC-Neo selection cassette are shown. White
boxes indicate murine sequence; black boxes indicate human
sequence.
[0029] FIG. 5A shows a schematic (not drawn to scale) of the
strategy for screening of the first targeted mouse Ttr locus,
including loss-of-allele assays (7576mTU, 9090mTM, and 9090mTD),
gain of allele assays (7576hTU, 7576hTD, Neo), retention assays
(9090retU, 9090retU2, 9090retU3, 9090retD, 9090retD2, 9090retD3),
and CRISPR assays designed to cover the region that is disrupted by
the CRISPR guides (9090mTGU, mGU, 9090mTGD, and mGD). White boxes
indicate murine sequence; black boxes indicate human sequence.
[0030] FIG. 5B shows a schematic (not drawn to scale) of the
strategy for screening of the second targeted mouse Ttr locus,
including loss-of-allele assays (4552mTU, 9212mTU, 9090mTM,
9212mTD), gain of allele assays (7655hTU, 7576hTD, Neo), retention
assays (9204mretU, 9204mretD), and CRISPR assays designed to cover
the region that is disrupted by the CRISPR guides (mGU, mGD, and
9212mTGD). White boxes indicate murine sequence; black boxes
indicate human sequence.
[0031] FIG. 6 shows beta-actin (Actb), beta-2-microglobulin (B2M),
Mus musculus transthyretin (Mm Ttr), and Homo sapiens transthyretin
(Hs TTR) mRNA expression in liver samples from (1) F0 generation
mice homozygous for the first version of the humanized mouse Ttr
locus (MAID 7576; F0 allele from FIG. 3), (2) liver samples from
wild type mice, (3) spleen samples from F0 generation mice
homozygous for the first version of the humanized mouse Ttr locus,
and (4) spleen samples from wild type mice. Lower Ct values
indicate higher expression.
[0032] FIGS. 7A and 7B show results of ELISA assays for human TTR
protein levels (FIG. 7A) and mouse TTR protein levels (FIG. 7B) in
serum and cerebrospinal fluid (CSF). The samples tested include
serum and CSF from F0 generation mice homozygous for the first
version of the humanized mouse Ttr locus (MAID 7576; F0 allele from
FIG. 3), human serum and CSF controls, and mouse (F1H4) serum and
CSF controls.
[0033] FIG. 7C shows results of ELISA assays for (1) human TTR and
(2) mouse TTR protein levels in serum. The samples tested include
serum samples from F0 generation mice homozygous for the first
version of the humanized mouse Ttr locus (MAID 7576; F0 allele from
FIG. 3) generated from a first clone (clone 7576C-G7), F0
generation mice homozygous for the first version of the humanized
mouse Ttr locus (MAID 7576; F0 allele from FIG. 3) generated from a
second clone (clone 7576A-A5), and wild type mice (F1H4). Mouse
serum and human serum were used as controls.
[0034] FIG. 8 shows human TTR protein expression as determined by
western blot in serum samples from wild type mice (F1H4), F0
generation mice homozygous for the first version of the humanized
mouse Ttr locus (MAID 7576; F0 allele from FIG. 3) generated from a
first clone (clone 7576C-G7), and F0 generation mice homozygous for
the first version of the humanized mouse Ttr locus generated from a
second clone (7576A-A5). Mouse serum was used as a negative
control, and human serum was used as a positive control. Mouse IgG
was used as a loading control.
[0035] FIG. 9 shows human TTR protein expression as determined by
western blot in liver and kidney samples from wild type mice
(F1H4), F0 generation mice homozygous for the first version of the
humanized mouse Ttr locus (MAID 7576; F0 allele from FIG. 3)
generated from a first clone (clone 7576C-G7), and F0 generation
mice homozygous for the first version of the humanized mouse Ttr
locus generated from a second clone (7576A-A5). Mouse serum was
used as a negative control, and human serum was used as a positive
control. GAPDH was used as a loading control.
[0036] FIG. 10 shows percent genome editing (total number of
insertions or deletions observed over the total number of sequences
read in the PCR reaction from a pool of lysed cells) at the
humanized mouse Ttr locus as determined by next-generation
sequencing (NGS) in primary hepatocytes isolated from F0 generation
mice homozygous for the first version of the humanized mouse Ttr
locus (MAID 7576; F0 allele from FIG. 3). The samples tested
included untreated hepatocytes and hepatocytes treated with lipid
nanoparticles containing Cas9 mRNA and guide RNAs designed to
target human TTR.
[0037] FIGS. 11A-11H show serum chemistry analysis of alanine
aminotransferase (ALT) (FIG. 11A), aspartate aminotransferase (AST)
(FIG. 11B), triglycerides (FIG. 11C), cholesterol (FIG. 11 D),
high-density lipoprotein (HDL) (FIG. 11E), low-density lipoprotein
(LDL) (FIG. 11F), non-esterified fatty acids (NEFA) (FIG. 11G), and
albumin (FIG. 11H) 14 days post-injection of lipid nanoparticles
containing Cas9 mRNA and guide RNAs designed to target human TTR
into F0 generation mice homozygous for the first version of the
humanized mouse Ttr locus (MAID 7576; F0 allele from FIG. 3). U/L
refers to units per liter, mg/dL refers to milligrams per
deciliter, mEq/L refers to milliequivalents per liter, and g/dL
refers to grams per deciliter.
[0038] FIG. 12 shows percent genome editing (total number of
insertions or deletions observed over the total number of sequences
read in the PCR reaction from a pool of lysed cells) at the
humanized mouse Ttr locus as determined by next-generation
sequencing (NGS) in samples from liver 14 days post-injection of
buffer control or lipid nanoparticles containing Cas9 mRNA and
guide RNAs designed to target human TTR into F0 generation mice
homozygous for the first version of the humanized mouse Ttr locus
(MAID 7576; F0 allele from FIG. 3).
[0039] FIG. 13 shows results of an ELISA assaying serum levels of
human TTR in wild type mice (F1H4), mice in which human TTR
plasmids were introduced by hydrodynamic delivery (HDD), and mice
in which a chimeric mouse/human TTR plasmid (region encoded by exon
1 is mouse, region encoded by exons 2-4 is human) was introduced by
HDD. Two negative controls are shown, and human serum was used as a
positive control.
[0040] FIG. 14 shows results of an ELISA assaying human TTR levels
in liver lysates 8 days post-injection of buffer control or lipid
nanoparticles containing Cas9 mRNA and human TTR guide RNA 1
designed to target human TTR into F2 generation mice homozygous for
the first version of the humanized mouse Ttr locus (MAID 7576; F1
allele from FIG. 3; derived from clone 7576B-F10).
[0041] FIGS. 15A and 15B show results of an ELISA assaying human
TTR levels in serum samples (1:5000 dilution in FIG. 15A, and
1:10000 dilution in FIG. 15B) 8 days post-injection of buffer
control or lipid nanoparticles containing Cas9 mRNA and human TTR
guide RNA 1 designed to target human TTR into F2 generation mice
homozygous for the first version of the humanized mouse Ttr locus
(MAID 7576; F1 allele from FIG. 3; derived from clone
7576B-F10).
[0042] FIG. 16 shows results of an ELISA assaying human TTR levels
in blood plasma samples of hTTR.sup.7577/7577, hTTR.sup.7655/7655,
hTTR.sup.7655/7656, and hTTR.sup.7656/7656, and hTTR.sup.7656/WT
mice.
[0043] FIGS. 17A and 17B show results of an ELISA assaying human
TTR and mouse TTR levels in blood plasma samples of hTTR.sup.WT/WT
and hTTR.sup.7577/7577 mice (3 months of age). Human serum was used
as a control.
[0044] FIG. 17C shows mTTR (1) and hTTR (2) mRNA expression in
liver samples from 3-month old hTTR.sup.WT/WT and
hTTR.sup.7577/7577 mice. Lower Ct values indicate higher
expression.
[0045] FIG. 18 shows show results of an ELISA assaying human TTR
levels in blood plasma samples of wild type (F1H4),
hTTR.sup.7577/7577 (hTTR v1), and hTTR.sup.7656/7656 (hTTRv2) mice
(ages 2-3 months).
[0046] FIG. 19 shows percent genome editing at the humanized mouse
Ttr locus as determined by next-generation sequencing (NGS) in
samples from liver post-injection of buffer control or lipid
nanoparticles containing Cas9 mRNA and guide RNAs designed to
target human TTR into mice homozygous for the first version of the
humanized mouse Ttr locus.
[0047] FIG. 20 shows results of an ELISA assaying human TTR levels
in serum samples post-injection of buffer control or lipid
nanoparticles containing Cas9 mRNA and guide RNAs designed to
target human TTR into mice homozygous for the first version of the
humanized mouse Ttr locus.
DEFINITIONS
[0048] The terms "protein," "polypeptide," and "peptide," used
interchangeably herein, include polymeric forms of amino acids of
any length, including coded and non-coded amino acids and
chemically or biochemically modified or derivatized amino acids.
The terms also include polymers that have been modified, such as
polypeptides having modified peptide backbones. The term "domain"
refers to any part of a protein or polypeptide having a particular
function or structure.
[0049] Proteins are said to have an "N-terminus" and a
"C-terminus." The term "N-terminus" relates to the start of a
protein or polypeptide, terminated by an amino acid with a free
amine group (--NH2). The term "C-terminus" relates to the end of an
amino acid chain (protein or polypeptide), terminated by a free
carboxyl group (--COOH).
[0050] The terms "nucleic acid" and "polynucleotide," used
interchangeably herein, include polymeric forms of nucleotides of
any length, including ribonucleotides, deoxyribonucleotides, or
analogs or modified versions thereof. They include single-,
double-, and multi-stranded DNA or RNA, genomic DNA, cDNA, DNA-RNA
hybrids, and polymers comprising purine bases, pyrimidine bases, or
other natural, chemically modified, biochemically modified,
non-natural, or derivatized nucleotide bases.
[0051] Nucleic acids are said to have "5' ends" and "3' ends"
because mononucleotides are reacted to make oligonucleotides in a
manner such that the 5' phosphate of one mononucleotide pentose
ring is attached to the 3' oxygen of its neighbor in one direction
via a phosphodiester linkage. An end of an oligonucleotide is
referred to as the "5' end" if its 5' phosphate is not linked to
the 3' oxygen of a mononucleotide pentose ring. An end of an
oligonucleotide is referred to as the "3' end" if its 3' oxygen is
not linked to a 5' phosphate of another mononucleotide pentose
ring. A nucleic acid sequence, even if internal to a larger
oligonucleotide, also may be said to have 5' and 3' ends. In either
a linear or circular DNA molecule, discrete elements are referred
to as being "upstream" or 5' of the "downstream" or 3'
elements.
[0052] The term "genomically integrated" refers to a nucleic acid
that has been introduced into a cell such that the nucleotide
sequence integrates into the genome of the cell. Any protocol may
be used for the stable incorporation of a nucleic acid into the
genome of a cell.
[0053] The term "expression vector" or "expression construct" or
"expression cassette" refers to a recombinant nucleic acid
containing a desired coding sequence operably linked to appropriate
nucleic acid sequences necessary for the expression of the operably
linked coding sequence in a particular host cell or organism.
Nucleic acid sequences necessary for expression in prokaryotes
usually include a promoter, an operator (optional), and a ribosome
binding site, as well as other sequences. Eukaryotic cells are
generally known to utilize promoters, enhancers, and termination
and polyadenylation signals, although some elements may be deleted
and other elements added without sacrificing the necessary
expression.
[0054] The term "targeting vector" refers to a recombinant nucleic
acid that can be introduced by homologous recombination,
non-homologous-end-joining-mediated ligation, or any other means of
recombination to a target position in the genome of a cell.
[0055] The term "viral vector" refers to a recombinant nucleic acid
that includes at least one element of viral origin and includes
elements sufficient for or permissive of packaging into a viral
vector particle. The vector and/or particle can be utilized for the
purpose of transferring DNA, RNA, or other nucleic acids into cells
either ex vivo or in vivo. Numerous forms of viral vectors are
known.
[0056] The term "isolated" with respect to proteins, nucleic acids,
and cells includes proteins, nucleic acids, and cells that are
relatively purified with respect to other cellular or organism
components that may normally be present in situ, up to and
including a substantially pure preparation of the protein, nucleic
acid, or cell. The term "isolated" also includes proteins and
nucleic acids that have no naturally occurring counterpart or
proteins or nucleic acids that have been chemically synthesized and
are thus substantially uncontaminated by other proteins or nucleic
acids. The term "isolated" also includes proteins, nucleic acids,
or cells that have been separated or purified from most other
cellular components or organism components with which they are
naturally accompanied (e.g., other cellular proteins, nucleic
acids, or cellular or extracellular components).
[0057] The term "wild type" includes entities having a structure
and/or activity as found in a normal (as contrasted with mutant,
diseased, altered, or so forth) state or context. Wild type genes
and polypeptides often exist in multiple different forms (e.g.,
alleles).
[0058] The term "endogenous sequence" refers to a nucleic acid
sequence that occurs naturally within a cell or non-human animal.
For example, an endogenous Ttr sequence of a non-human animal
refers to a native Ttr sequence that naturally occurs at the Ttr
locus in the non-human animal.
[0059] "Exogenous" molecules or sequences include molecules or
sequences that are not normally present in a cell in that form.
Normal presence includes presence with respect to the particular
developmental stage and environmental conditions of the cell. An
exogenous molecule or sequence, for example, can include a mutated
version of a corresponding endogenous sequence within the cell,
such as a humanized version of the endogenous sequence, or can
include a sequence corresponding to an endogenous sequence within
the cell but in a different form (i.e., not within a chromosome).
In contrast, endogenous molecules or sequences include molecules or
sequences that are normally present in that form in a particular
cell at a particular developmental stage under particular
environmental conditions.
[0060] The term "heterologous" when used in the context of a
nucleic acid or a protein indicates that the nucleic acid or
protein comprises at least two segments that do not naturally occur
together in the same molecule. For example, the term
"heterologous," when used with reference to segments of a nucleic
acid or segments of a protein, indicates that the nucleic acid or
protein comprises two or more sub-sequences that are not found in
the same relationship to each other (e.g., joined together) in
nature. As one example, a "heterologous" region of a nucleic acid
vector is a segment of nucleic acid within or attached to another
nucleic acid molecule that is not found in association with the
other molecule in nature. For example, a heterologous region of a
nucleic acid vector could include a coding sequence flanked by
sequences not found in association with the coding sequence in
nature. Likewise, a "heterologous" region of a protein is a segment
of amino acids within or attached to another peptide molecule that
is not found in association with the other peptide molecule in
nature (e.g., a fusion protein, or a protein with a tag).
Similarly, a nucleic acid or protein can comprise a heterologous
label or a heterologous secretion or localization sequence.
[0061] "Codon optimization" takes advantage of the degeneracy of
codons, as exhibited by the multiplicity of three-base pair codon
combinations that specify an amino acid, and generally includes a
process of modifying a nucleic acid sequence for enhanced
expression in particular host cells by replacing at least one codon
of the native sequence with a codon that is more frequently or most
frequently used in the genes of the host cell while maintaining the
native amino acid sequence. For example, a nucleic acid encoding a
Cas9 protein can be modified to substitute codons having a higher
frequency of usage in a given prokaryotic or eukaryotic cell,
including a bacterial cell, a yeast cell, a human cell, a non-human
cell, a mammalian cell, a rodent cell, a mouse cell, a rat cell, a
hamster cell, or any other host cell, as compared to the naturally
occurring nucleic acid sequence. Codon usage tables are readily
available, for example, at the "Codon Usage Database." These tables
can be adapted in a number of ways. See Nakamura et al. (2000)
Nucleic Acids Research 28:292, herein incorporated by reference in
its entirety for all purposes. Computer algorithms for codon
optimization of a particular sequence for expression in a
particular host are also available (see, e.g., Gene Forge).
[0062] The term "locus" refers to a specific location of a gene (or
significant sequence), DNA sequence, polypeptide-encoding sequence,
or position on a chromosome of the genome of an organism. For
example, a "Ttr locus" may refer to the specific location of a Ttr
gene, Ttr DNA sequence, transthyretin-encoding sequence, or Ttr
position on a chromosome of the genome of an organism that has been
identified as to where such a sequence resides. A "Ttr locus" may
comprise a regulatory element of a Ttr gene, including, for
example, an enhancer, a promoter, 5' and/or 3' untranslated region
(UTR), or a combination thereof.
[0063] The term "gene" refers to a DNA sequence in a chromosome
that codes for a product (e.g., an RNA product and/or a polypeptide
product) and includes the coding region interrupted with non-coding
introns and sequence located adjacent to the coding region on both
the 5' and 3' ends such that the gene corresponds to the
full-length mRNA (including the 5' and 3' untranslated sequences).
The term "gene" also includes other non-coding sequences including
regulatory sequences (e.g., promoters, enhancers, and transcription
factor binding sites), polyadenylation signals, internal ribosome
entry sites, silencers, insulating sequence, and matrix attachment
regions. These sequences may be close to the coding region of the
gene (e.g., within 10 kb) or at distant sites, and they influence
the level or rate of transcription and translation of the gene.
[0064] The term "allele" refers to a variant form of a gene. Some
genes have a variety of different forms, which are located at the
same position, or genetic locus, on a chromosome. A diploid
organism has two alleles at each genetic locus. Each pair of
alleles represents the genotype of a specific genetic locus.
Genotypes are described as homozygous if there are two identical
alleles at a particular locus and as heterozygous if the two
alleles differ.
[0065] The "coding region" or "coding sequence" of a gene consists
of the portion of a gene's DNA or RNA, composed of exons, that
codes for a protein. The region begins at the start codon on the 5'
end and ends at the stop codon on the 3' end.
[0066] A "promoter" is a regulatory region of DNA usually
comprising a TATA box capable of directing RNA polymerase II to
initiate RNA synthesis at the appropriate transcription initiation
site for a particular polynucleotide sequence. A promoter may
additionally comprise other regions which influence the
transcription initiation rate. The promoter sequences disclosed
herein modulate transcription of an operably linked polynucleotide.
A promoter can be active in one or more of the cell types disclosed
herein (e.g., a eukaryotic cell, a non-human mammalian cell, a
human cell, a rodent cell, a pluripotent cell, a one-cell stage
embryo, a differentiated cell, or a combination thereof). A
promoter can be, for example, a constitutively active promoter, a
conditional promoter, an inducible promoter, a temporally
restricted promoter (e.g., a developmentally regulated promoter),
or a spatially restricted promoter (e.g., a cell-specific or
tissue-specific promoter). Examples of promoters can be found, for
example, in WO 2013/176772, herein incorporated by reference in its
entirety for all purposes.
[0067] "Operable linkage" or being "operably linked" includes
juxtaposition of two or more components (e.g., a promoter and
another sequence element) such that both components function
normally and allow the possibility that at least one of the
components can mediate a function that is exerted upon at least one
of the other components. For example, a promoter can be operably
linked to a coding sequence if the promoter controls the level of
transcription of the coding sequence in response to the presence or
absence of one or more transcriptional regulatory factors. Operable
linkage can include such sequences being contiguous with each other
or acting in trans (e.g., a regulatory sequence can act at a
distance to control transcription of the coding sequence).
[0068] "Complementarity" of nucleic acids means that a nucleotide
sequence in one strand of nucleic acid, due to orientation of its
nucleobase groups, forms hydrogen bonds with another sequence on an
opposing nucleic acid strand. The complementary bases in DNA are
typically A with T and C with G. In RNA, they are typically C with
G and U with A. Complementarity can be perfect or
substantial/sufficient. Perfect complementarity between two nucleic
acids means that the two nucleic acids can form a duplex in which
every base in the duplex is bonded to a complementary base by
Watson-Crick pairing. "Substantial" or "sufficient" complementary
means that a sequence in one strand is not completely and/or
perfectly complementary to a sequence in an opposing strand, but
that sufficient bonding occurs between bases on the two strands to
form a stable hybrid complex in set of hybridization conditions
(e.g., salt concentration and temperature). Such conditions can be
predicted by using the sequences and standard mathematical
calculations to predict the Tm (melting temperature) of hybridized
strands, or by empirical determination of Tm by using routine
methods. Tm includes the temperature at which a population of
hybridization complexes formed between two nucleic acid strands are
50% denatured (i.e., a population of double-stranded nucleic acid
molecules becomes half dissociated into single strands). At a
temperature below the Tm, formation of a hybridization complex is
favored, whereas at a temperature above the Tm, melting or
separation of the strands in the hybridization complex is favored.
Tm may be estimated for a nucleic acid having a known G+C content
in an aqueous 1 M NaCl solution by using, e.g., Tm=81.5+0.41(%
G+C), although other known Tm computations take into account
nucleic acid structural characteristics.
[0069] "Hybridization condition" includes the cumulative
environment in which one nucleic acid strand bonds to a second
nucleic acid strand by complementary strand interactions and
hydrogen bonding to produce a hybridization complex. Such
conditions include the chemical components and their concentrations
(e.g., salts, chelating agents, formamide) of an aqueous or organic
solution containing the nucleic acids, and the temperature of the
mixture. Other factors, such as the length of incubation time or
reaction chamber dimensions may contribute to the environment. See,
e.g., Sambrook et al., Molecular Cloning, A Laboratory Manual,
2.sup.nd ed., pp. 1.90-1.91, 9.47-9.51, 11.47-11.57 (Cold Spring
Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989), herein
incorporated by reference in its entirety for all purposes.
[0070] Hybridization requires that the two nucleic acids contain
complementary sequences, although mismatches between bases are
possible. The conditions appropriate for hybridization between two
nucleic acids depend on the length of the nucleic acids and the
degree of complementation, variables which are well known. The
greater the degree of complementation between two nucleotide
sequences, the greater the value of the melting temperature (Tm)
for hybrids of nucleic acids having those sequences. For
hybridizations between nucleic acids with short stretches of
complementarity (e.g. complementarity over 35 or fewer, 30 or
fewer, 25 or fewer, 22 or fewer, 20 or fewer, or 18 or fewer
nucleotides) the position of mismatches becomes important (see
Sambrook et al., supra, 11.7-11.8). Typically, the length for a
hybridizable nucleic acid is at least about 10 nucleotides.
Illustrative minimum lengths for a hybridizable nucleic acid
include at least about 15 nucleotides, at least about 20
nucleotides, at least about 22 nucleotides, at least about 25
nucleotides, and at least about 30 nucleotides. Furthermore, the
temperature and wash solution salt concentration may be adjusted as
necessary according to factors such as length of the region of
complementation and the degree of complementation.
[0071] The sequence of polynucleotide need not be 100%
complementary to that of its target nucleic acid to be specifically
hybridizable. Moreover, a polynucleotide may hybridize over one or
more segments such that intervening or adjacent segments are not
involved in the hybridization event (e.g., a loop structure or
hairpin structure). A polynucleotide (e.g., gRNA) can comprise at
least 70%, at least 80%, at least 90%, at least 95%, at least 99%,
or 100% sequence complementarity to a target region within the
target nucleic acid sequence to which they are targeted. For
example, a gRNA in which 18 of 20 nucleotides are complementary to
a target region, and would therefore specifically hybridize, would
represent 90% complementarity. In this example, the remaining
noncomplementary nucleotides may be clustered or interspersed with
complementary nucleotides and need not be contiguous to each other
or to complementary nucleotides.
[0072] Percent complementarity between particular stretches of
nucleic acid sequences within nucleic acids can be determined
routinely using BLAST programs (basic local alignment search tools)
and PowerBLAST programs (Altschul et al. (1990) J. Mol. Biol.
215:403-410; Zhang and Madden (1997) Genome Res. 7:649-656, each of
which is herein incorporated by reference in its entirety for all
purposes) or by using the Gap program (Wisconsin Sequence Analysis
Package, Version 8 for Unix, Genetics Computer Group, University
Research Park, Madison Wis.), using default settings, which uses
the algorithm of Smith and Waterman (1981) Adv. Appl. Math.
2:482-489, herein incorporated by reference in its entirety for all
purposes.
[0073] The methods and compositions provided herein employ a
variety of different components. Some components throughout the
description can have active variants and fragments. Such components
include, for example, Cas proteins, CRISPR RNAs, tracrRNAs, and
guide RNAs. Biological activity for each of these components is
described elsewhere herein. The term "functional" refers to the
innate ability of a protein or nucleic acid (or a fragment or
variant thereof) to exhibit a biological activity or function. Such
biological activities or functions can include, for example, the
ability of a Cas protein to bind to a guide RNA and to a target DNA
sequence. The biological functions of functional fragments or
variants may be the same or may in fact be changed (e.g., with
respect to their specificity or selectivity or efficacy) in
comparison to the original, but with retention of the basic
biological function.
[0074] The term "variant" refers to a nucleotide sequence differing
from the sequence most prevalent in a population (e.g., by one
nucleotide) or a protein sequence different from the sequence most
prevalent in a population (e.g., by one amino acid).
[0075] The term "fragment" when referring to a protein means a
protein that is shorter or has fewer amino acids than the
full-length protein. The term "fragment" when referring to a
nucleic acid means a nucleic acid that is shorter or has fewer
nucleotides than the full-length nucleic acid. A fragment can be,
for example, an N-terminal fragment (i.e., removal of a portion of
the C-terminal end of the protein), a C-terminal fragment (i.e.,
removal of a portion of the N-terminal end of the protein), or an
internal fragment.
[0076] "Sequence identity" or "identity" in the context of two
polynucleotides or polypeptide sequences makes reference to the
residues in the two sequences that are the same when aligned for
maximum correspondence over a specified comparison window. When
percentage of sequence identity is used in reference to proteins,
residue positions which are not identical often differ by
conservative amino acid substitutions, where amino acid residues
are substituted for other amino acid residues with similar chemical
properties (e.g., charge or hydrophobicity) and therefore do not
change the functional properties of the molecule. When sequences
differ in conservative substitutions, the percent sequence identity
may be adjusted upwards to correct for the conservative nature of
the substitution. Sequences that differ by such conservative
substitutions are said to have "sequence similarity" or
"similarity." Means for making this adjustment are well known.
Typically, this involves scoring a conservative substitution as a
partial rather than a full mismatch, thereby increasing the
percentage sequence identity. Thus, for example, where an identical
amino acid is given a score of 1 and a non-conservative
substitution is given a score of zero, a conservative substitution
is given a score between zero and 1. The scoring of conservative
substitutions is calculated, e.g., as implemented in the program
PC/GENE (Intelligenetics, Mountain View, Calif.).
[0077] "Percentage of sequence identity" includes the value
determined by comparing two optimally aligned sequences (greatest
number of perfectly matched residues) over a comparison window,
wherein the portion of the polynucleotide sequence in the
comparison window may comprise additions or deletions (i.e., gaps)
as compared to the reference sequence (which does not comprise
additions or deletions) for optimal alignment of the two sequences.
The percentage is calculated by determining the number of positions
at which the identical nucleic acid base or amino acid residue
occurs in both sequences to yield the number of matched positions,
dividing the number of matched positions by the total number of
positions in the window of comparison, and multiplying the result
by 100 to yield the percentage of sequence identity. Unless
otherwise specified (e.g., the shorter sequence includes a linked
heterologous sequence), the comparison window is the full length of
the shorter of the two sequences being compared.
[0078] Unless otherwise stated, sequence identity/similarity values
include the value obtained using GAP Version 10 using the following
parameters: % identity and % similarity for a nucleotide sequence
using GAP Weight of 50 and Length Weight of 3, and the
nwsgapdna.cmp scoring matrix; % identity and % similarity for an
amino acid sequence using GAP Weight of 8 and Length Weight of 2,
and the BLOSUM62 scoring matrix; or any equivalent program thereof
"Equivalent program" includes any sequence comparison program that,
for any two sequences in question, generates an alignment having
identical nucleotide or amino acid residue matches and an identical
percent sequence identity when compared to the corresponding
alignment generated by GAP Version 10.
[0079] The term "conservative amino acid substitution" refers to
the substitution of an amino acid that is normally present in the
sequence with a different amino acid of similar size, charge, or
polarity. Examples of conservative substitutions include the
substitution of a non-polar (hydrophobic) residue such as
isoleucine, valine, or leucine for another non-polar residue.
Likewise, examples of conservative substitutions include the
substitution of one polar (hydrophilic) residue for another such as
between arginine and lysine, between glutamine and asparagine, or
between glycine and serine. Additionally, the substitution of a
basic residue such as lysine, arginine, or histidine for another,
or the substitution of one acidic residue such as aspartic acid or
glutamic acid for another acidic residue are additional examples of
conservative substitutions. Examples of non-conservative
substitutions include the substitution of a non-polar (hydrophobic)
amino acid residue such as isoleucine, valine, leucine, alanine, or
methionine for a polar (hydrophilic) residue such as cysteine,
glutamine, glutamic acid or lysine and/or a polar residue for a
non-polar residue. Typical amino acid categorizations are
summarized in Table 1 below.
TABLE-US-00001 TABLE 1 Amino Acid Categorizations. Alanine Ala A
Nonpolar Neutral 1.8 Arginine Arg R Polar Positive -4.5 Asparagine
Asn N Polar Neutral -3.5 Aspartic acid Asp D Polar Negative -3.5
Cysteine Cys C Nonpolar Neutral 2.5 Glutamic acid Glu E Polar
Negative -3.5 Glutamine Gln Q Polar Neutral -3.5 Glycine Gly G
Nonpolar Neutral -0.4 Histidine His H Polar Positive -3.2
Isoleucine Ile I Nonpolar Neutral 4.5 Leucine Leu L Nonpolar
Neutral 3.8 Lysine Lys K Polar Positive -3.9 Methionine Met M
Nonpolar Neutral 1.9 Phenylalanine Phe F Nonpolar Neutral 2.8
Proline Pro P Nonpolar Neutral -1.6 Serine Ser S Polar Neutral -0.8
Threonine Thr T Polar Neutral -0.7 Tryptophan Trp W Nonpolar
Neutral -0.9 Tyrosine Tyr Y Polar Neutral -1.3 Valine Val V
Nonpolar Neutral 4.2
[0080] A "homologous" sequence (e.g., nucleic acid sequence)
includes a sequence that is either identical or substantially
similar to a known reference sequence, such that it is, for
example, at least 50%, at least 55%, at least 60%, at least 65%, at
least 70%, at least 75%, at least 80%, at least 85%, at least 90%,
at least 95%, at least 96%, at least 97%, at least 98%, at least
99%, or 100% identical to the known reference sequence. Homologous
sequences can include, for example, orthologous sequence and
paralogous sequences. Homologous genes, for example, typically
descend from a common ancestral DNA sequence, either through a
speciation event (orthologous genes) or a genetic duplication event
(paralogous genes). "Orthologous" genes include genes in different
species that evolved from a common ancestral gene by speciation.
Orthologs typically retain the same function in the course of
evolution. "Paralogous" genes include genes related by duplication
within a genome. Paralogs can evolve new functions in the course of
evolution.
[0081] The term "in vitro" includes artificial environments and to
processes or reactions that occur within an artificial environment
(e.g., a test tube). The term "in vivo" includes natural
environments (e.g., a cell or organism or body) and to processes or
reactions that occur within a natural environment. The term "ex
vivo" includes cells that have been removed from the body of an
individual and to processes or reactions that occur within such
cells.
[0082] The term "reporter gene" refers to a nucleic acid having a
sequence encoding a gene product (typically an enzyme) that is
easily and quantifiably assayed when a construct comprising the
reporter gene sequence operably linked to an endogenous or
heterologous promoter and/or enhancer element is introduced into
cells containing (or which can be made to contain) the factors
necessary for the activation of the promoter and/or enhancer
elements. Examples of reporter genes include, but are not limited,
to genes encoding beta-galactosidase (lacZ), the bacterial
chloramphenicol acetyltransferase (cat) genes, firefly luciferase
genes, genes encoding beta-glucuronidase (GUS), and genes encoding
fluorescent proteins. A "reporter protein" refers to a protein
encoded by a reporter gene.
[0083] The term "fluorescent reporter protein" as used herein means
a reporter protein that is detectable based on fluorescence wherein
the fluorescence may be either from the reporter protein directly,
activity of the reporter protein on a fluorogenic substrate, or a
protein with affinity for binding to a fluorescent tagged compound.
Examples of fluorescent proteins include green fluorescent proteins
(e.g., GFP, GFP-2, tagGFP, turboGFP, eGFP, Emerald, Azami Green,
Monomeric Azami Green, CopGFP, AceGFP, and ZsGreen1), yellow
fluorescent proteins (e.g., YFP, eYFP, Citrine, Venus, YPet,
PhiYFP, and ZsYellow1), blue fluorescent proteins (e.g., BFP, eBFP,
eBFP2, Azurite, mKalamal, GFPuv, Sapphire, and T-sapphire), cyan
fluorescent proteins (e.g., CFP, eCFP, Cerulean, CyPet, AmCyanl,
and Midoriishi-Cyan), red fluorescent proteins (e.g., RFP, mKate,
mKate2, mPlum, DsRed monomer, mCherry, mRFP1, DsRed-Express,
DsRed2, DsRed-Monomer, HcRed-Tandem, HcRed1, AsRed2, eqFP611,
mRaspberry, mStrawberry, and Jred), orange fluorescent proteins
(e.g., mOrange, mKO, Kusabira-Orange, Monomeric Kusabira-Orange,
mTangerine, and tdTomato), and any other suitable fluorescent
protein whose presence in cells can be detected by flow cytometry
methods.
[0084] Repair in response to double-strand breaks (DSBs) occurs
principally through two conserved DNA repair pathways: homologous
recombination (HR) and non-homologous end joining (NHEJ). See
Kasparek & Humphrey (2011) Seminars in Cell & Dev. Biol.
22:886-897, herein incorporated by reference in its entirety for
all purposes. Likewise, repair of a target nucleic acid mediated by
an exogenous donor nucleic acid can include any process of exchange
of genetic information between the two polynucleotides.
[0085] The term "recombination" includes any process of exchange of
genetic information between two polynucleotides and can occur by
any mechanism. Recombination can occur via homology directed repair
(HDR) or homologous recombination (HR). HDR or HR includes a form
of nucleic acid repair that can require nucleotide sequence
homology, uses a "donor" molecule as a template for repair of a
"target" molecule (i.e., the one that experienced the double-strand
break), and leads to transfer of genetic information from the donor
to target. Without wishing to be bound by any particular theory,
such transfer can involve mismatch correction of heteroduplex DNA
that forms between the broken target and the donor, and/or
synthesis-dependent strand annealing, in which the donor is used to
resynthesize genetic information that will become part of the
target, and/or related processes. In some cases, the donor
polynucleotide, a portion of the donor polynucleotide, a copy of
the donor polynucleotide, or a portion of a copy of the donor
polynucleotide integrates into the target DNA. See Wang et al.
(2013) Cell 153:910-918; Mandalos et al. (2012) PLOS ONE
7:e45768:1-9; and Wang et al. (2013) Nat Biotechnol. 31:530-532,
each of which is herein incorporated by reference in its entirety
for all purposes.
[0086] NHEJ includes the repair of double-strand breaks in a
nucleic acid by direct ligation of the break ends to one another or
to an exogenous sequence without the need for a homologous
template. Ligation of non-contiguous sequences by NHEJ can often
result in deletions, insertions, or translocations near the site of
the double-strand break. For example, NHEJ can also result in the
targeted integration of an exogenous donor nucleic acid through
direct ligation of the break ends with the ends of the exogenous
donor nucleic acid (i.e., NHEJ-based capture). Such NHEJ-mediated
targeted integration can be preferred for insertion of an exogenous
donor nucleic acid when homology directed repair (HDR) pathways are
not readily usable (e.g., in non-dividing cells, primary cells, and
cells which perform homology-based DNA repair poorly). In addition,
in contrast to homology-directed repair, knowledge concerning large
regions of sequence identity flanking the cleavage site is not
needed, which can be beneficial when attempting targeted insertion
into organisms that have genomes for which there is limited
knowledge of the genomic sequence. The integration can proceed via
ligation of blunt ends between the exogenous donor nucleic acid and
the cleaved genomic sequence, or via ligation of sticky ends (i.e.,
having 5' or 3' overhangs) using an exogenous donor nucleic acid
that is flanked by overhangs that are compatible with those
generated by a nuclease agent in the cleaved genomic sequence. See,
e.g., US 2011/020722, WO 2014/033644, WO 2014/089290, and Maresca
et al. (2013) Genome Res. 23(3):539-546, each of which is herein
incorporated by reference in its entirety for all purposes. If
blunt ends are ligated, target and/or donor resection may be needed
to generation regions of microhomology needed for fragment joining,
which may create unwanted alterations in the target sequence.
[0087] The term "antigen-binding protein" includes any protein that
binds to an antigen. Examples of antigen-binding proteins include
an antibody, an antigen-binding fragment of an antibody, a
multispecific antibody (e.g., a bi-specific antibody), an scFV, a
bis-scFV, a diabody, a triabody, a tetrabody, a V-NAR, a VHH, a VL,
a F(ab), a F(ab).sub.2, a DVD (dual variable domain antigen-binding
protein), an SVD (single variable domain antigen-binding protein),
a bispecific T-cell engager (BiTE), or a Davisbody (U.S. Pat. No.
8,586,713, herein incorporated by reference herein in its entirety
for all purposes).
[0088] The term "antigen" refers to a substance, whether an entire
molecule or a domain within a molecule, which is capable of
eliciting production of antibodies with binding specificity to that
substance. The term antigen also includes substances, which in wild
type host organisms would not elicit antibody production by virtue
of self-recognition, but can elicit such a response in a host
animal with appropriate genetic engineering to break immunological
tolerance.
[0089] The term "epitope" refers to a site on an antigen to which
an antigen-binding protein (e.g., antibody) binds. An epitope can
be formed from contiguous amino acids or noncontiguous amino acids
juxtaposed by tertiary folding of one or more proteins. Epitopes
formed from contiguous amino acids (also known as linear epitopes)
are typically retained on exposure to denaturing solvents whereas
epitopes formed by tertiary folding (also known as conformational
epitopes) are typically lost on treatment with denaturing solvents.
An epitope typically includes at least 3, and more usually, at
least 5 or 8-10 amino acids in a unique spatial conformation.
Methods of determining spatial conformation of epitopes include,
for example, x-ray crystallography and 2-dimensional nuclear
magnetic resonance. See, e.g., Epitope Mapping Protocols, in
Methods in Molecular Biology, Vol. 66, Glenn E. Morris, Ed. (1996),
herein incorporated by reference in its entirety for all
purposes.
[0090] An antibody paratope as described herein generally comprises
at a minimum a complementarity determining region (CDR) that
specifically recognizes the heterologous epitope (e.g., a CDR3
region of a heavy and/or light chain variable domain).
[0091] The term "antibody" includes immunoglobulin molecules
comprising four polypeptide chains, two heavy (H) chains and two
light (L) chains inter-connected by disulfide bonds. Each heavy
chain comprises a heavy chain variable domain and a heavy chain
constant region (C.sub.H). The heavy chain constant region
comprises three domains: C.sub.H1, C.sub.H2 and C.sub.H3. Each
light chain comprises a light chain variable domain and a light
chain constant region (CO. The heavy chain and light chain variable
domains can be further subdivided into regions of hypervariability,
termed complementarity determining regions (CDR), interspersed with
regions that are more conserved, termed framework regions (FR).
Each heavy and light chain variable domain comprises three CDRs and
four FRs, arranged from amino-terminus to carboxy-terminus in the
following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4 (heavy chain
CDRs may be abbreviated as HCDR1, HCDR2 and HCDR3; light chain CDRs
may be abbreviated as LCDR1, LCDR2 and LCDR3). The term "high
affinity" antibody refers to an antibody that has a K.sub.D with
respect to its target epitope about of 10.sup.-9 M or lower (e.g.,
about 1.times.10.sup.-9 M, 1.times.10.sup.-10 M, 1.times.10.sup.-11
M, or about 1.times.10.sup.-12 M). In one embodiment, K.sub.D is
measured by surface plasmon resonance, e.g., BIACORE.TM.; in
another embodiment, K.sub.D is measured by ELISA.
[0092] Specific binding of an antigen-binding protein to its target
antigen includes binding with an affinity of at least 10.sup.6,
10.sup.7, 10.sup.8, 10.sup.9, or 10.sup.10 M.sup.-1. Specific
binding is detectably higher in magnitude and distinguishable from
non-specific binding occurring to at least one unrelated target.
Specific binding can be the result of formation of bonds between
particular functional groups or particular spatial fit (e.g., lock
and key type) whereas non-specific binding is usually the result of
van der Waals forces. Specific binding does not however necessarily
imply that an antigen-binding protein binds one and only one
target.
[0093] The term "antisense RNA" refers to a single-stranded RNA
that is complementary to a messenger RNA strand transcribed in a
cell.
[0094] The term "small interfering RNA (siRNA)" refers to a
typically double-stranded RNA molecule that induces the RNA
interference (RNAi) pathway. These molecules can vary in length
(generally between 18-30 base pairs) and contain varying degrees of
complementarity to their target mRNA in the antisense strand. Some,
but not all, siRNAs have unpaired overhanging bases on the 5' or 3'
end of the sense strand and/or the antisense strand. The term
"siRNA" includes duplexes of two separate strands, as well as
single strands that can form hairpin structures comprising a duplex
region. The double-stranded structure can be, for example, less
than 20, 25, 30, 35, 40, 45, or 50 nucleotides in length. For
example, the double-stranded structure can be from about 21-23
nucleotides in length, from about 19-25 nucleotides in length, or
from about 19-23 nucleotides in length.
[0095] The term "short hairpin RNA (shRNA)" refers to a single
strand of RNA bases that self-hybridizes in a hairpin structure and
can induce the RNA interference (RNAi) pathway upon processing.
These molecules can vary in length (generally about 50-90
nucleotides in length, or in some cases up to greater than 250
nucleotides in length, e.g., for microRNA-adapted shRNA). shRNA
molecules are processed within the cell to form siRNAs, which in
turn can knock down gene expression. shRNAs can be incorporated
into vectors. The term "shRNA" also refers to a DNA molecule from
which a short, hairpin RNA molecule may be transcribed.
[0096] Compositions or methods "comprising" or "including" one or
more recited elements may include other elements not specifically
recited. For example, a composition that "comprises" or "includes"
a protein may contain the protein alone or in combination with
other ingredients. The transitional phrase "consisting essentially
of" means that the scope of a claim is to be interpreted to
encompass the specified elements recited in the claim and those
that do not materially affect the basic and novel characteristic(s)
of the claimed invention. Thus, the term "consisting essentially
of" when used in a claim of this invention is not intended to be
interpreted to be equivalent to "comprising."
[0097] "Optional" or "optionally" means that the subsequently
described event or circumstance may or may not occur and that the
description includes instances in which the event or circumstance
occurs and instances in which it does not.
[0098] Designation of a range of values includes all integers
within or defining the range, and all subranges defined by integers
within the range.
[0099] Unless otherwise apparent from the context, the term "about"
encompasses values within a standard margin of error of measurement
(e.g., SEM) of a stated value.
[0100] The term "and/or" refers to and encompasses any and all
possible combinations of one or more of the associated listed
items, as well as the lack of combinations when interpreted in the
alternative ("or").
[0101] The term "or" refers to any one member of a particular list
and also includes any combination of members of that list.
[0102] The singular forms of the articles "a," "an," and "the"
include plural references unless the context clearly dictates
otherwise. For example, the term "a protein" or "at least one
protein" can include a plurality of proteins, including mixtures
thereof.
[0103] Statistically significant means p.ltoreq.0.05.
DETAILED DESCRIPTION
I. Overview
[0104] Disclosed herein are non-human animal genomes, non-human
animal cells, and non-human animals comprising in their genome a
humanized TTR locus and methods of using such non-human animal
cells and non-human animals. Non-human animal cells or non-human
animals comprising a humanized TTR locus express a human
transthyretin protein or a chimeric transthyretin protein
comprising one or more fragments of a human transthyretin protein.
Such non-human animal cells and non-human animals can be used to
assess delivery or efficacy of human-TTR-targeting agents (e.g.,
CRISPR/Cas9 genome editing agents) ex vivo or in vivo and can be
used in methods of optimizing the delivery of efficacy of such
agents ex vivo or in vivo.
[0105] In some of the non-human animal cells and non-human animals
disclosed herein, most or all of the human TTR genomic DNA is
inserted into the corresponding orthologous non-human animal Ttr
locus. In some of the non-human animal cells and non-human animals
disclosed herein, most or all of the non-human animal Ttr genomic
DNA is replaced one-for-one with corresponding orthologous human
TTR genomic DNA. Compared to non-human animals with cDNA
insertions, expression levels should be higher when the intron-exon
structure and splicing machinery are maintained because conserved
regulator elements are more likely to be left intact, and spliced
transcripts that undergo RNA processing are more stable than cDNAs.
In contrast, insertion of human TTR cDNA (e.g., along with
insertion of an artificial beta-globin intron in the 5' UTR) into a
non-human animal Ttr locus would abolish conserved regulatory
elements such as those contained within the first exon and intron
of the non-human animal Ttr. Replacing the non-human animal genomic
sequence with the corresponding orthologous human genomic sequence
or inserting human TTR genomic sequence in the corresponding
orthologous non-human Ttr locus is more likely to result in
faithful expression of the transgene from the endogenous Ttr locus.
Similarly, transgenic non-human animals with transgenic insertion
of human-TTR-coding sequences at a random genomic locus rather than
the endogenous non-human-animal Ttr locus will not as accurately
reflect the endogenous regulation of Ttr expression. A humanized
TTR allele resulting from replacing most or all of the non-human
animal genomic DNA one-for-one with corresponding orthologous human
genomic DNA or inserting human TTR genomic sequence in the
corresponding orthologous non-human Ttr locus will provide the true
human target or a close approximation of the true human target of
human-TTR-targeting reagents (e.g., CRISPR/Cas9 reagents designed
to target human TTR), thereby enabling testing of the efficacy and
mode of action of such agents in live animals as well as
pharmacokinetic and pharmacodynamics studies in a setting where the
humanized protein and humanized gene are the only version of TTR
present.
II. Non-Human Animals Comprising a Humanized TTR Locus
[0106] The cells and non-human animals disclosed herein comprise in
their genome a humanized TTR locus. Cells or non-human animals
comprising a humanized TTR locus express a human transthyretin
protein or a partially humanized, chimeric transthyretin protein in
which one or more fragments of the native transthyretin protein
have been replaced with corresponding fragments from human
transthyretin.
[0107] A. Transthyretin (TTR)
[0108] The cells and non-human animals described herein comprise a
humanized transthyretin (Ttr) locus. Transthyretin (TTR) is a
127-amino acid, 55 kDa serum and cerebrospinal fluid transport
protein primarily synthesized by the liver but also produced by the
choroid plexus. It has also been referred to as prealbumin,
thyroxine binding prealbumin, ATTR, TBPA, CTS, CTS1, HEL111,
HsT2651, and PALB. In its native state, TTR exists as a tetramer.
In homozygotes, homo-tetramers comprise identical 127-amino-acid
beta-sheet-rich subunits. In heterozygotes, TTR tetramers can be
made up of variant and/or wild-type subunits, typically combined in
a statistical fashion. TTR is responsible for carrying thyroxine
(T4) and retinol-bound RBP (retinol-binding protein) in both the
serum and the cerebrospinal fluid.
[0109] Unless otherwise apparent from context, reference to human
transthyretin (TTR) or its fragments or domains includes the
natural, wild type human amino acid sequences including isoforms
and allelic variants thereof. Transthyretin precursor protein
includes a signal sequence (typically 20 amino acids), whereas the
mature transthyretin protein does not. Exemplary TTR polypeptide
sequences are designated by Accession Numbers NP_000362.1 (NCBI)
and P02766.1 (UniProt) (identical, each set forth SEQ ID NO: 1).
Residues may be numbered according to UniProt Accession Number
P02766.1, with the first amino acid of the mature protein (i.e.,
not including the 20 amino acid signal sequence) designated residue
1. In any other TTR protein, residues are numbered according to the
corresponding residues in UniProt Accession Number P02766.1 on
maximum alignment.
[0110] The human TTR gene is located on chromosome 18 and includes
four exons and three introns. An exemplary human TTR gene is from
residues 5001-12258 in the sequence designated by GenBank Accession
Number NG_009490.1 (SEQ ID NO: 3). The four exons in SEQ ID NO: 3
include residues 1-205, 1130-1260, 3354-3489, and 6802-7258,
respectively. The TTR coding sequence in SEQ ID NO: 3 includes
residues 137-205, 1130-1260, 3354-3489, and 6802-6909. An exemplary
human TTR mRNA is designated by NCBI Accession Number NM_000371.3
(SEQ ID NO: 4).
[0111] The mouse Ttr gene is located and chromosome 18 and also
includes four exons and three introns. An exemplary mouse Ttr gene
is from residues 20665250 to 20674326 the sequence designated by
GenBank Accession Number NC_000084.6 (SEQ ID NO: 5). The four exons
in SEQ ID NO: 5 include residues 1-258, 1207-1337, 4730-4865, and
8382-9077, respectively. The Ttr coding sequence in SEQ ID NO: 5
includes residues 190-258, 1207-1337, 4730-4865, and 8382-8489. An
exemplary mouse TTR protein is designated by UniProt Accession
Number P07309.1 or NCBI Accession Number NP_038725.1 (identical,
each set forth SEQ ID NO: 6). An exemplary mouse Ttr mRNA is
designated by NCBI Accession Number NM_013697.5 (SEQ ID NO: 7).
[0112] An exemplary rat TTR protein is designated by UniProt
Accession Number P02767. An exemplary pig TTR protein is designated
by UniProt Accession Number P50390. An exemplary chicken TTR
protein is designated by UniProt Accession Number P27731. An
exemplary cow TTR protein is designated by UniProt Accession Number
O46375. An exemplary sheep TTR protein is designated by UniProt
Accession Number P12303. An exemplary chimpanzee TTR protein
designated by UniProt Accession Number Q5U7I5. An exemplary
orangutan TTR protein is designated by UniProt Accession Number
Q5NVS2. An exemplary rabbit TTR protein is designated by UniProt
Accession Number P07489. An exemplary cynomolgus monkey (macaque)
TTR protein is designated by UniProt Accession Number Q8HXW1.
[0113] Transthyretin (TTR) amyloidosis is a systemic disorder
characterized by pathogenic, misfolded TTR and the extracellular
deposition of amyloid fibrils composed of TTR. TTR amyloidosis is
generally caused by destabilization of the native TTR tetramer form
(due to environmental or genetic conditions), leading to
dissociation, misfolding, and aggregation of TTR into amyloid
fibrils that accumulate in various organs and tissues, causing
progressive dysfunction. The dissociated monomers have a propensity
to form misfolded protein aggregates and amyloid fibrils.
[0114] In humans, both wild-type TTR tetramers and mixed tetramers
made up of mutant and wild-type subunits can dissociate, misfold,
and aggregate, with the process of amyloidogenesis leading to the
degeneration of post-mitotic tissue. Thus, TTR amyloidoses
encompass diseases caused by pathogenic misfolded TTR resulting
from mutations in TTR or resulting from non-mutated, misfolded
TTR.
[0115] Senile systemic amyloidosis (SSA) and senile cardiac
amyloidosis (SCA) are age-related types of amyloidosis that result
from the deposition of wild-type TTR amyloid outside and within the
cardiomyocytes of the heart. TTR amyloidosis is also the most
common form of hereditary (familial) amyloidosis, which is caused
by mutations that destabilize the TTR protein. TTR amyloidoses
associated with point mutations in the TTR gene include familial
amyloid polyneuropathy (FAP), familial amyloid cardiomyopathy
(FAC), and central nervous system selective amyloidosis (CNSA).
[0116] B. Humanized TTR Loci
[0117] A humanized TTR locus disclosed herein can be a Ttr locus in
which the entire Ttr gene is replaced with the corresponding
orthologous human TTR sequence, or it can be a Ttr locus in which
only a portion of the Ttr gene is replaced with the corresponding
orthologous human TTR sequence (i.e., humanized). A humanized TTR
locus can also comprise human TTR sequence inserted into an
endogenous Ttr locus without replacing the corresponding
orthologous endogenous sequence. A human TTR sequence corresponding
to a particular segment of endogenous Ttr sequence refers to the
region of human TTR that aligns with the particular segment of
endogenous Ttr sequence when human TTR and the endogenous Ttr are
optimally aligned. Optionally, the human TTR sequence is modified
to be codon-optimized based on codon usage in the non-human animal.
Replaced or inserted (i.e., humanized) regions can include coding
regions such as an exon, non-coding regions such as an intron,
untranslated regions, or regulatory regions (e.g., a promoter, an
enhancer, or a transcriptional repressor-binding element), or any
combination thereof.
[0118] A humanized TTR locus is one in which a region of the
endogenous Ttr locus has been deleted and replaced with a
corresponding orthologous human TTR sequence (e.g., orthologous
wild type human TTR sequence). Alternatively, a humanized TTR locus
is one in which a region of the human TTR locus has been inserted
into a corresponding endogenous non-human-animal Ttr locus. As one
example, the replaced or inserted region of the endogenous Ttr
locus can comprise both a coding sequence (i.e., all or part of an
exon) and a non-coding sequence (i.e., all or part of intron), such
as at least one exon and at least one intron. For example, the
replaced or inserted region can comprise at least one exon and at
least one intron. The replaced or inserted region comprising both
coding sequence and non-coding sequence can be a contiguous region
of the endogenous Ttr locus, meaning there is no intervening
sequence between the replaced or inserted coding sequence and the
replaced or inserted non-coding sequence. For example, the replaced
or inserted region can comprise at least one exon and at least one
adjacent intron. The replaced or inserted region can comprise one
exon, two exons, three exons, four exons, or all exons of the
endogenous Ttr locus. The inserted human TTR sequence can comprise
one exon, two exons, three exons, four exons, or all exons of a
human TTR gene. Likewise, the replaced region can comprise one
intron, two introns, three introns, or all introns of the
endogenous Ttr locus. The inserted human TTR sequence can comprise
one intron, two introns, three introns, or all introns of a human
TTR gene. Optionally, one or more introns and/or one or more exons
of the endogenous Ttr locus remain unmodified (i.e., not deleted
and replaced). For example, the first exon of the endogenous Ttr
locus can remain unmodified. Similarly, the first exon and the
first intron of the endogenous Ttr locus can remain unmodified.
[0119] In one specific example, the entire coding sequence for the
transthyretin precursor protein can be deleted and replaced with
the corresponding orthologous human TTR sequence. For example, the
region of the endogenous Ttr locus beginning at the start codon and
ending at the stop codon can be deleted and replaced with the
corresponding orthologous human TTR sequence. In another specific
example, the entire coding sequence for the human transthyretin
precursor protein can be inserted. For example, the region of the
human TTR locus beginning at the start codon and ending at the stop
codon can be inserted.
[0120] Flanking untranslated regions including regulatory sequences
can also be humanized. The first exon of a Ttr locus typically
include a 5' untranslated region upstream of the start codon.
Likewise, the last exon of a Ttr locus typically includes a 3'
untranslated region downstream of the stop codon. Regions upstream
of the Ttr start codon and downstream of the Ttr stop codon can
either be unmodified or can be deleted and replaced with the
corresponding orthologous human TTR sequence. For example, the 5'
untranslated region (UTR), the 3'UTR, or both the 5' UTR and the 3'
UTR can be humanized, or the 5' UTR, the 3'UTR, or both the 5' UTR
and the 3' UTR can remain endogenous. In one specific example, the
5' UTR remains endogenous. In another specific example, the 3' UTR
is humanized, but the 5' UTR remains endogenous. In another
specific example, the 5' UTR remains endogenous, and a human TTR 3'
UTR is inserted into the endogenous Ttr locus. For example, the
human TTR 3' UTR can replace the endogenous 3' UTR or can be
inserted without replacing the endogenous 3' UTR (e.g., it can be
inserted upstream of the endogenous 3' UTR).
[0121] One or more regions of the endogenous Ttr locus encoding one
or more domains of the transthyretin precursor protein can be
humanized. Likewise, one or more regions of the endogenous Ttr
locus encoding one or more domains of the transthyretin precursor
protein can remain unmodified (i.e., not deleted and replaced). For
example, transthyretin precursor proteins typically have a signal
peptide at the N-terminus. The signal peptide can be, for example,
about 20 amino acids in length. The region of the endogenous Ttr
locus encoding the signal peptide can remain unmodified (i.e., not
deleted and replaced), or can be deleted and replaced with the
corresponding orthologous human TTR sequence. Similarly, a region
of the endogenous Ttr locus encoding an epitope recognized by an
anti-human-TTR antigen-binding protein can be humanized.
[0122] Depending on the extent of replacement by corresponding
orthologous sequences or the extent of insertion of human TTR
sequences, regulatory sequences, such as a promoter, can be
endogenous or supplied by the replacing or inserted human
orthologous sequence. For example, the humanized TTR locus can
include the endogenous non-human animal Ttr promoter. The coding
sequence for the transthyretin precursor protein at the genetically
modified endogenous Ttr locus can be operably linked to the
endogenous Ttr promoter. For example, the human TTR sequence can be
operably linked to the endogenous Ttr promoter.
[0123] As a specific example, the humanized TTR locus can be one in
which the region of the endogenous Ttr locus being deleted and
replaced with the corresponding orthologous human TTR sequence or
the region of the human TTR locus being inserted comprises,
consists essentially of, or consists of the region from the Ttr
start codon to the stop codon. The human TTR sequence being
inserted can further comprise a human TTR 3' UTR. For example, the
human TTR sequence at the humanized TTR locus can comprise, consist
essentially of, or consist of the region from the TTR start codon
to the end of the 3' UTR. Optionally, the Ttr coding sequence in
the modified endogenous Ttr locus is operably linked to the
endogenous Ttr promoter. The human TTR sequence at the humanized
TTR locus can comprise, consist essentially of, or consist of a
sequence that is at least 85%, 90%, 95%, 96%, 97%, 98%, 99%, or
100% identical to SEQ ID NO: 18. The humanized TTR locus can
comprise, consist essentially of, or consist of a sequence that is
at least 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to
SEQ ID NO: 14 or 15. The coding sequence (CDS) at the humanized TTR
locus can comprise, consist essentially of, or consist of a
sequence that is at least 85%, 90%, 95%, 96%, 97%, 98%, 99%, or
100% identical to SEQ ID NO: 90 (or degenerates thereof that encode
the same protein). The resulting human transthyretin precursor
protein encoded by the humanized TTR locus can comprise, consist
essentially of, or consist of a sequence that is at least 85%, 90%,
95%, 96%, 97%, 98%, 99%, or 100% identical to SEQ ID NO: 1.
[0124] As another specific example, the humanized TTR locus can be
one in which the region of the endogenous Ttr locus being deleted
and replaced with the corresponding orthologous human TTR sequence
or the region of the human TTR locus being inserted comprises,
consists essentially of, or consists of the region from the start
of the second Ttr exon to the stop codon. The human TTR sequence
being inserted can further comprise a human TTR 3' UTR. For
example, the human TTR sequence at the humanized TTR locus can
comprise, consist essentially of, or consist of the region from the
start of the second human TTR exon to the end of the 3' UTR.
Optionally, the Ttr coding sequence in the modified endogenous Ttr
locus is operably linked to the endogenous Ttr promoter. The human
TTR sequence at the humanized TTR locus can comprise, consist
essentially of, or consist of a sequence that is at least 85%, 90%,
95%, 96%, 97%, 98%, 99%, or 100% identical to SEQ ID NO: 19. The
humanized TTR locus can comprise, consist essentially of, or
consist of a sequence that is at least 85%, 90%, 95%, 96%, 97%,
98%, 99%, or 100% identical to SEQ ID NO: 16 or 17. The coding
sequence (CDS) at the humanized TTR locus can comprise, consist
essentially of, or consist of a sequence that is at least 85%, 90%,
95%, 96%, 97%, 98%, 99%, or 100% identical to SEQ ID NO: 91 (or
degenerates thereof that encode the same protein). The resulting
chimeric transthyretin precursor protein encoded by the humanized
TTR locus can comprise, consist essentially of, or consist of a
sequence that is at least 85%, 90%, 95%, 96%, 97%, 98%, 99%, or
100% identical to SEQ ID NO: 2.
[0125] TTR protein expressed from a humanized TTR locus can be an
entirely human TTR protein or a chimeric endogenous/human TTR
protein (e.g., if the non-human animal is a mouse, a chimeric
mouse/human TTR protein). For example, the signal peptide of the
transthyretin precursor protein can be endogenous, and the
remainder of the protein can be human. Alternatively, the
N-terminus of the transthyretin precursor protein can be
endogenous, and the remainder of the protein can be human. For
example, the N-terminal 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
17, 18, 19, 20, 21, 22, 23, 24, or 25 amino acids can be
endogenous, and the remainder can be human. In a specific example,
the 23 amino acids at the N-terminus are endogenous, and the
remainder of the protein is human.
[0126] Optionally, a humanized TTR locus can comprise other
elements. Examples of such elements can include selection
cassettes, reporter genes, recombinase recognition sites, or other
elements. As one example, a humanized TTR locus can comprise a
removable selection cassette (e.g., a self-deleting selection
cassette) flanked by recombinase recognition sequences (e.g., loxP
sites). Alternatively, the humanized TTR locus can lack other
elements (e.g., can lack a selection cassette and/or can lack a
reporter gene). Examples of suitable reporter genes and reporter
proteins are disclosed elsewhere herein. Examples of suitable
selection markers include neomycin phosphotransferase (neo.sub.r),
hygromycin B phosphotransferase (hyg.sub.r),
puromycin-N-acetyltransferase (puro.sub.r), blasticidin S deaminase
(bsr.sub.r), xanthine/guanine phosphoribosyl transferase (gpt), and
herpes simplex virus thymidine kinase (HSV-k). Examples of
recombinases include Cre, Flp, and Dre recombinases. One example of
a Cre recombinase gene is Crei, in which two exons encoding the Cre
recombinase are separated by an intron to prevent its expression in
a prokaryotic cell. Such recombinases can further comprise a
nuclear localization signal to facilitate localization to the
nucleus (e.g., NLS-Crei). Recombinase recognition sites include
nucleotide sequences that are recognized by a site-specific
recombinase and can serve as a substrate for a recombination event.
Examples of recombinase recognition sites include FRT, FRT11,
FRT71, attp, att, rox, and lox sites such as loxP, lox511, lox2272,
lox66, lox71, loxM2, and lox5171.
[0127] Other elements such as reporter genes or selection cassettes
can be self-deleting cassettes flanked by recombinase recognition
sites. See, e.g., U.S. Pat. No. 8,697,851 and US 2013/0312129, each
of which is herein incorporated by reference in its entirety for
all purposes. As an example, the self-deleting cassette can
comprise a Crei gene (comprises two exons encoding a Cre
recombinase, which are separated by an intron) operably linked to a
mouse Prm1 promoter and a neomycin resistance gene operably linked
to a human ubiquitin promoter. By employing the Prm1 promoter, the
self-deleting cassette can be deleted specifically in male germ
cells of F0 animals. The polynucleotide encoding the selection
marker can be operably linked to a promoter active in a cell being
targeted. Examples of promoters are described elsewhere herein. As
another specific example, a self-deleting selection cassette can
comprise a hygromycin resistance gene coding sequence operably
linked to one or more promoters (e.g., both human ubiquitin and EM7
promoters) followed by a polyadenylation signal, followed by a Crei
coding sequence operably linked to one or more promoters (e.g., an
mPrm1 promoter), followed by another polyadenylation signal,
wherein the entire cassette is flanked by loxP sites.
[0128] The humanized TTR locus can also be a conditional allele.
For example, the conditional allele can be a multifunctional
allele, as described in US 2011/0104799, herein incorporated by
reference in its entirety for all purposes. For example, the
conditional allele can comprise: (a) an actuating sequence in sense
orientation with respect to transcription of a target gene; (b) a
drug selection cassette (DSC) in sense or antisense orientation;
(c) a nucleotide sequence of interest (NSI) in antisense
orientation; and (d) a conditional by inversion module (COIN, which
utilizes an exon-splitting intron and an invertible gene-trap-like
module) in reverse orientation. See, e.g., US 2011/0104799. The
conditional allele can further comprise recombinable units that
recombine upon exposure to a first recombinase to form a
conditional allele that (i) lacks the actuating sequence and the
DSC; and (ii) contains the NSI in sense orientation and the COIN in
antisense orientation. See, e.g., US 2011/0104799.
[0129] C. Non-Human Animal Genomes, Non-Human Animal Cells, and
Non-Human Animals Comprising a Humanized TTR Locus
[0130] Non-human animal genomes, non-human animal cells, and
non-human animals comprising a humanized TTR locus as described
elsewhere herein are provided. The genomes, cells, or non-human
animals can be heterozygous or homozygous for the humanized TTR
locus. A diploid organism has two alleles at each genetic locus.
Each pair of alleles represents the genotype of a specific genetic
locus. Genotypes are described as homozygous if there are two
identical alleles at a particular locus and as heterozygous if the
two alleles differ.
[0131] The non-human animal genomes or cells provided herein can
be, for example, any non-human cell comprising a Ttr locus or a
genomic locus homologous or orthologous to the human TTR locus. The
genomes can be from or the cells can be eukaryotic cells, which
include, for example, animal cells, mammalian cells, non-human
mammalian cells, and human cells. The term "animal" includes
mammals, fishes, and birds. A mammalian cell can be, for example, a
non-human mammalian cell, a rodent cell, a rat cell, a mouse cell,
or a hamster cell. Other non-human mammals include, for example,
non-human primates, monkeys, apes, orangutans, cats, dogs, rabbits,
horses, livestock (e.g., bovine species such as cows, steer, and so
forth; ovine species such as sheep, goats, and so forth; and
porcine species such as pigs and boars). Domesticated animals and
agricultural animals are also included. The term "non-human"
excludes humans.
[0132] The cells can also be any type of undifferentiated or
differentiated state. For example, a cell can be a totipotent cell,
a pluripotent cell (e.g., a human pluripotent cell or a non-human
pluripotent cell such as a mouse embryonic stem (ES) cell or a rat
ES cell), or a non-pluripotent cell. Totipotent cells include
undifferentiated cells that can give rise to any cell type, and
pluripotent cells include undifferentiated cells that possess the
ability to develop into more than one differentiated cell types.
Such pluripotent and/or totipotent cells can be, for example, ES
cells or ES-like cells, such as an induced pluripotent stem (iPS)
cells. ES cells include embryo-derived totipotent or pluripotent
cells that are capable of contributing to any tissue of the
developing embryo upon introduction into an embryo. ES cells can be
derived from the inner cell mass of a blastocyst and are capable of
differentiating into cells of any of the three vertebrate germ
layers (endoderm, ectoderm, and mesoderm).
[0133] The cells provided herein can also be germ cells (e.g.,
sperm or oocytes). The cells can be mitotically competent cells or
mitotically-inactive cells, meiotically competent cells or
meiotically-inactive cells. Similarly, the cells can also be
primary somatic cells or cells that are not a primary somatic cell.
Somatic cells include any cell that is not a gamete, germ cell,
gametocyte, or undifferentiated stem cell. For example, the cells
can be liver cells, such as hepatoblasts or hepatocytes.
[0134] Suitable cells provided herein also include primary cells.
Primary cells include cells or cultures of cells that have been
isolated directly from an organism, organ, or tissue. Primary cells
include cells that are neither transformed nor immortal. They
include any cell obtained from an organism, organ, or tissue which
was not previously passed in tissue culture or has been previously
passed in tissue culture but is incapable of being indefinitely
passed in tissue culture. Such cells can be isolated by
conventional techniques and include, for example, hepatocytes.
[0135] Other suitable cells provided herein include immortalized
cells. Immortalized cells include cells from a multicellular
organism that would normally not proliferate indefinitely but, due
to mutation or alteration, have evaded normal cellular senescence
and instead can keep undergoing division. Such mutations or
alterations can occur naturally or be intentionally induced. A
specific example of an immortalized cell line is the HepG2 human
liver cancer cell line. Numerous types of immortalized cells are
well known. Immortalized or primary cells include cells that are
typically used for culturing or for expressing recombinant genes or
proteins.
[0136] The cells provided herein also include one-cell stage
embryos (i.e., fertilized oocytes or zygotes). Such one-cell stage
embryos can be from any genetic background (e.g., BALB/c, C57BL/6,
129, or a combination thereof for mice), can be fresh or frozen,
and can be derived from natural breeding or in vitro
fertilization.
[0137] The cells provided herein can be normal, healthy cells, or
can be diseased or mutant-bearing cells.
[0138] In a specific example, the non-human animal cells are
embryonic stem (ES) cells or liver cells, such as mouse or rat ES
cells or liver cells.
[0139] Non-human animals comprising a humanized TTR locus as
described herein can be made by the methods described elsewhere
herein. The term "animal" includes mammals, fishes, and birds.
Non-human mammals include, for example, non-human primates,
monkeys, apes, orangutans, cats, dogs, horses, rabbits, rodents
(e.g., mice, rats, hamsters, and guinea pigs), and livestock (e.g.,
bovine species such as cows and steer; ovine species such as sheep
and goats; and porcine species such as pigs and boars).
Domesticated animals and agricultural animals are also included.
The term "non-human animal" excludes humans. Preferred non-human
animals include, for example, rodents, such as mice and rats.
[0140] The non-human animals can be from any genetic background.
For example, suitable mice can be from a 129 strain, a C57BL/6
strain, a mix of 129 and C57BL/6, a BALB/c strain, or a Swiss
Webster strain. Examples of 129 strains include 129P1, 129P2,
129P3, 129X1, 129S1 (e.g., 129S1/SV, 129S1/Svlm), 129S2, 129S4,
129S5, 129S9/SvEvH, 129S6 (129/SvEvTac), 129S7, 129S8, 129T1, and
129T2. See, e.g., Festing et al. (1999) Mammalian Genome 10:836,
herein incorporated by reference in its entirety for all purposes.
Examples of C57BL strains include C57BL/A, C57BL/An, C57BL/GrFa,
C57BL/Kal_wN, C57BL/6, C57BL/6J, C57BL/6ByJ, C57BL/6NJ, C57BL/10,
C57BL/10ScSn, C57BL/10Cr, and C57BL/O1a. Suitable mice can also be
from a mix of an aforementioned 129 strain and an aforementioned
C57BL/6 strain (e.g., 50% 129 and 50% C57BL/6). Likewise, suitable
mice can be from a mix of aforementioned 129 strains or a mix of
aforementioned BL/6 strains (e.g., the 129S6 (129/SvEvTac)
strain).
[0141] Similarly, rats can be from any rat strain, including, for
example, an ACI rat strain, a Dark Agouti (DA) rat strain, a Wistar
rat strain, a LEA rat strain, a Sprague Dawley (SD) rat strain, or
a Fischer rat strain such as Fisher F344 or Fisher F6. Rats can
also be obtained from a strain derived from a mix of two or more
strains recited above. For example, a suitable rat can be from a DA
strain or an ACI strain. The ACI rat strain is characterized as
having black agouti, with white belly and feet and an RT1.sup.av1
haplotype. Such strains are available from a variety of sources
including Harlan Laboratories. The Dark Agouti (DA) rat strain is
characterized as having an agouti coat and an RT1.sup.av1
haplotype. Such rats are available from a variety of sources
including Charles River and Harlan Laboratories. Some suitable rats
can be from an inbred rat strain. See, e.g., US 2014/0235933,
herein incorporated by reference in its entirety for all
purposes.
III. Methods of Using Non-Human Animals Comprising a Humanized TTR
Locus for Assessing Efficacy of Human-TTR-Targeting Reagents In
Vivo or Ex Vivo
[0142] Various methods are provided for using the non-human animals
comprising a humanized TTR locus as described elsewhere herein for
assessing or optimizing delivery or efficacy of human-TTR-targeting
reagents (e.g., therapeutic molecules or complexes) in vivo or ex
vivo. Because the non-human animals comprise a humanized TTR locus,
the non-human animals will more accurately reflect the efficacy of
a human TTR-targeting reagent. Such non-human animals are
particularly useful for testing genome-editing reagents designed to
target the human TTR gene because the non-human animals disclosed
herein comprise humanized endogenous Ttr loci rather than
transgenic insertions of human TTR sequence at random genomic loci,
and the humanized endogenous Ttr loci comprise orthologous human
genomic TTR sequence from both coding and non-coding regions rather
than an artificial cDNA sequence.
[0143] A. Methods of Testing Efficacy of Human-TTR-Targeting
Reagents In Vivo or Ex Vivo
[0144] Various methods are provided for assessing delivery or
efficacy of human-TTR-targeting reagents in vivo using non-human
animals comprising a humanized TTR locus as described elsewhere
herein. Such methods can comprise: (a) introducing into the
non-human animal a human-TTR-targeting reagent (i.e., administering
the human-TTR-targeting reagent to the non-human animal); and (b)
assessing the activity of the human-TTR-targeting reagent.
[0145] The human-TTR-targeting reagent can be any biological or
chemical agent that targets the human TTR locus (the human TTR
gene), the human TTR mRNA, or the human transthyretin protein.
Examples of human-TTR-targeting reagents are disclosed elsewhere
herein and include, for example, genome-editing agents. For
example, the human-TTR-targeting reagent can be a TTR-targeting
nucleic acid (e.g., CRISPR/Cas guide RNAs, short hairpin RNAs
(shRNAs), or small interfering RNAs (siRNAs)) or nucleic acid
encoding a TTR-targeting protein (e.g., a Cas proteins such as
Cas9, a ZFN, or a TALEN). Alternatively, the human-TTR-targeting
reagent can be a TTR-targeting antibody or antigen-binding protein,
or any other large molecule or small molecule that targets human
TTR.
[0146] Such human-TTR-targeting reagents can be administered by any
delivery method (e.g., AAV, LNP, or HDD) as disclosed in more
detail elsewhere herein and by any route of administration. Means
of delivering therapeutic complexes and molecules and routes of
administration are disclosed in more detail elsewhere herein. In
particular methods, the reagents delivered via AAV-mediated
delivery. For example, AAV8 can be used to target the liver. In
other particular methods, the reagents are delivered by
LNP-mediated delivery. In other particular methods, the reagents
are delivered by hydrodynamic delivery (HDD). The dose can be any
suitable dose. For example, in some methods in which the reagents
(e.g., Cas9 mRNA and gRNA) are delivered by LNP-mediated delivery,
the dose can be between about 0.01 and about 10 mg/kg, about 0.01
and about 5 mg/kg, between about 0.01 and about 4 mg/kg, between
about 0.01 and about 3 mg/kg, between about 0.01 and about 2 mg/kg,
between about 0.01 and about 1 mg/kg, between about 0.1 and about
10 mg/kg, between about 0.1 and about 6 mg/kg; between about 0.1
and about 5 mg/kg, between about 0.1 and about 4 mg/kg, between
about 0.1 and about 3 mg/kg, between about 0.1 and about 2 mg/kg,
between about 0.1 and about 1 mg/kg, between about 0.3 and about 10
mg/kg, between about 0.3 and about 6 mg/kg; between about 0.3 and
about 5 mg/kg, between about 0.3 and about 4 mg/kg, between about
0.3 and about 3 mg/kg, between about 0.3 and about 2 mg/kg, between
about 0.3 and about 1 mg/kg, about 0.1 mg/kg, about 0.3 mg/kg,
about 1 mg/kg, about 2 mg/kg, or about 3 mg/kg. In a specific
example, the dose is between about 0.1 and about 6 mg/kg; between
about 0.1 and about 3 mg/kg, or between about 0.1 and about 2
mg/kg. In a specific example, the human-TTR-targeting reagent is a
genome editing reagent, the LNP dose is about 1 mg/kg, and the
percent genome editing at the humanized TTR locus is between about
70% and about 80%. In another specific example, the
human-TTR-targeting reagent is a genome editing reagent, the LNP
dose is about 0.3 mg/kg, and the percent editing is between about
50% and about 80%. In another specific example, the
human-TTR-targeting reagent is a genome editing reagent, the LNP
dose is about 0.1 mg/kg, and the percent editing is between about
20% and about 80%. In another specific example, the LNP dose is
about 1 mg/kg, and the serum TTR levels are reduced to between
about 0% and about 10% or between about 0% and about 35% of control
levels. In another specific example, the LNP dose is about 0.3
mg/kg, and the serum TTR levels are reduced to between about 0% and
about 20% or about 0% and about 95% of control levels. In another
specific example, the LNP dose is about 0.1 mg/kg, and the serum
TTR levels are reduced to between about 0% and about 60% or about
0% and about 99% of control levels.
[0147] Methods for assessing activity of the human-TTR-targeting
reagent are well-known and are provided elsewhere herein.
Assessment of activity can be in any cell type, any tissue type, or
any organ type as disclosed elsewhere herein. In some methods,
assessment of activity is in liver cells. If the TTR-targeting
reagent is a genome editing reagent (e.g., a nuclease agent), such
methods can comprise assessing modification of the humanized TTR
locus. As one example, the assessing can comprise measuring
non-homologous end joining (NHEJ) activity at the humanized TTR
locus. This can comprise, for example, measuring the frequency of
insertions or deletions within the humanized TTR locus. For
example, the assessing can comprise sequencing the humanized TTR
locus in one or more cells isolated from the non-human animal
(e.g., next-generation sequencing). Assessment can comprise
isolating a target organ (e.g., liver) or tissue from the non-human
animal and assessing modification of humanized TTR locus in the
target organ or tissue. Assessment can also comprise assessing
modification of humanized TTR locus in two or more different cell
types within the target organ or tissue. Similarly, assessment can
comprise isolating a non-target organ or tissue (e.g., two or more
non-target organs or tissues) from the non-human animal and
assessing modification of humanized TTR locus in the non-target
organ or tissue.
[0148] Such methods can also comprise measuring expression levels
of the mRNA produced by the humanized TTR locus, or by measuring
expression levels of the protein encoded by the humanized TTR
locus. For example, protein levels can be measured in a particular
cell, tissue, or organ type (e.g., liver), or secreted levels can
be measured in the serum. Methods for assessing expression of Ttr
mRNA or protein expressed from the humanized TTR locus are provided
elsewhere herein and are well-known.
[0149] The various methods provided above for assessing activity in
vivo can also be used to assess the activity of human-TTR-targeting
reagents ex vivo as described elsewhere herein.
[0150] As one example, if the human-TTR-targeting reagent is a
genome editing reagent (e.g., a nuclease agent), percent editing at
the humanized TTR locus can be assessed (e.g., in liver cells). For
example, the percent editing (e.g., total number of insertions or
deletions observed over the total number of sequences read in the
PCR reaction from a pool of lysed cells) can be at least about 10%,
at least about 20%, at least about 30%, at least about 40%, at
least about 50%, at least about 60%, at least about 70%, at least
about 80%, at least about 90%, at least about 95%, at least about
99%, or, for example, between about 1% and about 99%, between about
10% and about 99%, between about 20% and about 99%, between about
30% and about 99%, between about 40% and about 99%, between about
50% and about 99%, between about 60% and about 99%, between about
1% and about 90%, between about 10% and about 90%, between about
20% and about 90%, between about 30% and about 90%, between about
40% and about 90%, between about 50% and about 90%, between about
60% and about 90%, between about 1% and about 80%, between about
10% and about 80%, between about 20% and about 80%, between about
30% and about 80%, between about 40% and about 80%, between about
50% and about 80%, or between about 60% and about 80%.
[0151] As another example, serum TTR levels can be assessed. For
example, serum TTR levels can be reduced by at least about 10%, at
least about 20%, at least about 30%, at least about 40%, at least
about 50%, at least about 60%, at least about 65%, at least about
70%, at least about 80%, at least about 90%, at least about 95%, at
least about 99%, or, for example, between about 1% and about 99%,
between about 10% and about 99%, between about 20% and about 99%,
between about 30% and about 99%, between about 40% and about 99%,
between about 50% and about 99%, between about 60% and about 99%,
between about 70% and about 99%, between about 80% and about 99%,
between about 1% and about 90%, between about 10% and about 90%,
between about 20% and about 90%, between about 30% and about 90%,
between about 40% and about 90%, between about 50% and about 90%,
between about 60% and about 90%, between about 70% and about 90%,
or between about 80% and about 90%.
[0152] In some methods, the human-TTR-targeting reagent is a
nuclease agent, such as a CRISPR/Cas nuclease agent, that targets
the human TTR gene. Such methods can comprise, for example: (a)
introducing into the non-human animal a nuclease agent designed to
cleave the human TTR gene (e.g., Cas protein such as Cas9 and a
guide RNA designed to target a guide RNA target sequence in the
human TTR gene); and (b) assessing modification of the humanized
TTR locus.
[0153] In the case of a CRISPR/Cas nuclease, for example,
modification of the humanized TTR locus will be induced when the
guide RNA forms a complex with the Cas protein and directs the Cas
protein to the humanized TTR locus, and the Cas/guide RNA complex
cleaves the guide RNA target sequence, triggering repair by the
cell (e.g., via non-homologous end joining (NHEJ) if no donor
sequence is present).
[0154] Optionally, two or more guide RNAs can be introduced, each
designed to target a different guide RNA target sequence within the
human TTR gene. For example, two guide RNAs can be designed to
excise a genomic sequence between the two guide RNA target
sequences. Modification of the humanized TTR locus will be induced
when the first guide RNA forms a complex with the Cas protein and
directs the Cas protein to the humanized TTR locus, the second
guide RNA forms a complex with the Cas protein and directs the Cas
protein to the humanized TTR locus, the first Cas/guide RNA complex
cleaves the first guide RNA target sequence, and the second
Cas/guide RNA complex cleaves the second guide RNA target sequence,
resulting in excision of the intervening sequence.
[0155] Optionally, an exogenous donor nucleic acid capable of
recombining with and modifying a human TTR gene is also introduced
into the non-human animal. Optionally, the nuclease agent or Cas
protein can be tethered to the exogenous donor nucleic acid as
described elsewhere herein. Modification of the humanized TTR locus
will be induced, for example, when the guide RNA forms a complex
with the Cas protein and directs the Cas protein to the humanized
TTR locus, the Cas/guide RNA complex cleaves the guide RNA target
sequence, and the humanized TTR locus recombines with the exogenous
donor nucleic acid to modify the humanized TTR locus. The exogenous
donor nucleic acid can recombine with the humanized TTR locus, for
example, via homology-directed repair (HDR) or via NHEJ-mediated
insertion. Any type of exogenous donor nucleic acid can be used,
examples of which are provided elsewhere herein.
[0156] B. Methods of Optimizing Delivery or Efficacy of
Human-TTR-Targeting Reagent In Vivo or Ex Vivo
[0157] Various methods are provided for optimizing delivery of
human-TTR-targeting reagents to a cell or non-human animal or
optimizing the activity or efficacy of human-TTR-targeting reagents
in vivo. Such methods can comprise, for example: (a) performing the
method of testing the efficacy of a human-TTR-targeting reagent as
described above a first time in a first non-human animal or first
cell comprising a humanized TTR locus; (b) changing a variable and
performing the method a second time in a second non-human animal
(i.e., of the same species) or a second cell comprising a humanized
TTR locus with the changed variable; and (c) comparing the activity
of the human-TTR-targeting reagent in step (a) with the activity of
the human-TTR-targeting reagent in step (b), and selecting the
method resulting in the higher activity.
[0158] Methods of measuring delivery, efficacy, or activity of
human-TTR-targeting reagents are disclosed elsewhere herein. For
example, such methods can comprise measuring modification of the
humanized TTR locus. More effective modification of the humanized
TTR locus can mean different things depending on the desired effect
within the non-human animal or cell. For example, more effective
modification of the humanized TTR locus can mean one or more or all
of higher levels of modification, higher precision, higher
consistency, or higher specificity. Higher levels of modification
(i.e., higher efficacy) of the humanized TTR locus refers to a
higher percentage of cells is targeted within a particular target
cell type, within a particular target tissue, or within a
particular target organ (e.g., liver). Higher precision refers to
more precise modification of the humanized TTR locus (e.g., a
higher percentage of targeted cells having the same modification or
having the desired modification without extra unintended insertions
and deletions (e.g., NHEJ indels)). Higher consistency refers to
more consistent modification of the humanized TTR locus among
different types of targeted cells, tissues, or organs if more than
one type of cell, tissue, or organ is being targeted (e.g.,
modification of a greater number of cell types within the liver).
If a particular organ is being targeted, higher consistency can
also refer to more consistent modification throughout all locations
within the organ (e.g., the liver). Higher specificity can refer to
higher specificity with respect to the genomic locus or loci
targeted, higher specificity with respect to the cell type
targeted, higher specificity with respect to the tissue type
targeted, or higher specificity with respect to the organ targeted.
For example, increased genomic locus specificity refers to less
modification of off-target genomic loci (e.g., a lower percentage
of targeted cells having modifications at unintended, off-target
genomic loci instead of or in addition to modification of the
target genomic locus). Likewise, increased cell type, tissue, or
organ type specificity refers to less modification of off-target
cell types, tissue types, or organ types if a particular cell type,
tissue type, or organ type is being targeted (e.g., when a
particular organ is targeted (e.g., the liver), there is less
modification of cells in organs or tissues that are not intended
targets).
[0159] The variable that is changed can be any parameter. As one
example, the changed variable can be the packaging or the delivery
method by which the human-TTR-targeting reagent or reagents are
introduced into the cell or non-human animal. Examples of delivery
methods, such as LNP, HDD, and AAV, are disclosed elsewhere herein.
For example, the changed variable can be the AAV serotype.
Similarly, the administering can comprise LNP-mediated delivery,
and the changed variable can be the LNP formulation. As another
example, the changed variable can be the route of administration
for introduction of the human-TTR-targeting reagent or reagents
into the cell or non-human animal. Examples of routes of
administration, such as intravenous, intravitreal,
intraparenchymal, and nasal instillation, are disclosed elsewhere
herein.
[0160] As another example, the changed variable can be the
concentration or amount of the human-TTR-targeting reagent or
reagents introduced. As another example, the changed variable can
be the concentration or the amount of one human-TTR-targeting
reagent introduced (e.g., guide RNA, Cas protein, or exogenous
donor nucleic acid) relative to the concentration or the amount
another human-TTR-targeting reagent introduced (e.g., guide RNA,
Cas protein, or exogenous donor nucleic acid).
[0161] As another example, the changed variable can be the timing
of introducing the human-TTR-targeting reagent or reagents relative
to the timing of assessing the activity or efficacy of the
reagents. As another example, the changed variable can be the
number of times or frequency with which the human-TTR-targeting
reagent or reagents are introduced. As another example, the changed
variable can be the timing of introduction of one
human-TTR-targeting reagent introduced (e.g., guide RNA, Cas
protein, or exogenous donor nucleic acid) relative to the timing of
introduction of another human-TTR-targeting reagent introduced
(e.g., guide RNA, Cas protein, or exogenous donor nucleic
acid).
[0162] As another example, the changed variable can be the form in
which the human-TTR-targeting reagent or reagents are introduced.
For example, a guide RNA can be introduced in the form of DNA or in
the form of RNA. A Cas protein (e.g., Cas9) can be introduced in
the form of DNA, in the form of RNA, or in the form of a protein
(e.g., complexed with a guide RNA). An exogenous donor nucleic acid
can be DNA, RNA, single-stranded, double-stranded, linear,
circular, and so forth. Similarly, each of the components can
comprise various combinations of modifications for stability, to
reduce off-target effects, to facilitate delivery, and so forth. As
another example, the changed variable can be the
human-TTR-targeting reagent or reagents that are introduced (e.g.,
introducing a different guide RNA with a different sequence,
introducing a different Cas protein (e.g., introducing a different
Cas protein with a different sequence, or a nucleic acid with a
different sequence but encoding the same Cas protein amino acid
sequence), or introducing a different exogenous donor nucleic acid
with a different sequence).
[0163] In a specific example, the human-TTR-targeting reagent
comprises a Cas protein and a guide RNA designed to target a guide
RNA target sequence in a human TTR gene. In such methods, the
changed variable can be the guide RNA sequence and/or the guide RNA
target sequence. In some such methods, the Cas protein and the
guide RNA can each be administered in the form of RNA, and the
changed variable can be the ratio of Cas mRNA to guide RNA (e.g.,
in an LNP formulation). In some such methods, the changed variable
can be guide RNA modifications (e.g., a guide RNA with a
modification is compared to a guide RNA without the
modification).
[0164] C. Human-TTR-Targeting Reagents
[0165] A human-TTR-targeting reagent can be any reagent that
targets a human TTR gene, a human TTR mRNA, or a human TTR protein.
For example, it can be a genome editing reagent such as a nuclease
agent that cleaves a target sequence within the human TTR gene, it
can be an antisense oligonucleotide targeting a human TTR mRNA, it
can be an antigen-binding protein targeting an epitope of a human
TTR protein, or it can be a small molecule targeting human TTR.
Human-TTR-targeting reagents in the methods disclosed herein can be
known human-TTR-targeting reagents, can be putative-TTR-targeting
reagents (e.g., candidate reagents designed to target human TTR),
or can be reagents being screened for human-TTR-targeting
activity.
[0166] (1) Nuclease Agents Targeting Human TTR Gene
[0167] A human-TTR-targeting reagent can be a genome editing
reagent such as a nuclease agent that cleaves a target sequence
within the human TTR gene. A nuclease target sequence includes a
DNA sequence at which a nick or double-strand break is induced by a
nuclease agent. The target sequence for a nuclease agent can be
endogenous (or native) to the cell or the target sequence can be
exogenous to the cell. A target sequence that is exogenous to the
cell is not naturally occurring in the genome of the cell. The
target sequence can also exogenous to the polynucleotides of
interest that one desires to be positioned at the target locus. In
some cases, the target sequence is present only once in the genome
of the host cell.
[0168] The length of the target sequence can vary, and includes,
for example, target sequences that are about 30-36 bp for a zinc
finger nuclease (ZFN) pair (i.e., about 15-18 bp for each ZFN),
about 36 bp for a Transcription Activator-Like Effector Nuclease
(TALEN), or about 20 bp for a CRISPR/Cas9 guide RNA.
[0169] Any nuclease agent that induces a nick or double-strand
break at a desired target sequence can be used in the methods and
compositions disclosed herein. A naturally occurring or native
nuclease agent can be employed so long as the nuclease agent
induces a nick or double-strand break in a desired target sequence.
Alternatively, a modified or engineered nuclease agent can be
employed. An "engineered nuclease agent" includes a nuclease that
is engineered (modified or derived) from its native form to
specifically recognize and induce a nick or double-strand break in
the desired target sequence. Thus, an engineered nuclease agent can
be derived from a native, naturally occurring nuclease agent or it
can be artificially created or synthesized. The engineered nuclease
can induce a nick or double-strand break in a target sequence, for
example, wherein the target sequence is not a sequence that would
have been recognized by a native (non-engineered or non-modified)
nuclease agent. The modification of the nuclease agent can be as
little as one amino acid in a protein cleavage agent or one
nucleotide in a nucleic acid cleavage agent. Producing a nick or
double-strand break in a target sequence or other DNA can be
referred to herein as "cutting" or "cleaving" the target sequence
or other DNA.
[0170] Active variants and fragments of the exemplified target
sequences are also provided. Such active variants can comprise at
least 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%, 98%, 99% or more sequence identity to the given target
sequence, wherein the active variants retain biological activity
and hence are capable of being recognized and cleaved by a nuclease
agent in a sequence-specific manner. Assays to measure the
double-strand break of a target sequence by a nuclease agent are
well-known. See, e.g., Frendewey et al. (2010) Methods in
Enzymology 476:295-307, which is incorporated by reference herein
in its entirety for all purposes.
[0171] The target sequence of the nuclease agent can be positioned
anywhere in or near the Ttr locus. The target sequence can be
located within a coding region of the Ttr gene, or within
regulatory regions that influence the expression of the gene. A
target sequence of the nuclease agent can be located in an intron,
an exon, a promoter, an enhancer, a regulatory region, or any
non-protein coding region.
[0172] One type of nuclease agent is a Transcription Activator-Like
Effector Nuclease (TALEN). TAL effector nucleases are a class of
sequence-specific nucleases that can be used to make double-strand
breaks at specific target sequences in the genome of a prokaryotic
or eukaryotic organism. TAL effector nucleases are created by
fusing a native or engineered transcription activator-like (TAL)
effector, or functional part thereof, to the catalytic domain of an
endonuclease, such as, for example, FokI. The unique, modular TAL
effector DNA binding domain allows for the design of proteins with
potentially any given DNA recognition specificity. Thus, the DNA
binding domains of the TAL effector nucleases can be engineered to
recognize specific DNA target sites and thus, used to make
double-strand breaks at desired target sequences. See WO
2010/079430; Morbitzer et al. (2010) PNAS 10.1073/pnas.1013133107;
Scholze & Boch (2010) Virulence 1:428-432; Christian et al.
Genetics (2010) 186:757-761; Li et al. (2010) Nuc. Acids Res.
(2010) doi:10.1093/nar/gkq704; and Miller et al. (2011) Nature
Biotechnology 29:143-148, each of which is herein incorporated by
reference in its entirety.
[0173] Examples of suitable TAL nucleases, and methods for
preparing suitable TAL nucleases, are disclosed, e.g., in US
2011/0239315 A1, US 2011/0269234 A1, US 2011/0145940 A1, US
2003/0232410 A1, US 2005/0208489 A1, US 2005/0026157 A1, US
2005/0064474 A1, US 2006/0188987 A1, and US 2006/0063231 A1, each
of which is herein incorporated by reference in its entirety. In
various embodiments, TAL effector nucleases are engineered that cut
in or near a target nucleic acid sequence in, e.g., a locus of
interest or a genomic locus of interest, wherein the target nucleic
acid sequence is at or near a sequence to be modified by a
targeting vector. The TAL nucleases suitable for use with the
various methods and compositions provided herein include those that
are specifically designed to bind at or near target nucleic acid
sequences to be modified by targeting vectors as described
herein.
[0174] In some TALENs, each monomer of the TALEN comprises 33-35
TAL repeats that recognize a single base pair via two hypervariable
residues. In some TALENs, the nuclease agent is a chimeric protein
comprising a TAL-repeat-based DNA binding domain operably linked to
an independent nuclease such as a FokI endonuclease. For example,
the nuclease agent can comprise a first TAL-repeat-based DNA
binding domain and a second TAL-repeat-based DNA binding domain,
wherein each of the first and the second TAL-repeat-based DNA
binding domains is operably linked to a FokI nuclease, wherein the
first and the second TAL-repeat-based DNA binding domain recognize
two contiguous target DNA sequences in each strand of the target
DNA sequence separated by a spacer sequence of varying length
(12-20 bp), and wherein the FokI nuclease subunits dimerize to
create an active nuclease that makes a double strand break at a
target sequence.
[0175] The nuclease agent employed in the various methods and
compositions disclosed herein can further comprise a zinc-finger
nuclease (ZFN). In some ZFNs, each monomer of the ZFN comprises 3
or more zinc finger-based DNA binding domains, wherein each zinc
finger-based DNA binding domain binds to a 3 bp subsite. In other
ZFNs, the ZFN is a chimeric protein comprising a zinc finger-based
DNA binding domain operably linked to an independent nuclease such
as a FokI endonuclease. For example, the nuclease agent can
comprise a first ZFN and a second ZFN, wherein each of the first
ZFN and the second ZFN is operably linked to a FokI nuclease
subunit, wherein the first and the second ZFN recognize two
contiguous target DNA sequences in each strand of the target DNA
sequence separated by about 5-7 bp spacer, and wherein the FokI
nuclease subunits dimerize to create an active nuclease that makes
a double strand break. See, e.g., US20060246567; US20080182332;
US20020081614; US20030021776; WO/2002/057308A2; US20130123484;
US20100291048; WO/2011/017293A2; and Gaj et al. (2013) Trends in
Biotechnology, 31(7):397-405, each of which is herein incorporated
by reference.
[0176] Another type of nuclease agent is a meganuclease.
Meganucleases have been classified into four families based on
conserved sequence motifs, the families are the LAGLIDADG, GIY-YIG,
H-N-H, and His-Cys box families. These motifs participate in the
coordination of metal ions and hydrolysis of phosphodiester bonds.
Meganucleases are notable for their long target sequences, and for
tolerating some sequence polymorphisms in their DNA substrates.
Meganuclease domains, structure and function are known, see for
example, Guhan and Muniyappa (2003) Crit Rev Biochem Mol Biol
38:199-248; Lucas et al., (2001) Nucleic Acids Res 29:960-9; Jurica
and Stoddard, (1999) Cell Mol Life Sci 55:1304-26; Stoddard, (2006)
Q Rev Biophys 38:49-95; and Moure et al., (2002) Nat Struct Biol
9:764. In some examples, a naturally occurring variant and/or
engineered derivative meganuclease is used. Methods for modifying
the kinetics, cofactor interactions, expression, optimal
conditions, and/or target sequence specificity, and screening for
activity are known. See, e.g., Epinat et al., (2003) Nucleic Acids
Res 31:2952-62; Chevalier et al., (2002) Mol Cell 10:895-905;
Gimble et al., (2003) Mol Biol 334:993-1008; Seligman et al.,
(2002) Nucleic Acids Res 30:3870-9; Sussman et al., (2004) J Mol
Biol 342:31-41; Rosen et al., (2006) Nucleic Acids Res 34:4791-800;
Chames et al., (2005) Nucleic Acids Res 33:e178; Smith et al.,
(2006) Nucleic Acids Res 34:e149; Gruen et al., (2002) Nucleic
Acids Res 30:e29; Chen and Zhao, (2005) Nucleic Acids Res 33:e154;
WO2005105989; WO2003078619; WO2006097854; WO2006097853;
WO2006097784; and WO2004031346, each of which is herein
incorporated by reference in its entirety.
[0177] Any meganuclease can be used, including, for example,
I-SceI, I-SceII, I-SceIII, I-SceIV, I-SceV, I-SceVI, I-SceVII,
I-CeuI, I-CeuAIIP, I-CreI, I-CrepsbIP, I-CrepsbIIP, I-CrepsbIIIP,
I-CrepsbIVP, I-TliI, I-PpoI, PI-PspI, F-SceI, F-SceII, F-SuvI,
F-TevI, F-TevII, I-AmaI, I-AniI, I-ChuI, I-CmoeI, I-CpaI, I-CpaII,
I-CsmI, I-CvuI, I-CvuAIP, I-DdiI, I-DdiII, I-DirI, I-DmoI, I-HmuI,
I-HmuII, I-HsNIP, I-LlaI, I-MsoI, I-NaaI, I-NanI, I-NcIIP, I-NgrIP,
I-NitI, I-NjaI, I-Nsp236IP, I-PakI, I-PboIP, I-PcuIP, I-PcuAI,
I-PcuVI, I-PgrIP, I-PobIP, I-PorI, I-PorIIP, I-PbpIP, I-SpBetaIP,
I-ScaI, I-SexIP, I-SneIP, I-SpomI, I-SpomCP, I-SpomIP, I-SpomIIP,
I-SquIP, I-Ssp6803I, I-SthPhiJP, I-SthPhiST3P, I-SthPhiSTe3bP,
I-TdeIP, I-TevI, I-TevII, I-TevIII, I-UarAP, I-UarHGPAIP,
I-UarHGPA13P, I-VinIP, I-ZbiIP, PI-MtuI, PI-MtuHIP PI-MtuHIIP,
PI-PfuI, PI-PfuII, PI-PkoI, PI-PkoII, PI-Rma43812IP, PI-SpBetaIP,
PI-SceI, PI-TfuI, PI-TfuII, PI-ThyI, PI-TliI, PI-TliII, or any
active variants or fragments thereof.
[0178] Meganucleases can recognize, for example, double-stranded
DNA sequences of 12 to 40 base pairs. In some cases, the
meganuclease recognizes one perfectly matched target sequence in
the genome.
[0179] Some meganucleases are homing nucleases. One type of homing
nuclease is a LAGLIDADG family of homing nucleases including, for
example, I-SceI, I-CreI, and I-Dmol.
[0180] Nuclease agents can further comprise CRISPR/Cas systems as
described in more detail below.
[0181] Active variants and fragments of nuclease agents (i.e., an
engineered nuclease agent) are also provided. Such active variants
can comprise at least 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%,
94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the
native nuclease agent, wherein the active variants retain the
ability to cut at a desired target sequence and hence retain nick
or double-strand-break-inducing activity. For example, any of the
nuclease agents described herein can be modified from a native
endonuclease sequence and designed to recognize and induce a nick
or double-strand break at a target sequence that was not recognized
by the native nuclease agent. Thus, some engineered nucleases have
a specificity to induce a nick or double-strand break at a target
sequence that is different from the corresponding native nuclease
agent target sequence. Assays for nick or
double-strand-break-inducing activity are known and generally
measure the overall activity and specificity of the endonuclease on
DNA substrates containing the target sequence.
[0182] The nuclease agent may be introduced into a cell or
non-human animal by any known means. A polypeptide encoding the
nuclease agent may be directly introduced into the cell or
non-human animal. Alternatively, a polynucleotide encoding the
nuclease agent can be introduced into the cell or non-human animal.
When a polynucleotide encoding the nuclease agent is introduced,
the nuclease agent can be transiently, conditionally, or
constitutively expressed within the cell. The polynucleotide
encoding the nuclease agent can be contained in an expression
cassette and be operably linked to a conditional promoter, an
inducible promoter, a constitutive promoter, or a tissue-specific
promoter. Examples of promoters are discussed in further detail
elsewhere herein. Alternatively, the nuclease agent can be
introduced into the cell as an mRNA encoding the nuclease
agent.
[0183] A polynucleotide encoding a nuclease agent can be stably
integrated in the genome of a cell and operably linked to a
promoter active in the cell. Alternatively, a polynucleotide
encoding a nuclease agent can be in a targeting vector.
[0184] When the nuclease agent is provided to the cell through the
introduction of a polynucleotide encoding the nuclease agent, such
a polynucleotide encoding a nuclease agent can be modified to
substitute codons having a higher frequency of usage in the cell of
interest, as compared to the naturally occurring polynucleotide
sequence encoding the nuclease agent. For example, the
polynucleotide encoding the nuclease agent can be modified to
substitute codons having a higher frequency of usage in a given
eukaryotic cell of interest, including a human cell, a non-human
cell, a mammalian cell, a rodent cell, a mouse cell, a rat cell or
any other host cell of interest, as compared to the naturally
occurring polynucleotide sequence.
[0185] (2) CRISPR/Cas Systems Targeting Human TTR Gene
[0186] A particular type of human-TTR-targeting reagent can be a
CRISPR/Cas system that targets the human TTR gene. CRISPR/Cas
systems include transcripts and other elements involved in the
expression of, or directing the activity of, Cas genes. A
CRISPR/Cas system can be, for example, a type I, a type II, or a
type III system. Alternatively, a CRISPR/Cas system can be a type V
system (e.g., subtype V-A or subtype V-B). CRISPR/Cas systems used
in the compositions and methods disclosed herein can be
non-naturally occurring. A "non-naturally occurring" system
includes anything indicating the involvement of the hand of man,
such as one or more components of the system being altered or
mutated from their naturally occurring state, being at least
substantially free from at least one other component with which
they are naturally associated in nature, or being associated with
at least one other component with which they are not naturally
associated. For example, non-naturally occurring CRISPR/Cas systems
can employ CRISPR complexes comprising a gRNA and a Cas protein
that do not naturally occur together, a Cas protein that does not
occur naturally, or a gRNA that does not occur naturally.
[0187] Cas Proteins and Polynucleotides Encoding Cas Proteins.
[0188] Cas proteins generally comprise at least one RNA recognition
or binding domain that can interact with guide RNAs (gRNAs,
described in more detail below). Cas proteins can also comprise
nuclease domains (e.g., DNase or RNase domains), DNA-binding
domains, helicase domains, protein-protein interaction domains,
dimerization domains, and other domains. Some such domains (e.g.,
DNase domains) can be from a native Cas protein. Other such domains
can be added to make a modified Cas protein. A nuclease domain
possesses catalytic activity for nucleic acid cleavage, which
includes the breakage of the covalent bonds of a nucleic acid
molecule. Cleavage can produce blunt ends or staggered ends, and it
can be single-stranded or double-stranded. For example, a wild type
Cas9 protein will typically create a blunt cleavage product.
Alternatively, a wild type Cpf1 protein (e.g., FnCpf1) can result
in a cleavage product with a 5-nucleotide 5' overhang, with the
cleavage occurring after the 18th base pair from the PAM sequence
on the non-targeted strand and after the 23rd base on the targeted
strand. A Cas protein can have full cleavage activity to create a
double-strand break at a target genomic locus (e.g., a
double-strand break with blunt ends), or it can be a nickase that
creates a single-strand break at a target genomic locus.
[0189] Examples of Cas proteins include Cas1, Cas1B, Cas2, Cas3,
Cas4, Cas5, Cas5e (CasD), Cas6, Cas6e, Cas6f, Cas7, Cas8a1, Cas8a2,
Cas8b, Cas8c, Cas9 (Csn1 or Csx12), Cas10, Cas10d, CasF, CasG,
CasH, Csy1, Csy2, Csy3, Cse1 (CasA), Cse2 (CasB), Cse3 (CasE), Cse4
(CasC), Csc1, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1,
Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10,
Csx16, CsaX, Csx3, Csx1, Csx15, Csf1, Csf2, Csf3, Csf4, and Cu1966,
and homologs or modified versions thereof.
[0190] An exemplary Cas protein is a Cas9 protein or a protein
derived from Cas9 protein. Cas9 proteins are from a type II
CRISPR/Cas system and typically share four key motifs with a
conserved architecture. Motifs 1, 2, and 4 are RuvC-like motifs,
and motif 3 is an HNH motif. Exemplary Cas9 proteins are from
Streptococcus pyogenes, Streptococcus thermophilus, Streptococcus
sp., Staphylococcus aureus, Nocardiopsis dassonvillei, Streptomyces
pristinaespiralis, Streptomyces viridochromogenes, Streptomyces
viridochromogenes, Streptosporangium roseum, Streptosporangium
roseum, Alicyclobacillus acidocaldarius, Bacillus pseudomycoides,
Bacillus selenitireducens, Exiguobacterium sibiricum, Lactobacillus
delbrueckii, Lactobacillus salivarius, Microscilla marina,
Burkholderiales bacterium, Polaromonas naphthalenivorans,
Polaromonas sp., Crocosphaera watsonii, Cyanothece sp., Microcystis
aeruginosa, Synechococcus sp., Acetohalobium arabaticum, Ammonifex
degensii, Caldicelulosiruptor becscii, Candidatus Desulforudis,
Clostridium botulinum, Clostridium difficile, Finegoldia magna,
Natranaerobius thermophilus, Pelotomaculum thermopropionicum,
Acidithiobacillus caldus, Acidithiobacillus ferrooxidans,
Allochromatium vinosum, Marinobacter sp., Nitrosococcus halophilus,
Nitrosococcus watsoni, Pseudoalteromonas haloplanktis,
Ktedonobacter racemifer, Methanohalobium evestigatum, Anabaena
variabilis, Nodularia spumigena, Nostoc sp., Arthrospira maxima,
Arthrospira platensis, Arthrospira sp., Lyngbya sp Microcoleus
chthonoplastes, Oscillatoria sp Petrotoga mobilis, Thermosipho
africanus, Acaryochloris marina, Neisseria meningitidis, or
Campylobacter jejuni. Additional examples of the Cas9 family
members are described in WO 2014/131833, herein incorporated by
reference in its entirety for all purposes. Cas9 from S. pyogenes
(SpCas9) (assigned SwissProt accession number Q99ZW2) is an
exemplary Cas9 protein. Cas9 from S. aureus (SaCas9) (assigned
UniProt accession number J7RUA5) is another exemplary Cas9 protein.
Cas9 from Campylobacter jejuni (CjCas9) (assigned UniProt accession
number Q0P897) is another exemplary Cas9 protein. See, e.g., Kim et
al. (2017) Nat. Comm. 8:14500, herein incorporated by reference in
its entirety for all purposes. SaCas9 is smaller than SpCas9, and
CjCas9 is smaller than both SaCas9 and SpCas9. An exemplary Cas9
protein sequence can comprise, consist essentially of, or consist
of SEQ ID NO: 94. An exemplary DNA encoding the Cas9 protein can
comprise, consist essentially of, or consist of SEQ ID NO: 93.
[0191] Another example of a Cas protein is a Cpf1 (CRISPR from
Prevotella and Francisella 1) protein. Cpf1 is a large protein
(about 1300 amino acids) that contains a RuvC-like nuclease domain
homologous to the corresponding domain of Cas9 along with a
counterpart to the characteristic arginine-rich cluster of Cas9.
However, Cpf1 lacks the HNH nuclease domain that is present in Cas9
proteins, and the RuvC-like domain is contiguous in the Cpf1
sequence, in contrast to Cas9 where it contains long inserts
including the HNH domain. See, e.g., Zetsche et al. (2015) Cell
163(3):759-771, herein incorporated by reference in its entirety
for all purposes. Exemplary Cpf1 proteins are from Francisella
tularensis 1, Francisella tularensis subsp. novicida, Prevotella
albensis, Lachnospiraceae bacterium MC2017 1, Butyrivibrio
proteoclasticus, Peregrinibacteria bacterium GW2011_GWA2_33_10,
Parcubacteria bacterium GW2011_GWC2_44_17, Smithella sp. SCADC,
Acidaminococcus sp. BV3L6, Lachnospiraceae bacterium MA2020,
Candidatus Methanoplasma termitum, Eubacterium eligens, Moraxella
bovoculi 237, Leptospira inadai, Lachnospiraceae bacterium ND2006,
Porphyromonas crevioricanis 3, Prevotella disiens, and
Porphyromonas macacae. Cpf1 from Francisella novicida U112 (FnCpf1;
assigned UniProt accession number A0Q7Q2) is an exemplary Cpf1
protein.
[0192] Cas proteins can be wild type proteins (i.e., those that
occur in nature), modified Cas proteins (i.e., Cas protein
variants), or fragments of wild type or modified Cas proteins. Cas
proteins can also be active variants or fragments with respect to
catalytic activity of wild type or modified Cas proteins. Active
variants or fragments with respect to catalytic activity can
comprise at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,
98%, 99% or more sequence identity to the wild type or modified Cas
protein or a portion thereof, wherein the active variants retain
the ability to cut at a desired cleavage site and hence retain
nick-inducing or double-strand-break-inducing activity. Assays for
nick-inducing or double-strand-break-inducing activity are known
and generally measure the overall activity and specificity of the
Cas protein on DNA substrates containing the cleavage site.
[0193] Cas proteins can be modified to increase or decrease one or
more of nucleic acid binding affinity, nucleic acid binding
specificity, and enzymatic activity. Cas proteins can also be
modified to change any other activity or property of the protein,
such as stability. For example, one or more nuclease domains of the
Cas protein can be modified, deleted, or inactivated, or a Cas
protein can be truncated to remove domains that are not essential
for the function of the protein or to optimize (e.g., enhance or
reduce) the activity or a property of the Cas protein.
[0194] One example of a modified Cas protein is the modified
SpCas9-HF1 protein, which is a high-fidelity variant of
Streptococcus pyogenes Cas9 harboring alterations
(N497A/R661A/Q695A/Q926A) designed to reduce non-specific DNA
contacts. See, e.g., Kleinstiver et al. (2016) Nature
529(7587):490-495, herein incorporated by reference in its entirety
for all purposes. Another example of a modified Cas protein is the
modified eSpCas9 variant (K848A/K1003A/R1060A) designed to reduce
off-target effects. See, e.g., Slaymaker et al. (2016) Science
351(6268):84-88, herein incorporated by reference in its entirety
for all purposes. Other SpCas9 variants include K855A and
K810A/K1003A/R1060A.
[0195] Cas proteins can comprise at least one nuclease domain, such
as a DNase domain. For example, a wild type Cpf1 protein generally
comprises a RuvC-like domain that cleaves both strands of target
DNA, perhaps in a dimeric configuration. Cas proteins can also
comprise at least two nuclease domains, such as DNase domains. For
example, a wild type Cas9 protein generally comprises a RuvC-like
nuclease domain and an HNH-like nuclease domain. The RuvC and HNH
domains can each cut a different strand of double-stranded DNA to
make a double-stranded break in the DNA. See, e.g., Jinek et al.
(2012) Science 337:816-821, herein incorporated by reference in its
entirety for all purposes.
[0196] One or more or all of the nuclease domains can be deleted or
mutated so that they are no longer functional or have reduced
nuclease activity. For example, if one of the nuclease domains is
deleted or mutated in a Cas9 protein, the resulting Cas9 protein
can be referred to as a nickase and can generate a single-strand
break at a guide RNA target sequence within a double-stranded DNA
but not a double-strand break (i.e., it can cleave the
complementary strand or the non-complementary strand, but not
both). If both of the nuclease domains are deleted or mutated, the
resulting Cas protein (e.g., Cas9) will have a reduced ability to
cleave both strands of a double-stranded DNA (e.g., a nuclease-null
or nuclease-inactive Cas protein, or a catalytically dead Cas
protein (dCas)). An example of a mutation that converts Cas9 into a
nickase is a D10A (aspartate to alanine at position 10 of Cas9)
mutation in the RuvC domain of Cas9 from S. pyogenes. Likewise,
H939A (histidine to alanine at amino acid position 839), H840A
(histidine to alanine at amino acid position 840), or N863A
(asparagine to alanine at amino acid position N863) in the HNH
domain of Cas9 from S. pyogenes can convert the Cas9 into a
nickase. Other examples of mutations that convert Cas9 into a
nickase include the corresponding mutations to Cas9 from S.
thermophilus. See, e.g., Sapranauskas et al. (2011) Nucleic Acids
Research 39:9275-9282 and WO 2013/141680, each of which is herein
incorporated by reference in its entirety for all purposes. Such
mutations can be generated using methods such as site-directed
mutagenesis, PCR-mediated mutagenesis, or total gene synthesis.
Examples of other mutations creating nickases can be found, for
example, in WO 2013/176772 and WO 2013/142578, each of which is
herein incorporated by reference in its entirety for all purposes.
If all of the nuclease domains are deleted or mutated in a Cas
protein (e.g., both of the nuclease domains are deleted or mutated
in a Cas9 protein), the resulting Cas protein (e.g., Cas9) will
have a reduced ability to cleave both strands of a double-stranded
DNA (e.g., a nuclease-null or nuclease-inactive Cas protein). One
specific example is a D10A/H840A S. pyogenes Cas9 double mutant or
a corresponding double mutant in a Cas9 from another species when
optimally aligned with S. pyogenes Cas9. Another specific example
is a D10A/N863A S. pyogenes Cas9 double mutant or a corresponding
double mutant in a Cas9 from another species when optimally aligned
with S. pyogenes Cas9.
[0197] Examples of inactivating mutations in the catalytic domains
of Staphylococcus aureus Cas9 proteins are also known. For example,
the Staphyloccocus aureus Cas9 enzyme (SaCas9) may comprise a
substitution at position N580 (e.g., N580A substitution) and a
substitution at position D10 (e.g., D10A substitution) to generate
a nuclease-inactive Cas protein. See, e.g., WO 2016/106236, herein
incorporated by reference in its entirety for all purposes.
[0198] Examples of inactivating mutations in the catalytic domains
of Cpf1 proteins are also known. With reference to Cpf1 proteins
from Francisella novicida U112 (FnCpf1), Acidaminococcus sp. BV3L6
(AsCpf1), Lachnospiraceae bacterium ND2006 (LbCpf1), and Moraxella
bovoculi 237 (MbCpf1 Cpf1), such mutations can include mutations at
positions 908, 993, or 1263 of AsCpf1 or corresponding positions in
Cpf1 orthologs, or positions 832, 925, 947, or 1180 of LbCpf1 or
corresponding positions in Cpf1 orthologs. Such mutations can
include, for example one or more of mutations D908A, E993A, and
D1263A of AsCpf1 or corresponding mutations in Cpf1 orthologs, or
D832A, E925A, D947A, and D1180A of LbCpf1 or corresponding
mutations in Cpf1 orthologs. See, e.g., US 2016/0208243, herein
incorporated by reference in its entirety for all purposes.
[0199] Cas proteins (e.g., nuclease-active Cas proteins or
nuclease-inactive Cas proteins) can also be operably linked to
heterologous polypeptides as fusion proteins. For example, a Cas
protein can be fused to a cleavage domain or an epigenetic
modification domain. See WO 2014/089290, herein incorporated by
reference in its entirety for all purposes. Cas proteins can also
be fused to a heterologous polypeptide providing increased or
decreased stability. The fused domain or heterologous polypeptide
can be located at the N-terminus, the C-terminus, or internally
within the Cas protein.
[0200] As one example, a Cas protein can be fused to one or more
heterologous polypeptides that provide for subcellular
localization. Such heterologous polypeptides can include, for
example, one or more nuclear localization signals (NLS) such as the
monopartite SV40 NLS and/or a bipartite alpha-importin NLS for
targeting to the nucleus, a mitochondrial localization signal for
targeting to the mitochondria, an ER retention signal, and the
like. See, e.g., Lange et al. (2007) J. Biol. Chem. 282:5101-5105,
herein incorporated by reference in its entirety for all purposes.
Such subcellular localization signals can be located at the
N-terminus, the C-terminus, or anywhere within the Cas protein. An
NLS can comprise a stretch of basic amino acids, and can be a
monopartite sequence or a bipartite sequence. Optionally, a Cas
protein can comprise two or more NLSs, including an NLS (e.g., an
alpha-importin NLS or a monopartite NLS) at the N-terminus and an
NLS (e.g., an SV40 NLS or a bipartite NLS) at the C-terminus. A Cas
protein can also comprise two or more NLSs at the N-terminus and/or
two or more NLSs at the C-terminus.
[0201] Cas proteins can also be operably linked to a
cell-penetrating domain or protein transduction domain. For
example, the cell-penetrating domain can be derived from the HIV-1
TAT protein, the TLM cell-penetrating motif from human hepatitis B
virus, MPG, Pep-1, VP22, a cell penetrating peptide from Herpes
simplex virus, or a polyarginine peptide sequence. See, e.g., WO
2014/089290 and WO 2013/176772, each of which is herein
incorporated by reference in its entirety for all purposes. The
cell-penetrating domain can be located at the N-terminus, the
C-terminus, or anywhere within the Cas protein.
[0202] Cas proteins can also be operably linked to a heterologous
polypeptide for ease of tracking or purification, such as a
fluorescent protein, a purification tag, or an epitope tag.
Examples of fluorescent proteins include green fluorescent proteins
(e.g., GFP, GFP-2, tagGFP, turboGFP, eGFP, Emerald, Azami Green,
Monomeric Azami Green, CopGFP, AceGFP, ZsGreen1), yellow
fluorescent proteins (e.g., YFP, eYFP, Citrine, Venus, YPet,
PhiYFP, ZsYellow1), blue fluorescent proteins (e.g., eBFP, eBFP2,
Azurite, mKalamal, GFPuv, Sapphire, T-sapphire), cyan fluorescent
proteins (e.g., eCFP, Cerulean, CyPet, AmCyanl, Midoriishi-Cyan),
red fluorescent proteins (e.g., mKate, mKate2, mPlum, DsRed
monomer, mCherry, mRFP1, DsRed-Express, DsRed2, DsRed-Monomer,
HcRed-Tandem, HcRed1, AsRed2, eqFP611, mRaspberry, mStrawberry,
Jred), orange fluorescent proteins (e.g., mOrange, mKO,
Kusabira-Orange, Monomeric Kusabira-Orange, mTangerine, tdTomato),
and any other suitable fluorescent protein. Examples of tags
include glutathione-S-transferase (GST), chitin binding protein
(CBP), maltose binding protein, thioredoxin (TRX), poly(NANP),
tandem affinity purification (TAP) tag, myc, AcV5, AU1, AU5, E,
ECS, E2, FLAG, hemagglutinin (HA), nus, Softag 1, Softag 3, Strep,
SBP, Glu-Glu, HSV, KT3, S, S1, T7, V5, VSV-G, histidine (His),
biotin carboxyl carrier protein (BCCP), and calmodulin.
[0203] Cas proteins can also be tethered to exogenous donor nucleic
acids or labeled nucleic acids. Such tethering (i.e., physical
linking) can be achieved through covalent interactions or
noncovalent interactions, and the tethering can be direct (e.g.,
through direct fusion or chemical conjugation, which can be
achieved by modification of cysteine or lysine residues on the
protein or intein modification), or can be achieved through one or
more intervening linkers or adapter molecules such as streptavidin
or aptamers. See, e.g., Pierce et al. (2005) Mini Rev. Med. Chem.
5(1):41-55; Duckworth et al. (2007) Angew. Chem. Int. Ed. Engl.
46(46):8819-8822; Schaeffer and Dixon (2009) Australian J. Chem.
62(10):1328-1332; Goodman et al. (2009) Chembiochem.
10(9):1551-1557; and Khatwani et al. (2012) Bioorg. Med. Chem.
20(14):4532-4539, each of which is herein incorporated by reference
in its entirety for all purposes. Noncovalent strategies for
synthesizing protein-nucleic acid conjugates include
biotin-streptavidin and nickel-histidine methods. Covalent
protein-nucleic acid conjugates can be synthesized by connecting
appropriately functionalized nucleic acids and proteins using a
wide variety of chemistries. Some of these chemistries involve
direct attachment of the oligonucleotide to an amino acid residue
on the protein surface (e.g., a lysine amine or a cysteine thiol),
while other more complex schemes require post-translational
modification of the protein or the involvement of a catalytic or
reactive protein domain. Methods for covalent attachment of
proteins to nucleic acids can include, for example, chemical
cross-linking of oligonucleotides to protein lysine or cysteine
residues, expressed protein-ligation, chemoenzymatic methods, and
the use of photoaptamers. The exogenous donor nucleic acid or
labeled nucleic acid can be tethered to the C-terminus, the
N-terminus, or to an internal region within the Cas protein. In one
example, the exogenous donor nucleic acid or labeled nucleic acid
is tethered to the C-terminus or the N-terminus of the Cas protein.
Likewise, the Cas protein can be tethered to the 5' end, the 3'
end, or to an internal region within the exogenous donor nucleic
acid or labeled nucleic acid. That is, the exogenous donor nucleic
acid or labeled nucleic acid can be tethered in any orientation and
polarity. For example, the Cas protein can be tethered to the 5'
end or the 3' end of the exogenous donor nucleic acid or labeled
nucleic acid.
[0204] Cas proteins can be provided in any form. For example, a Cas
protein can be provided in the form of a protein, such as a Cas
protein complexed with a gRNA. Alternatively, a Cas protein can be
provided in the form of a nucleic acid encoding the Cas protein,
such as an RNA (e.g., messenger RNA (mRNA)) or DNA. Optionally, the
nucleic acid encoding the Cas protein can be codon optimized for
efficient translation into protein in a particular cell or
organism. For example, the nucleic acid encoding the Cas protein
can be modified to substitute codons having a higher frequency of
usage in a bacterial cell, a yeast cell, a human cell, a non-human
cell, a mammalian cell, a rodent cell, a mouse cell, a rat cell, or
any other host cell of interest, as compared to the naturally
occurring polynucleotide sequence. When a nucleic acid encoding the
Cas protein is introduced into the cell, the Cas protein can be
transiently, conditionally, or constitutively expressed in the
cell.
[0205] Cas proteins provided as mRNAs can be modified for improved
stability and/or immunogenicity properties. The modifications may
be made to one or more nucleosides within the mRNA. Examples of
chemical modifications to mRNA nucleobases include pseudouridine,
1-methyl-pseudouridine, and 5-methyl-cytidine. For example, capped
and polyadenylated Cas mRNA containing N1-methyl pseudouridine can
be used. Likewise, Cas mRNAs can be modified by depletion of
uridine using synonymous codons.
[0206] Nucleic acids encoding Cas proteins can be stably integrated
in the genome of the cell and operably linked to a promoter active
in the cell. Alternatively, nucleic acids encoding Cas proteins can
be operably linked to a promoter in an expression construct.
Expression constructs include any nucleic acid constructs capable
of directing expression of a gene or other nucleic acid sequence of
interest (e.g., a Cas gene) and which can transfer such a nucleic
acid sequence of interest to a target cell. For example, the
nucleic acid encoding the Cas protein can be in a targeting vector
comprising a nucleic acid insert and/or a vector comprising a DNA
encoding a gRNA. Alternatively, it can be in a vector or plasmid
that is separate from the targeting vector comprising the nucleic
acid insert and/or separate from the vector comprising the DNA
encoding the gRNA. Promoters that can be used in an expression
construct include promoters active, for example, in one or more of
a eukaryotic cell, a human cell, a non-human cell, a mammalian
cell, a non-human mammalian cell, a rodent cell, a mouse cell, a
rat cell, a hamster cell, a rabbit cell, a pluripotent cell, an
embryonic stem (ES) cell, or a zygote. Such promoters can be, for
example, conditional promoters, inducible promoters, constitutive
promoters, or tissue-specific promoters. Optionally, the promoter
can be a bidirectional promoter driving expression of both a Cas
protein in one direction and a guide RNA in the other direction.
Such bidirectional promoters can consist of (1) a complete,
conventional, unidirectional Pol III promoter that contains 3
external control elements: a distal sequence element (DSE), a
proximal sequence element (PSE), and a TATA box; and (2) a second
basic Pol III promoter that includes a PSE and a TATA box fused to
the 5' terminus of the DSE in reverse orientation. For example, in
the H1 promoter, the DSE is adjacent to the PSE and the TATA box,
and the promoter can be rendered bidirectional by creating a hybrid
promoter in which transcription in the reverse direction is
controlled by appending a PSE and TATA box derived from the U6
promoter. See, e.g., US 2016/0074535, herein incorporated by
references in its entirety for all purposes. Use of a bidirectional
promoter to express genes encoding a Cas protein and a guide RNA
simultaneously allow for the generation of compact expression
cassettes to facilitate delivery.
[0207] Guide RNAs.
[0208] A "guide RNA" or "gRNA" is an RNA molecule that binds to a
Cas protein (e.g., Cas9 protein) and targets the Cas protein to a
specific location within a target DNA. Guide RNAs can comprise two
segments: a "DNA-targeting segment" and a "protein-binding
segment." "Segment" includes a section or region of a molecule,
such as a contiguous stretch of nucleotides in an RNA. Some gRNAs,
such as those for Cas9, can comprise two separate RNA molecules: an
"activator-RNA" (e.g., tracrRNA) and a "targeter-RNA" (e.g., CRISPR
RNA or crRNA). Other gRNAs are a single RNA molecule (single RNA
polynucleotide), which can also be called a "single-molecule gRNA,"
a "single-guide RNA," or an "sgRNA." See, e.g., WO 2013/176772, WO
2014/065596, WO 2014/089290, WO 2014/093622, WO 2014/099750, WO
2013/142578, and WO 2014/131833, each of which is herein
incorporated by reference in its entirety for all purposes. For
Cas9, for example, a single-guide RNA can comprise a crRNA fused to
a tracrRNA (e.g., via a linker). For Cpf1, for example, only a
crRNA is needed to achieve binding to and/or cleavage of a target
sequence. The terms "guide RNA" and "gRNA" include both
double-molecule (i.e., modular) gRNAs and single-molecule
gRNAs.
[0209] An exemplary two-molecule gRNA comprises a crRNA-like
("CRISPR RNA" or "targeter-RNA" or "crRNA" or "crRNA repeat")
molecule and a corresponding tracrRNA-like ("trans-acting CRISPR
RNA" or "activator-RNA" or "tracrRNA") molecule. A crRNA comprises
both the DNA-targeting segment (single-stranded) of the gRNA and a
stretch of nucleotides (i.e., the crRNA tail) that forms one half
of the dsRNA duplex of the protein-binding segment of the gRNA. An
example of a crRNA tail, located downstream (3') of the
DNA-targeting segment, comprises, consists essentially of, or
consists of GUUUUAGAGCUAUGCU (SEQ ID NO: 87). Any of the
DNA-targeting segments disclosed herein can be joined to the 5' end
of SEQ ID NO: 87 to form a crRNA.
[0210] A corresponding tracrRNA (activator-RNA) comprises a stretch
of nucleotides that forms the other half of the dsRNA duplex of the
protein-binding segment of the gRNA. A stretch of nucleotides of a
crRNA are complementary to and hybridize with a stretch of
nucleotides of a tracrRNA to form the dsRNA duplex of the
protein-binding domain of the gRNA. As such, each crRNA can be said
to have a corresponding tracrRNA. An example of a tracrRNA sequence
comprises, consists essentially of, or consists of
AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACC
GAGUCGGUGCUUU (SEQ ID NO: 88).
[0211] In systems in which both a crRNA and a tracrRNA are needed,
the crRNA and the corresponding tracrRNA hybridize to form a gRNA.
In systems in which only a crRNA is needed, the crRNA can be the
gRNA. The crRNA additionally provides the single-stranded
DNA-targeting segment that targets a guide RNA target sequence by
hybridizing to the opposite strand (i.e., the complementary
strand). If used for modification within a cell, the exact sequence
of a given crRNA or tracrRNA molecule can be designed to be
specific to the species in which the RNA molecules will be used.
See, e.g., Mali et al. (2013) Science 339:823-826; Jinek et al.
(2012) Science 337:816-821; Hwang et al. (2013) Nat. Biotechnol.
31:227-229; Jiang et al. (2013) Nat. Biotechnol. 31:233-239; and
Cong et al. (2013) Science 339:819-823, each of which is herein
incorporated by reference in its entirety for all purposes.
[0212] The DNA-targeting segment (crRNA) of a given gRNA comprises
a nucleotide sequence that is complementary to a sequence (i.e.,
the complementary strand of the guide RNA recognition sequence on
the strand opposite of the guide RNA target sequence) in a target
DNA. The DNA-targeting segment of a gRNA interacts with a target
DNA in a sequence-specific manner via hybridization (i.e., base
pairing). As such, the nucleotide sequence of the DNA-targeting
segment may vary and determines the location within the target DNA
with which the gRNA and the target DNA will interact. The
DNA-targeting segment of a subject gRNA can be modified to
hybridize to any desired sequence within a target DNA. Naturally
occurring crRNAs differ depending on the CRISPR/Cas system and
organism but often contain a targeting segment of between 21 to 72
nucleotides length, flanked by two direct repeats (DR) of a length
of between 21 to 46 nucleotides (see, e.g., WO 2014/131833, herein
incorporated by reference in its entirety for all purposes). In the
case of S. pyogenes, the DRs are 36 nucleotides long and the
targeting segment is 30 nucleotides long. The 3' located DR is
complementary to and hybridizes with the corresponding tracrRNA,
which in turn binds to the Cas protein.
[0213] The DNA-targeting segment can have a length of at least
about 12 nucleotides, at least about 15 nucleotides, at least about
17 nucleotides, at least about 18 nucleotides, at least about 19
nucleotides, at least about 20 nucleotides, at least about 25
nucleotides, at least about 30 nucleotides, at least about 35
nucleotides, or at least about 40 nucleotides. Such DNA-targeting
segments can have a length from about 12 nucleotides to about 100
nucleotides, from about 12 nucleotides to about 80 nucleotides,
from about 12 nucleotides to about 50 nucleotides, from about 12
nucleotides to about 40 nucleotides, from about 12 nucleotides to
about 30 nucleotides, from about 12 nucleotides to about 25
nucleotides, or from about 12 nucleotides to about 20 nucleotides.
For example, the DNA targeting segment can be from about 15
nucleotides to about 25 nucleotides (e.g., from about 17
nucleotides to about 20 nucleotides, or about 17 nucleotides, about
18 nucleotides, about 19 nucleotides, or about 20 nucleotides).
See, e.g., US 2016/0024523, herein incorporated by reference in its
entirety for all purposes. For Cas9 from S. pyogenes, a typical
DNA-targeting segment is between 16 and 20 nucleotides in length or
between 17 and 20 nucleotides in length. For Cas9 from S. aureus, a
typical DNA-targeting segment is between 21 and 23 nucleotides in
length. For Cpf1, a typical DNA-targeting segment is at least 16
nucleotides in length or at least 18 nucleotides in length.
[0214] TracrRNAs can be in any form (e.g., full-length tracrRNAs or
active partial tracrRNAs) and of varying lengths. They can include
primary transcripts or processed forms. For example, tracrRNAs (as
part of a single-guide RNA or as a separate molecule as part of a
two-molecule gRNA) may comprise, consist essentially of, or consist
of all or a portion of a wild type tracrRNA sequence (e.g., about
or more than about 20, 26, 32, 45, 48, 54, 63, 67, 85, or more
nucleotides of a wild type tracrRNA sequence). Examples of wild
type tracrRNA sequences from S. pyogenes include 171-nucleotide,
89-nucleotide, 75-nucleotide, and 65-nucleotide versions. See,
e.g., Deltcheva et al. (2011) Nature 471:602-607; WO 2014/093661,
each of which is herein incorporated by reference in its entirety
for all purposes. Examples of tracrRNAs within single-guide RNAs
(sgRNAs) include the tracrRNA segments found within +48, +54, +67,
and +85 versions of sgRNAs, where "+n" indicates that up to the +n
nucleotide of wild type tracrRNA is included in the sgRNA. See U.S.
Pat. No. 8,697,359, herein incorporated by reference in its
entirety for all purposes.
[0215] The percent complementarity between the DNA-targeting
segment and the complementary strand of the guide RNA recognition
sequence within the target DNA can be at least 60% (e.g., at least
65%, at least 70%, at least 75%, at least 80%, at least 85%, at
least 90%, at least 95%, at least 97%, at least 98%, at least 99%,
or 100%). The percent complementarity between the DNA-targeting
segment and the complementary strand of the guide RNA recognition
sequence within the target DNA can be at least 60% over about 20
contiguous nucleotides. As an example, the percent complementarity
between the DNA-targeting segment and the complementary strand of
the guide RNA recognition sequence within the target DNA is 100%
over the 14 contiguous nucleotides at the 5' end of the
complementary strand of the guide RNA recognition sequence within
the complementary strand of the target DNA and as low as 0% over
the remainder. In such a case, the DNA-targeting segment can be
considered to be 14 nucleotides in length. As another example, the
percent complementarity between the DNA-targeting segment and the
complementary strand of the guide RNA recognition sequence within
the target DNA is 100% over the seven contiguous nucleotides at the
5' end of the complementary strand of the guide RNA recognition
sequence within the complementary strand of the target DNA and as
low as 0% over the remainder. In such a case, the DNA-targeting
segment can be considered to be 7 nucleotides in length. In some
guide RNAs, at least 17 nucleotides within the DNA-targeting
segment are complementary to the target DNA. For example, the
DNA-targeting segment can be 20 nucleotides in length and can
comprise 1, 2, or 3 mismatches with the complementary strand of the
guide RNA recognition sequence. Preferably, the mismatches are not
adjacent to a protospacer adjacent motif (PAM) sequence (e.g., the
mismatches are in the 5' end of the DNA-targeting segment, or the
mismatches are at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
15, 16, 17, 18, or 19 base pairs away from the PAM sequence).
[0216] The protein-binding segment of a gRNA can comprise two
stretches of nucleotides that are complementary to one another. The
complementary nucleotides of the protein-binding segment hybridize
to form a double-stranded RNA duplex (dsRNA). The protein-binding
segment of a subject gRNA interacts with a Cas protein, and the
gRNA directs the bound Cas protein to a specific nucleotide
sequence within target DNA via the DNA-targeting segment.
[0217] Single-guide RNAs have the DNA-targeting segment and a
scaffold sequence (i.e., the protein-binding or Cas-binding
sequence of the guide RNA). For example, such guide RNAs have a 5'
DNA-targeting segment and a 3' scaffold sequence. Exemplary
scaffold sequences comprise, consist essentially of, or consist of:
GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGA
AAAAGUGGCACCGAGUCGGUGCU (version 1; SEQ ID NO: 89);
GUUGGAACCAUUCAAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCA
ACUUGAAAAAGUGGCACCGAGUCGGUGC (version 2; SEQ ID NO: 8);
GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGA
AAAAGUGGCACCGAGUCGGUGC (version 3; SEQ ID NO: 9); and
GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUCCGUU
AUCAACUUGAAAAAGUGGCACCGAGUCGGUGC (version 4; SEQ ID NO: 10). Guide
RNAs targeting any guide RNA target sequence can include, for
example, a DNA-targeting segment on the 5' end of the guide RNA
fused to any of the exemplary guide RNA scaffold sequences on the
3' end of the guide RNA. That is, any of the DNA-targeting segments
disclosed herein can be joined to the 5' end of any one of SEQ ID
NOS: 89, 8, 9, or 10 to form a single guide RNA (chimeric guide
RNA). Guide RNA versions 1, 2, 3, and 4 as disclosed elsewhere
herein refer to DNA-targeting segments (i.e., guide sequences or
guides) joined with scaffold versions 1, 2, 3, and 4,
respectively.
[0218] Guide RNAs can include modifications or sequences that
provide for additional desirable features (e.g., modified or
regulated stability; subcellular targeting; tracking with a
fluorescent label; a binding site for a protein or protein complex;
and the like). Examples of such modifications include, for example,
a 5' cap (e.g., a 7-methylguanylate cap (m7G)); a 3' polyadenylated
tail (i.e., a 3' poly(A) tail); a riboswitch sequence (e.g., to
allow for regulated stability and/or regulated accessibility by
proteins and/or protein complexes); a stability control sequence; a
sequence that forms a dsRNA duplex (i.e., a hairpin); a
modification or sequence that targets the RNA to a subcellular
location (e.g., nucleus, mitochondria, chloroplasts, and the like);
a modification or sequence that provides for tracking (e.g., direct
conjugation to a fluorescent molecule, conjugation to a moiety that
facilitates fluorescent detection, a sequence that allows for
fluorescent detection, and so forth); a modification or sequence
that provides a binding site for proteins (e.g., proteins that act
on DNA, including DNA methyltransferases, DNA demethylases, histone
acetyltransferases, histone deacetylases, and the like); and
combinations thereof. Other examples of modifications include
engineered stem loop duplex structures, engineered bulge regions,
engineered hairpins 3' of the stem loop duplex structure, or any
combination thereof. See, e.g., US 2015/0376586, herein
incorporated by reference in its entirety for all purposes. A bulge
can be an unpaired region of nucleotides within the duplex made up
of the crRNA-like region and the minimum tracrRNA-like region. A
bulge can comprise, on one side of the duplex, an unpaired
5'-XXXY-3' where X is any purine and Y can be a nucleotide that can
form a wobble pair with a nucleotide on the opposite strand, and an
unpaired nucleotide region on the other side of the duplex.
[0219] Unmodified nucleic acids can be prone to degradation.
Exogenous nucleic acids can also induce an innate immune response.
Modifications can help introduce stability and reduce
immunogenicity. Guide RNAs can comprise modified nucleosides and
modified nucleotides including, for example, one or more of the
following: (1) alteration or replacement of one or both of the
non-linking phosphate oxygens and/or of one or more of the linking
phosphate oxygens in the phosphodiester backbone linkage; (2)
alteration or replacement of a constituent of the ribose sugar such
as alteration or replacement of the 2' hydroxyl on the ribose
sugar; (3) replacement of the phosphate moiety with dephospho
linkers; (4) modification or replacement of a naturally occurring
nucleobase; (5) replacement or modification of the ribose-phosphate
backbone; (6) modification of the 3' end or 5' end of the
oligonucleotide (e.g., removal, modification or replacement of a
terminal phosphate group or conjugation of a moiety); and (7)
modification of the sugar. Other possible guide RNA modifications
include modifications of or replacement of uracils or poly-uracil
tracts. See, e.g., WO 2015/048577 and US 2016/0237455, each of
which is herein incorporated by reference in its entirety for all
purposes. Similar modifications can be made to Cas-encoding nucleic
acids, such as Cas mRNAs.
[0220] As one example, nucleotides at the 5' or 3' end of a guide
RNA can include phosphorothioate linkages (e.g., the bases can have
a modified phosphate group that is a phosphorothioate group). For
example, a guide RNA can include phosphorothioate linkages between
the 2, 3, or 4 terminal nucleotides at the 5' or 3' end of the
guide RNA. As another example, nucleotides at the 5' and/or 3' end
of a guide RNA can have 2'-O-methyl modifications. For example, a
guide RNA can include 2'-O-methyl modifications at the 2, 3, or 4
terminal nucleotides at the 5' and/or 3' end of the guide RNA
(e.g., the 5' end). See, e.g., WO 2017/173054 A1 and Finn et al.
(2018) Cell Reports 22:1-9, each of which is herein incorporated by
reference in its entirety for all purposes. In one specific
example, the guide RNA comprises 2'-O-methyl analogs and 3'
phosphorothioate internucleotide linkages at the first three 5' and
3' terminal RNA residues. In another specific example, the guide
RNA is modified such that all 2'OH groups that do not interact with
the Cas9 protein are replaced with 2'-O-methyl analogs, and the
tail region of the guide RNA, which has minimal interaction with
Cas9, is modified with 5' and 3' phosphorothioate internucleotide
linkages. See, e.g., Yin et al. (2017) Nat. Biotech.
35(12):1179-1187, herein incorporated by reference in its entirety
for all purposes. Other examples of modified guide RNAs are
provided, e.g., in WO 2018/107028 A1, herein incorporated by
reference in its entirety for all purposes.
[0221] Guide RNAs can be provided in any form. For example, the
gRNA can be provided in the form of RNA, either as two molecules
(separate crRNA and tracrRNA) or as one molecule (sgRNA), and
optionally in the form of a complex with a Cas protein. The gRNA
can also be provided in the form of DNA encoding the gRNA. The DNA
encoding the gRNA can encode a single RNA molecule (sgRNA) or
separate RNA molecules (e.g., separate crRNA and tracrRNA). In the
latter case, the DNA encoding the gRNA can be provided as one DNA
molecule or as separate DNA molecules encoding the crRNA and
tracrRNA, respectively.
[0222] When a gRNA is provided in the form of DNA, the gRNA can be
transiently, conditionally, or constitutively expressed in the
cell. DNAs encoding gRNAs can be stably integrated into the genome
of the cell and operably linked to a promoter active in the cell.
Alternatively, DNAs encoding gRNAs can be operably linked to a
promoter in an expression construct. For example, the DNA encoding
the gRNA can be in a vector comprising a heterologous nucleic acid,
such as a nucleic acid encoding a Cas protein. Alternatively, it
can be in a vector or a plasmid that is separate from the vector
comprising the nucleic acid encoding the Cas protein. Promoters
that can be used in such expression constructs include promoters
active, for example, in one or more of a eukaryotic cell, a human
cell, a non-human cell, a mammalian cell, a non-human mammalian
cell, a rodent cell, a mouse cell, a rat cell, a hamster cell, a
rabbit cell, a pluripotent cell, an embryonic stem (ES) cell, an
adult stem cell, a developmentally restricted progenitor cell, an
induced pluripotent stem (iPS) cell, or a one-cell stage embryo.
Such promoters can be, for example, conditional promoters,
inducible promoters, constitutive promoters, or tissue-specific
promoters. Such promoters can also be, for example, bidirectional
promoters. Specific examples of suitable promoters include an RNA
polymerase III promoter, such as a human U6 promoter, a rat U6
polymerase III promoter, or a mouse U6 polymerase III promoter.
[0223] Alternatively, gRNAs can be prepared by various other
methods. For example, gRNAs can be prepared by in vitro
transcription using, for example, T7 RNA polymerase (see, e.g., WO
2014/089290 and WO 2014/065596, each of which is herein
incorporated by reference in its entirety for all purposes). Guide
RNAs can also be a synthetically produced molecule prepared by
chemical synthesis.
[0224] Guide RNA Recognition Sequences and Guide RNA Target
Sequences.
[0225] The term "guide RNA recognition sequence" includes nucleic
acid sequences present in a target DNA to which a DNA-targeting
segment of a gRNA will bind, provided sufficient conditions for
binding exist. The term guide RNA recognition sequence as used
herein encompasses both strands of the target double-stranded DNA
(i.e., the sequence on the complementary strand to which the guide
RNA hybridizes and the corresponding sequence on the
non-complementary strand adjacent to the protospacer adjacent motif
(PAM)). The term "guide RNA target sequence" as used herein refers
specifically to the sequence on the non-complementary strand
adjacent to the PAM (i.e., upstream or 5' of the PAM). That is, the
guide RNA target sequence refers to the sequence on the
non-complementary strand corresponding to the sequence to which the
guide RNA hybridizes on the complementary strand. A guide RNA
target sequence is equivalent to the DNA-targeting segment of a
guide RNA, but with thymines instead of uracils. As one example, a
guide RNA target sequence for a Cas9 enzyme would refer to the
sequence on the non-complementary strand adjacent to the 5'-NGG-3'
PAM. Guide RNA recognition sequences include sequences to which a
guide RNA is designed to have complementarity, where hybridization
between the complementary strand of a guide RNA recognition
sequence and a DNA-targeting segment of a guide RNA promotes the
formation of a CRISPR complex. Full complementarity is not
necessarily required, provided that there is sufficient
complementarity to cause hybridization and promote formation of a
CRISPR complex. Guide RNA recognition sequences or guide RNA target
sequences also include cleavage sites for Cas proteins, described
in more detail below. A guide RNA recognition sequence or a guide
RNA target sequence can comprise any polynucleotide, which can be
located, for example, in the nucleus or cytoplasm of a cell or
within an organelle of a cell, such as a mitochondrion or
chloroplast.
[0226] The guide RNA recognition sequence within a target DNA can
be targeted by (i.e., be bound by, or hybridize with, or be
complementary to) a Cas protein or a gRNA. Suitable DNA/RNA binding
conditions include physiological conditions normally present in a
cell. Other suitable DNA/RNA binding conditions (e.g., conditions
in a cell-free system) are known (see, e.g., Molecular Cloning: A
Laboratory Manual, 3rd Ed. (Sambrook et al., Harbor Laboratory
Press 2001), herein incorporated by reference in its entirety for
all purposes). The strand of the target DNA that is complementary
to and hybridizes with the Cas protein or gRNA can be called the
"complementary strand," and the strand of the target DNA that is
complementary to the "complementary strand" (and is therefore not
complementary to the Cas protein or gRNA) can be called
"non-complementary strand" or "template strand."
[0227] The Cas protein can cleave the nucleic acid at a site within
or outside of the nucleic acid sequence present in the target DNA
to which the DNA-targeting segment of a gRNA will bind. The
"cleavage site" includes the position of a nucleic acid at which a
Cas protein produces a single-strand break or a double-strand
break. For example, formation of a CRISPR complex (comprising a
gRNA hybridized to the complementary strand of a guide RNA
recognition sequence and complexed with a Cas protein) can result
in cleavage of one or both strands in or near (e.g., within 1, 2,
3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or more base pairs from) the
nucleic acid sequence present in a target DNA to which a
DNA-targeting segment of a gRNA will bind. If the cleavage site is
outside of the nucleic acid sequence to which the DNA-targeting
segment of the gRNA will bind, the cleavage site is still
considered to be within the "guide RNA recognition sequence" or
guide RNA target sequence. The cleavage site can be on only one
strand or on both strands of a nucleic acid. Cleavage sites can be
at the same position on both strands of the nucleic acid (producing
blunt ends) or can be at different sites on each strand (producing
staggered ends (i.e., overhangs)). Staggered ends can be produced,
for example, by using two Cas proteins, each of which produces a
single-strand break at a different cleavage site on a different
strand, thereby producing a double-strand break. For example, a
first nickase can create a single-strand break on the first strand
of double-stranded DNA (dsDNA), and a second nickase can create a
single-strand break on the second strand of dsDNA such that
overhanging sequences are created. In some cases, the guide RNA
recognition sequence or guide RNA target sequence of the nickase on
the first strand is separated from the guide RNA recognition
sequence or guide RNA target sequence of the nickase on the second
strand by at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 40,
50, 75, 100, 250, 500, or 1,000 base pairs.
[0228] Site-specific binding and/or cleavage of target DNA by Cas
proteins can occur at locations determined by both (i) base-pairing
complementarity between the gRNA and the target DNA and (ii) a
short motif, called the protospacer adjacent motif (PAM), in the
target DNA. The PAM can flank the guide RNA target sequence on the
non-complementary strand opposite of the strand to which the guide
RNA hybridizes. Optionally, the guide RNA target sequence can be
flanked on the 3' end by the PAM. Alternatively, the guide RNA
target sequence can be flanked on the 5' end by the PAM. For
example, the cleavage site of Cas proteins can be about 1 to about
10 or about 2 to about 5 base pairs (e.g., 3 base pairs) upstream
or downstream of the PAM sequence. In some cases (e.g., when Cas9
from S. pyogenes or a closely related Cas9 is used), the PAM
sequence of the non-complementary strand can be 5'-N.sub.1GG-3',
where N.sub.1 is any DNA nucleotide and is immediately 3' of the
guide RNA recognition sequence of the non-complementary strand of
the target DNA (i.e., immediately 3' of the guide RNA target
sequence). As such, the PAM sequence of the complementary strand
would be 5'-CCN.sub.2-3', where N.sub.2 is any DNA nucleotide and
is immediately 5' of the guide RNA recognition sequence of the
complementary strand of the target DNA. In some such cases, N.sub.1
and N.sub.2 can be complementary and the N.sub.1-N.sub.2 base pair
can be any base pair (e.g., N.sub.1=C and N.sub.2=G; N.sub.1=G and
N.sub.2=C; N.sub.1=A and N.sub.2=T; or N.sub.1=T, and N.sub.2=A).
In the case of Cas9 from S. aureus, the PAM can be NNGRRT or NNGRR,
where N can be A, G, C, or T, and R can be G or A. In the case of
Cas9 from C. jejuni, the PAM can be, for example, NNNNACAC or
NNNNRYAC, where N can be A, G, C, or T, and R can be G or A. In
some cases (e.g., for FnCpf1), the PAM sequence can be upstream of
the 5' end and have the sequence 5'-TTN-3'.
[0229] Examples of guide RNA target sequences or guide RNA target
sequences in addition to a PAM sequence are provided below. For
example, the guide RNA target sequence can be a 20-nucleotide DNA
sequence immediately preceding an NGG motif recognized by a Cas9
protein. Examples of such guide RNA target sequences plus a PAM
sequence are GN.sub.19NGG (SEQ ID NO: 11) or N.sub.20NGG (SEQ ID
NO: 12). See, e.g., WO 2014/165825, herein incorporated by
reference in its entirety for all purposes. The guanine at the 5'
end can facilitate transcription by RNA polymerase in cells. Other
examples of guide RNA target sequences plus a PAM sequence can
include two guanine nucleotides at the 5' end (e.g., GGN.sub.20NGG;
SEQ ID NO: 13) to facilitate efficient transcription by T7
polymerase in vitro. See, e.g., WO 2014/065596, herein incorporated
by reference in its entirety for all purposes. Other guide RNA
target sequences plus a PAM sequence can have between 4-22
nucleotides in length of SEQ ID NOS: 11-13, including the 5' G or
GG and the 3' GG or NGG. Yet other guide RNA target sequences can
have between 14 and 20 nucleotides in length of SEQ ID NOS:
11-13.
[0230] The guide RNA recognition sequence or guide RNA target
sequence can be any nucleic acid sequence endogenous or exogenous
to a cell. The guide RNA recognition sequence or guide RNA target
sequence can be a sequence coding a gene product (e.g., a protein)
or a non-coding sequence (e.g., a regulatory sequence) or can
include both.
[0231] (3) Exogenous Donor Nucleic Acids Targeting Human TTR
Gene
[0232] The methods and compositions disclosed herein can utilize
exogenous donor nucleic acids to modify the humanized TTR locus
following cleavage of the humanized TTR locus with a nuclease
agent. In such methods, the nuclease agent protein cleaves the
humanized TTR locus to create a single-strand break (nick) or
double-strand break, and the exogenous donor nucleic acid
recombines the humanized TTR locus via non-homologous end joining
(NHEJ)-mediated ligation or through a homology-directed repair
event. Optionally, repair with the exogenous donor nucleic acid
removes or disrupts the nuclease target sequence so that alleles
that have been targeted cannot be re-targeted by the nuclease
agent.
[0233] Exogenous donor nucleic acids can comprise deoxyribonucleic
acid (DNA) or ribonucleic acid (RNA), they can be single-stranded
or double-stranded, and they can be in linear or circular form. For
example, an exogenous donor nucleic acid can be a single-stranded
oligodeoxynucleotide (ssODN). See, e.g., Yoshimi et al. (2016) Nat.
Commun. 7:10431, herein incorporated by reference in its entirety
for all purposes. An exemplary exogenous donor nucleic acid is
between about 50 nucleotides to about 5 kb in length, is between
about 50 nucleotides to about 3 kb in length, or is between about
50 to about 1,000 nucleotides in length. Other exemplary exogenous
donor nucleic acids are between about 40 to about 200 nucleotides
in length. For example, an exogenous donor nucleic acid can be
between about 50-60, 60-70, 70-80, 80-90, 90-100, 100-110, 110-120,
120-130, 130-140, 140-150, 150-160, 160-170, 170-180, 180-190, or
190-200 nucleotides in length. Alternatively, an exogenous donor
nucleic acid can be between about 50-100, 100-200, 200-300,
300-400, 400-500, 500-600, 600-700, 700-800, 800-900, or 900-1000
nucleotides in length. Alternatively, an exogenous donor nucleic
acid can be between about 1-1.5, 1.5-2, 2-2.5, 2.5-3, 3-3.5, 3.5-4,
4-4.5, or 4.5-5 kb in length. Alternatively, an exogenous donor
nucleic acid can be, for example, no more than 5 kb, 4.5 kb, 4 kb,
3.5 kb, 3 kb, 2.5 kb, 2 kb, 1.5 kb, 1 kb, 900 nucleotides, 800
nucleotides, 700 nucleotides, 600 nucleotides, 500 nucleotides, 400
nucleotides, 300 nucleotides, 200 nucleotides, 100 nucleotides, or
50 nucleotides in length. Exogenous donor nucleic acids (e.g.,
targeting vectors) can also be longer.
[0234] In one example, an exogenous donor nucleic acid is an ssODN
that is between about 80 nucleotides and about 200 nucleotides in
length. In another example, an exogenous donor nucleic acids is an
ssODN that is between about 80 nucleotides and about 3 kb in
length. Such an ssODN can have homology arms, for example, that are
each between about 40 nucleotides and about 60 nucleotides in
length. Such an ssODN can also have homology arms, for example,
that are each between about 30 nucleotides and 100 nucleotides in
length. The homology arms can be symmetrical (e.g., each 40
nucleotides or each 60 nucleotides in length), or they can be
asymmetrical (e.g., one homology arm that is 36 nucleotides in
length, and one homology arm that is 91 nucleotides in length).
[0235] Exogenous donor nucleic acids can include modifications or
sequences that provide for additional desirable features (e.g.,
modified or regulated stability; tracking or detecting with a
fluorescent label; a binding site for a protein or protein complex;
and so forth). Exogenous donor nucleic acids can comprise one or
more fluorescent labels, purification tags, epitope tags, or a
combination thereof. For example, an exogenous donor nucleic acid
can comprise one or more fluorescent labels (e.g., fluorescent
proteins or other fluorophores or dyes), such as at least 1, at
least 2, at least 3, at least 4, or at least 5 fluorescent labels.
Exemplary fluorescent labels include fluorophores such as
fluorescein (e.g., 6-carboxyfluorescein (6-FAM)), Texas Red, HEX,
Cy3, Cy5, Cy5.5, Pacific Blue,
5-(and-6)-carboxytetramethylrhodamine (TAMRA), and Cy7. A wide
range of fluorescent dyes are available commercially for labeling
oligonucleotides (e.g., from Integrated DNA Technologies). Such
fluorescent labels (e.g., internal fluorescent labels) can be used,
for example, to detect an exogenous donor nucleic acid that has
been directly integrated into a cleaved target nucleic acid having
protruding ends compatible with the ends of the exogenous donor
nucleic acid. The label or tag can be at the 5' end, the 3' end, or
internally within the exogenous donor nucleic acid. For example, an
exogenous donor nucleic acid can be conjugated at 5' end with the
IR700 fluorophore from Integrated DNA Technologies (5'IRDYE.RTM.
700).
[0236] Exogenous donor nucleic acids can also comprise nucleic acid
inserts including segments of DNA to be integrated at the humanized
TTR locus. Integration of a nucleic acid insert at a humanized TTR
locus can result in addition of a nucleic acid sequence of interest
to the humanized TTR locus, deletion of a nucleic acid sequence of
interest at the humanized TTR locus, or replacement of a nucleic
acid sequence of interest at the humanized TTR locus (i.e.,
deletion and insertion). Some exogenous donor nucleic acids are
designed for insertion of a nucleic acid insert at the humanized
TTR locus without any corresponding deletion at the humanized TTR
locus. Other exogenous donor nucleic acids are designed to delete a
nucleic acid sequence of interest at the humanized TTR locus
without any corresponding insertion of a nucleic acid insert. Yet
other exogenous donor nucleic acids are designed to delete a
nucleic acid sequence of interest at the humanized TTR locus and
replace it with a nucleic acid insert.
[0237] The nucleic acid insert or the corresponding nucleic acid at
the humanized TTR locus being deleted and/or replaced can be
various lengths. An exemplary nucleic acid insert or corresponding
nucleic acid at the humanized TTR locus being deleted and/or
replaced is between about 1 nucleotide to about 5 kb in length or
is between about 1 nucleotide to about 1,000 nucleotides in length.
For example, a nucleic acid insert or a corresponding nucleic acid
at the humanized TTR locus being deleted and/or replaced can be
between about 1-10, 10-20, 20-30, 30-40, 40-50, 50-60, 60-70,
70-80, 80-90, 90-100, 100-110, 110-120, 120-130, 130-140, 140-150,
150-160, 160-170, 170-180, 180-190, or 190-120 nucleotides in
length. Likewise, a nucleic acid insert or a corresponding nucleic
acid at the humanized TTR locus being deleted and/or replaced can
be between 1-100, 100-200, 200-300, 300-400, 400-500, 500-600,
600-700, 700-800, 800-900, or 900-1000 nucleotides in length.
Likewise, a nucleic acid insert or a corresponding nucleic acid at
the humanized TTR locus being deleted and/or replaced can be
between about 1-1.5, 1.5-2, 2-2.5, 2.5-3, 3-3.5, 3.5-4, 4-4.5, or
4.5-5 kb in length or longer.
[0238] The nucleic acid insert can comprise a sequence that is
homologous or orthologous to all or part of sequence targeted for
replacement. For example, the nucleic acid insert can comprise a
sequence that comprises one or more point mutations (e.g., 1, 2, 3,
4, 5, or more) compared with a sequence targeted for replacement at
the humanized TTR locus. Optionally, such point mutations can
result in a conservative amino acid substitution (e.g.,
substitution of aspartic acid [Asp, D] with glutamic acid [Glu, E])
in the encoded polypeptide.
[0239] Donor Nucleic Acids for Non-Homologous-End-Joining-Mediated
Insertion.
[0240] Some exogenous donor nucleic acids have short
single-stranded regions at the 5' end and/or the 3' end that are
complementary to one or more overhangs created by nuclease-mediated
cleavage at the humanized TTR locus. These overhangs can also be
referred to as 5' and 3' homology arms. For example, some exogenous
donor nucleic acids have short single-stranded regions at the 5'
end and/or the 3' end that are complementary to one or more
overhangs created by nuclease-mediated cleavage at 5' and/or 3'
target sequences at the humanized TTR locus. Some such exogenous
donor nucleic acids have a complementary region only at the 5' end
or only at the 3' end. For example, some such exogenous donor
nucleic acids have a complementary region only at the 5' end
complementary to an overhang created at a 5' target sequence at the
humanized TTR locus or only at the 3' end complementary to an
overhang created at a 3' target sequence at the humanized TTR
locus. Other such exogenous donor nucleic acids have complementary
regions at both the 5' and 3' ends. For example, other such
exogenous donor nucleic acids have complementary regions at both
the 5' and 3' ends e.g., complementary to first and second
overhangs, respectively, generated by nuclease-mediated cleavage at
the humanized TTR locus. For example, if the exogenous donor
nucleic acid is double-stranded, the single-stranded complementary
regions can extend from the 5' end of the top strand of the donor
nucleic acid and the 5' end of the bottom strand of the donor
nucleic acid, creating 5' overhangs on each end. Alternatively, the
single-stranded complementary region can extend from the 3' end of
the top strand of the donor nucleic acid and from the 3' end of the
bottom strand of the template, creating 3' overhangs.
[0241] The complementary regions can be of any length sufficient to
promote ligation between the exogenous donor nucleic acid and the
target nucleic acid. Exemplary complementary regions are between
about 1 to about 5 nucleotides in length, between about 1 to about
25 nucleotides in length, or between about 5 to about 150
nucleotides in length. For example, a complementary region can be
at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides in length.
Alternatively, the complementary region can be about 5-10, 10-20,
20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100-110,
110-120, 120-130, 130-140, or 140-150 nucleotides in length, or
longer.
[0242] Such complementary regions can be complementary to overhangs
created by two pairs of nickases. Two double-strand breaks with
staggered ends can be created by using first and second nickases
that cleave opposite strands of DNA to create a first double-strand
break, and third and fourth nickases that cleave opposite strands
of DNA to create a second double-strand break. For example, a Cas
protein can be used to nick first, second, third, and fourth guide
RNA target sequences corresponding with first, second, third, and
fourth guide RNAs. The first and second guide RNA target sequences
can be positioned to create a first cleavage site such that the
nicks created by the first and second nickases on the first and
second strands of DNA create a double-strand break (i.e., the first
cleavage site comprises the nicks within the first and second guide
RNA target sequences). Likewise, the third and fourth guide RNA
target sequences can be positioned to create a second cleavage site
such that the nicks created by the third and fourth nickases on the
first and second strands of DNA create a double-strand break (i.e.,
the second cleavage site comprises the nicks within the third and
fourth guide RNA target sequences). Preferably, the nicks within
the first and second guide RNA target sequences and/or the third
and fourth guide RNA target sequences can be off-set nicks that
create overhangs. The offset window can be, for example, at least
about 5 bp, 10 bp, 20 bp, 30 bp, 40 bp, 50 bp, 60 bp, 70 bp, 80 bp,
90 bp, 100 bp or more. See Ran et al. (2013) Cell 154:1380-1389;
Mali et al. (2013) Nat. Biotech. 31:833-838; and Shen et al. (2014)
Nat. Methods 11:399-404, each of which is herein incorporated by
reference in its entirety for all purposes. In such cases, a
double-stranded exogenous donor nucleic acid can be designed with
single-stranded complementary regions that are complementary to the
overhangs created by the nicks within the first and second guide
RNA target sequences and by the nicks within the third and fourth
guide RNA target sequences. Such an exogenous donor nucleic acid
can then be inserted by non-homologous-end-joining-mediated
ligation.
[0243] Donor Nucleic Acids for Insertion by Homology-Directed
Repair.
[0244] Some exogenous donor nucleic acids comprise homology arms.
If the exogenous donor nucleic acid also comprises a nucleic acid
insert, the homology arms can flank the nucleic acid insert. For
ease of reference, the homology arms are referred to herein as 5'
and 3' (i.e., upstream and downstream) homology arms. This
terminology relates to the relative position of the homology arms
to the nucleic acid insert within the exogenous donor nucleic acid.
The 5' and 3' homology arms correspond to regions within the
humanized TTR locus, which are referred to herein as "5' target
sequence" and "3' target sequence," respectively.
[0245] A homology arm and a target sequence "correspond" or are
"corresponding" to one another when the two regions share a
sufficient level of sequence identity to one another to act as
substrates for a homologous recombination reaction. The term
"homology" includes DNA sequences that are either identical or
share sequence identity to a corresponding sequence. The sequence
identity between a given target sequence and the corresponding
homology arm found in the exogenous donor nucleic acid can be any
degree of sequence identity that allows for homologous
recombination to occur. For example, the amount of sequence
identity shared by the homology arm of the exogenous donor nucleic
acid (or a fragment thereof) and the target sequence (or a fragment
thereof) can be at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%,
82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%, 96%, 97%, 98%, 99% or 100% sequence identity, such that the
sequences undergo homologous recombination. Moreover, a
corresponding region of homology between the homology arm and the
corresponding target sequence can be of any length that is
sufficient to promote homologous recombination. Exemplary homology
arms are between about 25 nucleotides to about 2.5 kb in length,
are between about 25 nucleotides to about 1.5 kb in length, or are
between about 25 to about 500 nucleotides in length. For example, a
given homology arm (or each of the homology arms) and/or
corresponding target sequence can comprise corresponding regions of
homology that are between about 25-30, 30-40, 40-50, 50-60, 60-70,
70-80, 80-90, 90-100, 100-150, 150-200, 200-250, 250-300, 300-350,
350-400, 400-450, or 450-500 nucleotides in length, such that the
homology arms have sufficient homology to undergo homologous
recombination with the corresponding target sequences within the
target nucleic acid. Alternatively, a given homology arm (or each
homology arm) and/or corresponding target sequence can comprise
corresponding regions of homology that are between about 0.5 kb to
about 1 kb, about 1 kb to about 1.5 kb, about 1.5 kb to about 2 kb,
or about 2 kb to about 2.5 kb in length. For example, the homology
arms can each be about 750 nucleotides in length. The homology arms
can be symmetrical (each about the same size in length), or they
can be asymmetrical (one longer than the other).
[0246] When a nuclease agent is used in combination with an
exogenous donor nucleic acid, the 5' and 3' target sequences are
preferably located in sufficient proximity to the nuclease cleavage
site (e.g., within sufficient proximity to a the nuclease target
sequence) so as to promote the occurrence of a homologous
recombination event between the target sequences and the homology
arms upon a single-strand break (nick) or double-strand break at
the nuclease cleavage site. The term "nuclease cleavage site"
includes a DNA sequence at which a nick or double-strand break is
created by a nuclease agent (e.g., a Cas9 protein complexed with a
guide RNA). The target sequences within the targeted locus that
correspond to the 5' and 3' homology arms of the exogenous donor
nucleic acid are "located in sufficient proximity" to a nuclease
cleavage site if the distance is such as to promote the occurrence
of a homologous recombination event between the 5' and 3' target
sequences and the homology arms upon a single-strand break or
double-strand break at the nuclease cleavage site. Thus, the target
sequences corresponding to the 5' and/or 3' homology arms of the
exogenous donor nucleic acid can be, for example, within at least 1
nucleotide of a given nuclease cleavage site or within at least 10
nucleotides to about 1,000 nucleotides of a given nuclease cleavage
site. As an example, the nuclease cleavage site can be immediately
adjacent to at least one or both of the target sequences.
[0247] The spatial relationship of the target sequences that
correspond to the homology arms of the exogenous donor nucleic acid
and the nuclease cleavage site can vary. For example, target
sequences can be located 5' to the nuclease cleavage site, target
sequences can be located 3' to the nuclease cleavage site, or the
target sequences can flank the nuclease cleavage site.
[0248] (4) Other Human-TTR-Targeting Reagents
[0249] The activity of any other known or putative
human-TTR-targeting reagent can also be assessed using the
non-human animals disclosed herein. Similarly, any other molecule
can be screened for human-TTR-targeting activity using the
non-human animals disclosed herein.
[0250] Examples of other human-TTR-targeting reagents include
antisense oligonucleotides (e.g., siRNAs or shRNAs) that act
through RNA interference (RNAi). Antisense oligonucleotides (ASOs)
or antisense RNAs are short synthetic strings of nucleotides
designed to prevent the expression of a targeted protein by
selectively binding to the RNA that encodes the targeted protein
and thereby preventing translation. These compounds bind to RNA
with high affinity and selectivity through well characterized
Watson-Crick base pairing (hybridization). RNA interference (RNAi)
is an endogenous cellular mechanism for controlling gene expression
in which small interfering RNAs (siRNAs) that are bound to the
RNA-induced silencing complex (RISC) mediate the cleavage of target
messenger RNA (mRNA). Examples of human-TTR-targeting antisense
oligonucleotides are known. See, e.g., Ackermann et al. (2012)
Amyloid Suppl 1:43-44 and Coelho et al. (2013) N. Engl. J. Med.
369(9):819-829, each of which is herein incorporated by reference
in its entirety for all purposes.
[0251] Other human-TTR-targeting reagents include antibodies or
antigen-binding proteins designed to specifically bind a human TTR
epitope.
[0252] Other human-TTR-targeting reagents include small-molecule
reagents. One example of such a small-molecule reagent is
tafamidis, which functions by kinetic stabilization of the
correctly folded tetrameric form of the transthyretin (TTR)
protein. See, e.g., Hammarstrom et al. (2003) Science 299:713-716,
herein incorporated by reference in its entirety for all
purposes.
[0253] D. Administering Human-TTR-Targeting Reagents to Non-Human
Animals or Cells
[0254] The methods disclosed herein can comprise introducing into a
non-human animal or cell various molecules (e.g.,
human-TTR-targeting reagents such as therapeutic molecules or
complexes), including nucleic acids, proteins, nucleic-acid-protein
complexes, or protein complexes. "Introducing" includes presenting
to the cell or non-human animal the molecule (e.g., nucleic acid or
protein) in such a manner that it gains access to the interior of
the cell or to the interior of cells within the non-human animal.
The introducing can be accomplished by any means, and two or more
of the components (e.g., two of the components, or all of the
components) can be introduced into the cell or non-human animal
simultaneously or sequentially in any combination. For example, a
Cas protein can be introduced into a cell or non-human animal
before introduction of a guide RNA, or it can be introduced
following introduction of the guide RNA. As another example, an
exogenous donor nucleic acid can be introduced prior to the
introduction of a Cas protein and a guide RNA, or it can be
introduced following introduction of the Cas protein and the guide
RNA (e.g., the exogenous donor nucleic acid can be administered
about 1, 2, 3, 4, 8, 12, 24, 36, 48, or 72 hours before or after
introduction of the Cas protein and the guide RNA). See, e.g., US
2015/0240263 and US 2015/0110762, each of which is herein
incorporated by reference in its entirety for all purposes. In
addition, two or more of the components can be introduced into the
cell or non-human animal by the same delivery method or different
delivery methods. Similarly, two or more of the components can be
introduced into a non-human animal by the same route of
administration or different routes of administration.
[0255] In some methods, components of a CRISPR/Cas system are
introduced into a non-human animal or cell. A guide RNA can be
introduced into a non-human animal or cell in the form of an RNA
(e.g., in vitro transcribed RNA) or in the form of a DNA encoding
the guide RNA. When introduced in the form of a DNA, the DNA
encoding a guide RNA can be operably linked to a promoter active in
a cell in the non-human animal. For example, a guide RNA may be
delivered via AAV and expressed in vivo under a U6 promoter. Such
DNAs can be in one or more expression constructs. For example, such
expression constructs can be components of a single nucleic acid
molecule. Alternatively, they can be separated in any combination
among two or more nucleic acid molecules (i.e., DNAs encoding one
or more CRISPR RNAs and DNAs encoding one or more tracrRNAs can be
components of a separate nucleic acid molecules).
[0256] Likewise, Cas proteins can be provided in any form. For
example, a Cas protein can be provided in the form of a protein,
such as a Cas protein complexed with a gRNA. Alternatively, a Cas
protein can be provided in the form of a nucleic acid encoding the
Cas protein, such as an RNA (e.g., messenger RNA (mRNA)) or DNA.
Optionally, the nucleic acid encoding the Cas protein can be codon
optimized for efficient translation into protein in a particular
cell or organism. For example, the nucleic acid encoding the Cas
protein can be modified to substitute codons having a higher
frequency of usage in a mammalian cell, a rodent cell, a mouse
cell, a rat cell, or any other host cell of interest, as compared
to the naturally occurring polynucleotide sequence. When a nucleic
acid encoding the Cas protein is introduced into a non-human
animal, the Cas protein can be transiently, conditionally, or
constitutively expressed in a cell in the non-human animal.
[0257] Nucleic acids encoding Cas proteins or guide RNAs can be
operably linked to a promoter in an expression construct.
Expression constructs include any nucleic acid constructs capable
of directing expression of a gene or other nucleic acid sequence of
interest (e.g., a Cas gene) and which can transfer such a nucleic
acid sequence of interest to a target cell. For example, the
nucleic acid encoding the Cas protein can be in a vector comprising
a DNA encoding one or more gRNAs. Alternatively, it can be in a
vector or plasmid that is separate from the vector comprising the
DNA encoding one or more gRNAs. Suitable promoters that can be used
in an expression construct include promoters active, for example,
in one or more of a eukaryotic cell, a human cell, a non-human
cell, a mammalian cell, a non-human mammalian cell, a rodent cell,
a mouse cell, a rat cell, a hamster cell, a rabbit cell, a
pluripotent cell, an embryonic stem (ES) cell, an adult stem cell,
a developmentally restricted progenitor cell, an induced
pluripotent stem (iPS) cell, or a one-cell stage embryo. Such
promoters can be, for example, conditional promoters, inducible
promoters, constitutive promoters, or tissue-specific promoters.
Optionally, the promoter can be a bidirectional promoter driving
expression of both a Cas protein in one direction and a guide RNA
in the other direction. Such bidirectional promoters can consist of
(1) a complete, conventional, unidirectional Pol III promoter that
contains 3 external control elements: a distal sequence element
(DSE), a proximal sequence element (PSE), and a TATA box; and (2) a
second basic Pol III promoter that includes a PSE and a TATA box
fused to the 5' terminus of the DSE in reverse orientation. For
example, in the H1 promoter, the DSE is adjacent to the PSE and the
TATA box, and the promoter can be rendered bidirectional by
creating a hybrid promoter in which transcription in the reverse
direction is controlled by appending a PSE and TATA box derived
from the U6 promoter. See, e.g., US 2016/0074535, herein
incorporated by references in its entirety for all purposes. Use of
a bidirectional promoter to express genes encoding a Cas protein
and a guide RNA simultaneously allows for the generation of compact
expression cassettes to facilitate delivery.
[0258] Molecules (e.g., Cas proteins or guide RNAs) introduced into
the non-human animal or cell can be provided in compositions
comprising a carrier increasing the stability of the introduced
molecules (e.g., prolonging the period under given conditions of
storage (e.g., -20.degree. C., 4.degree. C., or ambient
temperature) for which degradation products remain below a
threshold, such below 0.5% by weight of the starting nucleic acid
or protein; or increasing the stability in vivo). Non-limiting
examples of such carriers include poly(lactic acid) (PLA)
microspheres, poly(D,L-lactic-coglycolic-acid) (PLGA) microspheres,
liposomes, micelles, inverse micelles, lipid cochleates, and lipid
microtubules.
[0259] Various methods and compositions are provided herein to
allow for introduction of a nucleic acid or protein into a cell or
non-human animal. Methods for introducing nucleic acids into
various cell types are known and include, for example, stable
transfection methods, transient transfection methods, and
virus-mediated methods.
[0260] Transfection protocols as well as protocols for introducing
nucleic acid sequences into cells may vary. Non-limiting
transfection methods include chemical-based transfection methods
using liposomes; nanoparticles; calcium phosphate (Graham et al.
(1973) Virology 52 (2): 456-67, Bacchetti et al. (1977) Proc. Natl.
Acad. Sci. USA 74 (4): 1590-4, and Kriegler, M (1991). Transfer and
Expression: A Laboratory Manual. New York: W. H. Freeman and
Company. pp. 96-97); dendrimers; or cationic polymers such as
DEAE-dextran or polyethylenimine. Non-chemical methods include
electroporation, Sono-poration, and optical transfection.
Particle-based transfection includes the use of a gene gun, or
magnet-assisted transfection (Bertram (2006) Current Pharmaceutical
Biotechnology 7, 277-28). Viral methods can also be used for
transfection.
[0261] Introduction of nucleic acids or proteins into a cell can
also be mediated by electroporation, by intracytoplasmic injection,
by viral infection, by adenovirus, by adeno-associated virus, by
lentivirus, by retrovirus, by transfection, by lipid-mediated
transfection, or by nucleofection. Nucleofection is an improved
electroporation technology that enables nucleic acid substrates to
be delivered not only to the cytoplasm but also through the nuclear
membrane and into the nucleus. In addition, use of nucleofection in
the methods disclosed herein typically requires much fewer cells
than regular electroporation (e.g., only about 2 million compared
with 7 million by regular electroporation). In one example,
nucleofection is performed using the LONZA.RTM. NUCLEOFECTOR.TM.
system.
[0262] Introduction of nucleic acids or proteins into a cell (e.g.,
a zygote) can also be accomplished by microinjection. In zygotes
(i.e., one-cell stage embryos), microinjection can be into the
maternal and/or paternal pronucleus or into the cytoplasm. If the
microinjection is into only one pronucleus, the paternal pronucleus
is preferable due to its larger size. Microinjection of an mRNA is
preferably into the cytoplasm (e.g., to deliver mRNA directly to
the translation machinery), while microinjection of a Cas protein
or a polynucleotide encoding a Cas protein or encoding an RNA is
preferable into the nucleus/pronucleus. Alternatively,
microinjection can be carried out by injection into both the
nucleus/pronucleus and the cytoplasm: a needle can first be
introduced into the nucleus/pronucleus and a first amount can be
injected, and while removing the needle from the one-cell stage
embryo a second amount can be injected into the cytoplasm. If a Cas
protein is injected into the cytoplasm, the Cas protein preferably
comprises a nuclear localization signal to ensure delivery to the
nucleus/pronucleus. Methods for carrying out microinjection are
well known. See, e.g., Nagy et al. (Nagy A, Gertsenstein M,
Vintersten K, Behringer R., 2003, Manipulating the Mouse Embryo.
Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press);
see also Meyer et al. (2010) Proc. Natl. Acad. Sci. USA
107:15022-15026 and Meyer et al. (2012) Proc. Natl. Acad. Sci. USA
109:9354-9359.
[0263] Other methods for introducing nucleic acid or proteins into
a cell or non-human animal can include, for example, vector
delivery, particle-mediated delivery, exosome-mediated delivery,
lipid-nanoparticle-mediated delivery,
cell-penetrating-peptide-mediated delivery, or
implantable-device-mediated delivery. As specific examples, a
nucleic acid or protein can be introduced into a cell or non-human
animal in a carrier such as a poly(lactic acid) (PLA) microsphere,
a poly(D,L-lactic-coglycolic-acid) (PLGA) microsphere, a liposome,
a micelle, an inverse micelle, a lipid cochleate, or a lipid
microtubule. Some specific examples of delivery to a non-human
animal include hydrodynamic delivery, virus-mediated delivery
(e.g., adeno-associated virus (AAV)-mediated delivery), and
lipid-nanoparticle-mediated delivery.
[0264] Introduction of nucleic acids and proteins into cells or
non-human animals can be accomplished by hydrodynamic delivery
(HDD). Hydrodynamic delivery has emerged as a method for
intracellular DNA delivery in vivo. For gene delivery to
parenchymal cells, only essential DNA sequences need to be injected
via a selected blood vessel, eliminating safety concerns associated
with current viral and synthetic vectors. When injected into the
bloodstream, DNA is capable of reaching cells in the different
tissues accessible to the blood. Hydrodynamic delivery employs the
force generated by the rapid injection of a large volume of
solution into the incompressible blood in the circulation to
overcome the physical barriers of endothelium and cell membranes
that prevent large and membrane-impermeable compounds from entering
parenchymal cells. In addition to the delivery of DNA, this method
is useful for the efficient intracellular delivery of RNA,
proteins, and other small compounds in vivo. See, e.g., Bonamassa
et al. (2011) Pharm. Res. 28(4):694-701, herein incorporated by
reference in its entirety for all purposes.
[0265] Introduction of nucleic acids can also be accomplished by
virus-mediated delivery, such as AAV-mediated delivery or
lentivirus-mediated delivery. Other exemplary viruses/viral vectors
include retroviruses, adenoviruses, vaccinia viruses, poxviruses,
and herpes simplex viruses. The viruses can infect dividing cells,
non-dividing cells, or both dividing and non-dividing cells. The
viruses can integrate into the host genome or alternatively do not
integrate into the host genome. Such viruses can also be engineered
to have reduced immunity. The viruses can be replication-competent
or can be replication-defective (e.g., defective in one or more
genes necessary for additional rounds of virion replication and/or
packaging). Viruses can cause transient expression, long-lasting
expression (e.g., at least 1 week, 2 weeks, 1 month, 2 months, or 3
months), or permanent expression (e.g., of Cas9 and/or gRNA).
Exemplary viral titers (e.g., AAV titers) include 10.sup.12,
10.sup.13, 10.sup.14, 10.sup.15 and 10.sup.16 vector
genomes/mL.
[0266] The ssDNA AAV genome consists of two open reading frames,
Rep and Cap, flanked by two inverted terminal repeats that allow
for synthesis of the complementary DNA strand. When constructing an
AAV transfer plasmid, the transgene is placed between the two ITRs,
and Rep and Cap can be supplied in trans. In addition to Rep and
Cap, AAV can require a helper plasmid containing genes from
adenovirus. These genes (E4, E2a, and VA) mediated AAV replication.
For example, the transfer plasmid, Rep/Cap, and the helper plasmid
can be transfected into HEK293 cells containing the adenovirus gene
E1+ to produce infectious AAV particles. Alternatively, the Rep,
Cap, and adenovirus helper genes may be combined into a single
plasmid. Similar packaging cells and methods can be used for other
viruses, such as retroviruses.
[0267] Multiple serotypes of AAV have been identified. These
serotypes differ in the types of cells they infect (i.e., their
tropism), allowing preferential transduction of specific cell
types. Serotypes for CNS tissue include AAV1, AAV2, AAV4, AAV5,
AAV8, and AAV9. Serotypes for heart tissue include AAV1, AAV8, and
AAV9. Serotypes for kidney tissue include AAV2. Serotypes for lung
tissue include AAV4, AAV5, AAV6, and AAV9. Serotypes for pancreas
tissue include AAV8. Serotypes for photoreceptor cells include
AAV2, AAV5, and AAV8. Serotypes for retinal pigment epithelium
tissue include AAV1, AAV2, AAV4, AAV5, and AAV8. Serotypes for
skeletal muscle tissue include AAV1, AAV6, AAV7, AAV8, and AAV9.
Serotypes for liver tissue include AAV7, AAV8, and AAV9, and
particularly AAV8.
[0268] Tropism can be further refined through pseudotyping, which
is the mixing of a capsid and a genome from different viral
serotypes. For example AAV2/5 indicates a virus containing the
genome of serotype 2 packaged in the capsid from serotype 5. Use of
pseudotyped viruses can improve transduction efficiency, as well as
alter tropism. Hybrid capsids derived from different serotypes can
also be used to alter viral tropism. For example, AAV-DJ contains a
hybrid capsid from eight serotypes and displays high infectivity
across a broad range of cell types in vivo. AAV-DJ8 is another
example that displays the properties of AAV-DJ but with enhanced
brain uptake. AAV serotypes can also be modified through mutations.
Examples of mutational modifications of AAV2 include Y444F, Y500F,
Y730F, and S662V. Examples of mutational modifications of AAV3
include Y705F, Y731F, and T492V. Examples of mutational
modifications of AAV6 include S663V and T492V. Other
pseudotyped/modified AAV variants include AAV2/1, AAV2/6, AAV2/7,
AAV2/8, AAV2/9, AAV2.5, AAV8.2, and AAV/SASTG.
[0269] To accelerate transgene expression, self-complementary AAV
(scAAV) variants can be used. Because AAV depends on the cell's DNA
replication machinery to synthesize the complementary strand of the
AAV's single-stranded DNA genome, transgene expression may be
delayed. To address this delay, scAAV containing complementary
sequences that are capable of spontaneously annealing upon
infection can be used, eliminating the requirement for host cell
DNA synthesis. However, single-stranded AAV (ssAAV) vectors can
also be used.
[0270] To increase packaging capacity, longer transgenes may be
split between two AAV transfer plasmids, the first with a 3' splice
donor and the second with a 5' splice acceptor. Upon co-infection
of a cell, these viruses form concatemers, are spliced together,
and the full-length transgene can be expressed. Although this
allows for longer transgene expression, expression is less
efficient. Similar methods for increasing capacity utilize
homologous recombination. For example, a transgene can be divided
between two transfer plasmids but with substantial sequence overlap
such that co-expression induces homologous recombination and
expression of the full-length transgene.
[0271] Introduction of nucleic acids and proteins can also be
accomplished by lipid nanoparticle (LNP)-mediated delivery. For
example, LNP-mediated delivery can be used to deliver a combination
of Cas mRNA and guide RNA or a combination of Cas protein and guide
RNA. Delivery through such methods results in transient Cas
expression, and the biodegradable lipids improve clearance, improve
tolerability, and decrease immunogenicity. Lipid formulations can
protect biological molecules from degradation while improving their
cellular uptake. Lipid nanoparticles are particles comprising a
plurality of lipid molecules physically associated with each other
by intermolecular forces. These include microspheres (including
unilamellar and multilamellar vesicles, e.g., liposomes), a
dispersed phase in an emulsion, micelles, or an internal phase in a
suspension. Such lipid nanoparticles can be used to encapsulate one
or more nucleic acids or proteins for delivery. Formulations which
contain cationic lipids are useful for delivering polyanions such
as nucleic acids. Other lipids that can be included are neutral
lipids (i.e., uncharged or zwitterionic lipids), anionic lipids,
helper lipids that enhance transfection, and stealth lipids that
increase the length of time for which nanoparticles can exist in
vivo. Examples of suitable cationic lipids, neutral lipids, anionic
lipids, helper lipids, and stealth lipids can be found in WO
2016/010840 A1, herein incorporated by reference in its entirety
for all purposes. An exemplary lipid nanoparticle can comprise a
cationic lipid and one or more other components. In one example,
the other component can comprise a helper lipid such as
cholesterol. In another example, the other components can comprise
a helper lipid such as cholesterol and a neutral lipid such as
DSPC. In another example, the other components can comprise a
helper lipid such as cholesterol, an optional neutral lipid such as
DSPC, and a stealth lipid such as S010, S024, S027, S031, or
S033.
[0272] The LNP may contain one or more or all of the following: (i)
a lipid for encapsulation and for endosomal escape; (ii) a neutral
lipid for stabilization; (iii) a helper lipid for stabilization;
and (iv) a stealth lipid. See, e.g., Finn et al. (2018) Cell
Reports 22:1-9 and WO 2017/173054 A1, each of which is herein
incorporated by reference in its entirety for all purposes. In
certain LNPs, the cargo can include a guide RNA or a nucleic acid
encoding a guide RNA. In certain LNPs, the cargo can include an
mRNA encoding a Cas nuclease, such as Cas9, and a guide RNA or a
nucleic acid encoding a guide RNA.
[0273] The lipid for encapsulation and endosomal escape can be a
cationic lipid. The lipid can also be a biodegradable lipid, such
as a biodegradable ionizable lipid. One example of a suitable lipid
is Lipid A or LP01, which is
(9Z,12Z)-3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3-(diethylamino)propoxy-
)carbonyl)oxy)methyl)propyl octadeca-9,12-dienoate, also called
3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3-(diethylamino)propoxy)carbonyl-
)oxy)methyl)propyl (9Z,12Z)-octadeca-9,12-dienoate. See, e.g., Finn
et al. (2018) Cell Reports 22:1-9 and WO 2017/173054 A1, each of
which is herein incorporated by reference in its entirety for all
purposes. Another example of a suitable lipid is Lipid B, which is
((5-((dimethylamino)methyl)-1,3-phenylene)bis(oxy))bis(octane-8,1-diyl)bi-
s(decanoate), also called
((5-((dimethylamino)methyl)-1,3-phenylene)bis(oxy))bis(octane-8,1-diyl)bi-
s(decanoate). Another example of a suitable lipid is Lipid C, which
is
2-((4-(((3-(dimethylamino)propoxy)carbonyl)oxy)hexadecanoyl)oxy)propane-1-
,3-diyl(9Z,9'Z,12Z,12'Z)-bis(octadeca-9,12-dienoate). Another
example of a suitable lipid is Lipid D, which is
3-(((3-(dimethylamino)propoxy)carbonyl)oxy)-13-(octanoyloxy)tridecyl
3-octylundecanoate. Other suitable lipids include
heptatriaconta-6,9,28,31-tetraen-19-yl4-(dimethylamino)butanoate
(also known as Dlin-MC3-DMA (MC3))).
[0274] Some such lipids suitable for use in the LNPs described
herein are biodegradable in vivo. For example, LNPs comprising such
a lipid include those where at least 75% of the lipid is cleared
from the plasma within 8, 10, 12, 24, or 48 hours, or 3, 4, 5, 6,
7, or 10 days. As another example, at least 50% of the LNP is
cleared from the plasma within 8, 10, 12, 24, or 48 hours, or 3, 4,
5, 6, 7, or 10 days.
[0275] Such lipids may be ionizable depending upon the pH of the
medium they are in. For example, in a slightly acidic medium, the
lipids may be protonated and thus bear a positive charge.
Conversely, in a slightly basic medium, such as, for example, blood
where pH is approximately 7.35, the lipids may not be protonated
and thus bear no charge. In some embodiments, the lipids may be
protonated at a pH of at least about 9, 9.5, or 10. The ability of
such a lipid to bear a charge is related to its intrinsic pKa. For
example, the lipid may, independently, have a pKa in the range of
from about 5.8 to about 6.2.
[0276] Neutral lipids function to stabilize and improve processing
of the LNPs. Examples of suitable neutral lipids include a variety
of neutral, uncharged or zwitterionic lipids. Examples of neutral
phospholipids suitable for use in the present disclosure include,
but are not limited to, 5-heptadecylbenzene-1,3-diol (resorcinol),
dipalmitoylphosphatidylcholine (DPPC),
distearoylphosphatidylcholine (DSPC), phosphocholine (DOPC),
dimyristoylphosphatidylcholine (DMPC), phosphatidylcholine (PLPC),
1,2-distearoyl-sn-glycero-3-phosphocholine (DAPC),
phosphatidylethanolamine (PE), egg phosphatidylcholine (EPC),
dilauryloylphosphatidylcholine (DLPC),
dimyristoylphosphatidylcholine (DMPC), 1-myristoyl-2-palmitoyl
phosphatidylcholine (MPPC), 1-palmitoyl-2-myristoyl
phosphatidylcholine (PMPC), 1-palmitoyl-2-stearoyl
phosphatidylcholine (PSPC),
1,2-diarachidoyl-sn-glycero-3-phosphocholine (DBPC),
1-stearoyl-2-palmitoyl phosphatidylcholine (SPPC),
1,2-dieicosenoyl-sn-glycero-3-phosphocholine (DEPC),
palmitoyloleoyl phosphatidylcholine (POPC), lysophosphatidyl
choline, dioleoyl phosphatidylethanolamine (DOPE),
dilinoleoylphosphatidylcholine distearoylphosphatidylethanolamine
(DSPE), dimyristoyl phosphatidylethanolamine (DMPE), dipalmitoyl
phosphatidylethanolamine (DPPE), palmitoyloleoyl
phosphatidylethanolamine (POPE), lysophosphatidylethanolamine, and
combinations thereof. For example, the neutral phospholipid may be
selected from the group consisting of distearoylphosphatidylcholine
(DSPC) and dimyristoyl phosphatidyl ethanolamine (DMPE).
[0277] Helper lipids include lipids that enhance transfection. The
mechanism by which the helper lipid enhances transfection can
include enhancing particle stability. In certain cases, the helper
lipid can enhance membrane fusogenicity. Helper lipids include
steroids, sterols, and alkyl resorcinols. Examples of suitable
helper lipids suitable include cholesterol, 5-heptadecylresorcinol,
and cholesterol hemisuccinate. In one example, the helper lipid may
be cholesterol or cholesterol hemisuccinate.
[0278] Stealth lipids include lipids that alter the length of time
the nanoparticles can exist in vivo. Stealth lipids may assist in
the formulation process by, for example, reducing particle
aggregation and controlling particle size. Stealth lipids may
modulate pharmacokinetic properties of the LNP. Suitable stealth
lipids include lipids having a hydrophilic head group linked to a
lipid moiety.
[0279] The hydrophilic head group of stealth lipid can comprise,
for example, a polymer moiety selected from polymers based on PEG
(sometimes referred to as poly(ethylene oxide)), poly(oxazoline),
poly(vinyl alcohol), poly(glycerol), poly(N-vinylpyrrolidone),
polyaminoacids, and poly N-(2-hydroxypropyl)methacrylamide. The
term PEG means any polyethylene glycol or other polyalkylene ether
polymer. In certain LNP formulations, the PEG, is a PEG-2K, also
termed PEG 2000, which has an average molecular weight of about
2,000 daltons. See, e.g., WO 2017/173054 A1, herein incorporated by
reference in its entirety for all purposes.
[0280] The lipid moiety of the stealth lipid may be derived, for
example, from diacylglycerol or diacylglycamide, including those
comprising a dialkylglycerol or dialkylglycamide group having alkyl
chain length independently comprising from about C4 to about C40
saturated or unsaturated carbon atoms, wherein the chain may
comprise one or more functional groups such as, for example, an
amide or ester. The dialkylglycerol or dialkylglycamide group can
further comprise one or more substituted alkyl groups.
[0281] As one example, the stealth lipid may be selected from
PEG-dilauroylglycerol, PEG-dimyristoylglycerol (PEG-DMG),
PEG-dipalmitoylglycerol, PEG-distearoylglycerol (PEG-DSPE),
PEG-dilaurylglycamide, PEG-dimyristylglycamide,
PEG-dipalmitoylglycamide, and PEG-distearoylglycamide,
PEG-cholesterol
(1-[8'-(Cholest-5-en-3[beta]-oxy)carboxamido-3',6'-dioxaoctanyl]carbamoyl-
-[omega]-methyl-poly(ethylene glycol), PEG-DMB
(3,4-ditetradecoxylbenzyl-[omega]-methyl-poly(ethylene
glycol)ether),
1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene
glycol)-2000] (PEG2k-DMG),
1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene
glycol)-2000] (PEG2k-DSPE), 1,2-distearoyl-sn-glycerol, methoxypoly
ethylene glycol (PEG2k-DSG), poly(ethylene
glycol)-2000-dimethacrylate (PEG2k-DMA), and
1,2-distearyloxypropyl-3-amine-N-[methoxy(polyethylene
glycol)-2000] (PEG2k-DSA). In one particular example, the stealth
lipid may be PEG2k-DMG.
[0282] The LNPs can comprise different respective molar ratios of
the component lipids in the formulation. The mol-% of the CCD lipid
may be, for example, from about 30 mol-% to about 60 mol-%, from
about 35 mol-% to about 55 mol-%, from about 40 mol-% to about 50
mol-%, from about 42 mol-% to about 47 mol-%, or about 45%. The
mol-% of the helper lipid may be, for example, from about 30 mol-%
to about 60 mol-%, from about 35 mol-% to about 55 mol-%, from
about 40 mol-% to about 50 mol-%, from about 41 mol-% to about 46
mol-%, or about 44 mol-%. The mol-% of the neutral lipid may be,
for example, from about 1 mol-% to about 20 mol-%, from about 5
mol-% to about 15 mol-%, from about 7 mol-% to about 12 mol-%, or
about 9 mol-%. The mol-% of the stealth lipid may be, for example,
from about 1 mol-% to about 10 mol-%, from about 1 mol-% to about 5
mol-%, from about 1 mol-% to about 3 mol-%, about 2 mol-%, or about
1 mol-%.
[0283] The LNPs can have different ratios between the positively
charged amine groups of the biodegradable lipid (N) and the
negatively charged phosphate groups (P) of the nucleic acid to be
encapsulated. This may be mathematically represented by the
equation N/P. For example, the N/P ratio may be from about 0.5 to
about 100, from about 1 to about 50, from about 1 to about 25, from
about 1 to about 10, from about 1 to about 7, from about 3 to about
5, from about 4 to about 5, about 4, about 4.5, or about 5. The N/P
ratio can also be from about 4 to about 7 or from about 4.5 to
about 6. In specific examples, the N/P ratio can be 4.5 or can be
6.
[0284] In some LNPs, the cargo can comprise Cas mRNA and gRNA. The
Cas mRNA and gRNAs can be in different ratios. For example, the LNP
formulation can include a ratio of Cas mRNA to gRNA nucleic acid
ranging from about 25:1 to about 1:25, ranging from about 10:1 to
about 1:10, ranging from about 5:1 to about 1:5, or about 1:1.
Alternatively, the LNP formulation can include a ratio of Cas mRNA
to gRNA nucleic acid from about 1:1 to about 1:5, or about 10:1.
Alternatively, the LNP formulation can include a ratio of Cas mRNA
to gRNA nucleic acid of about 1:10, 25:1, 10:1, 5:1, 3:1, 1:1, 1:3,
1:5, 1:10, or 1:25. Alternatively, the LNP formulation can include
a ratio of Cas mRNA to gRNA nucleic acid of from about 1:1 to about
1:2. In specific examples, the ratio of Cas mRNA to gRNA can be
about 1:1 or about 1:2.
[0285] In some LNPs, the cargo can comprise exogenous donor nucleic
acid and gRNA. The exogenous donor nucleic acid and gRNAs can be in
different ratios. For example, the LNP formulation can include a
ratio of exogenous donor nucleic acid to gRNA nucleic acid ranging
from about 25:1 to about 1:25, ranging from about 10:1 to about
1:10, ranging from about 5:1 to about 1:5, or about 1:1.
Alternatively, the LNP formulation can include a ratio of exogenous
donor nucleic acid to gRNA nucleic acid from about 1:1 to about
1:5, about 5:1 to about 1:1, about 10:1, or about 1:10.
Alternatively, the LNP formulation can include a ratio of exogenous
donor nucleic acid to gRNA nucleic acid of about 1:10, 25:1, 10:1,
5:1, 3:1, 1:1, 1:3, 1:5, 1:10, or 1:25.
[0286] A specific example of a suitable LNP has a
nitrogen-to-phosphate (N/P) ratio of 4.5 and contains biodegradable
cationic lipid, cholesterol, DSPC, and PEG2k-DMG in a 45:44:9:2
molar ratio. The biodegradable cationic lipid can be
(9Z,12Z)-3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3-(diethylamino)propoxy-
)carbonyl)oxy)methyl)propyl octadeca-9,12-dienoate, also called
3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3-(diethylamino)propoxy)carbonyl-
)oxy)methyl)propyl (9Z,12Z)-octadeca-9,12-dienoate. See, e.g., Finn
et al. (2018) Cell Reports 22:1-9, herein incorporated by reference
in its entirety for all purposes. The Cas9 mRNA can be in a 1:1
ratio by weight to the guide RNA. Another specific example of a
suitable LNP contains Dlin-MC3-DMA (MC3), cholesterol, DSPC, and
PEG-DMG in a 50:38.5:10:1.5 molar ratio.
[0287] Another specific example of a suitable LNP has a
nitrogen-to-phosphate (N/P) ratio of 6 and contains biodegradable
cationic lipid, cholesterol, DSPC, and PEG2k-DMG in a 50:38:9:3
molar ratio. The biodegradable cationic lipid can be
(9Z,12Z)-3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3-(diethylamino)propoxy-
)carbonyl)oxy)methyl)propyl octadeca-9,12-dienoate, also called
3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3-(diethylamino)propoxy)carbonyl-
)oxy)methyl)propyl (9Z,12Z)-octadeca-9,12-dienoate. The Cas9 mRNA
can be in a 1:2 ratio by weight to the guide RNA.
[0288] The mode of delivery can be selected to decrease
immunogenicity. For example, a Cas protein and a gRNA may be
delivered by different modes (e.g., bi-modal delivery). These
different modes may confer different pharmacodynamics or
pharmacokinetic properties on the subject delivered molecule (e.g.,
Cas or nucleic acid encoding, gRNA or nucleic acid encoding, or
exogenous donor nucleic acid/repair template). For example, the
different modes can result in different tissue distribution,
different half-life, or different temporal distribution. Some modes
of delivery (e.g., delivery of a nucleic acid vector that persists
in a cell by autonomous replication or genomic integration) result
in more persistent expression and presence of the molecule, whereas
other modes of delivery are transient and less persistent (e.g.,
delivery of an RNA or a protein). Delivery of Cas proteins in a
more transient manner, for example as mRNA or protein, can ensure
that the Cas/gRNA complex is only present and active for a short
period of time and can reduce immunogenicity caused by peptides
from the bacterially-derived Cas enzyme being displayed on the
surface of the cell by MHC molecules. Such transient delivery can
also reduce the possibility of off-target modifications.
[0289] Administration in vivo can be by any suitable route
including, for example, parenteral, intravenous, oral,
subcutaneous, intra-arterial, intracranial, intrathecal,
intraperitoneal, topical, intranasal, or intramuscular. Systemic
modes of administration include, for example, oral and parenteral
routes. Examples of parenteral routes include intravenous,
intraarterial, intraosseous, intramuscular, intradermal,
subcutaneous, intranasal, and intraperitoneal routes. A specific
example is intravenous infusion. Nasal instillation and
intravitreal injection are other specific examples. Local modes of
administration include, for example, intrathecal,
intracerebroventricular, intraparenchymal (e.g., localized
intraparenchymal delivery to the striatum (e.g., into the caudate
or into the putamen), cerebral cortex, precentral gyms, hippocampus
(e.g., into the dentate gyrus or CA3 region), temporal cortex,
amygdala, frontal cortex, thalamus, cerebellum, medulla,
hypothalamus, tectum, tegmentum, or substantia nigra), intraocular,
intraorbital, subconjuctival, intravitreal, subretinal, and
transscleral routes. Significantly smaller amounts of the
components (compared with systemic approaches) may exert an effect
when administered locally (for example, intraparenchymal or
intravitreal) compared to when administered systemically (for
example, intravenously). Local modes of administration may also
reduce or eliminate the incidence of potentially toxic side effects
that may occur when therapeutically effective amounts of a
component are administered systemically.
[0290] Administration in vivo can be by any suitable route
including, for example, parenteral, intravenous, oral,
subcutaneous, intra-arterial, intracranial, intrathecal,
intraperitoneal, topical, intranasal, or intramuscular. A specific
example is intravenous infusion. Compositions comprising the guide
RNAs and/or Cas proteins (or nucleic acids encoding the guide RNAs
and/or Cas proteins) can be formulated using one or more
physiologically and pharmaceutically acceptable carriers, diluents,
excipients or auxiliaries. The formulation can depend on the route
of administration chosen. The term "pharmaceutically acceptable"
means that the carrier, diluent, excipient, or auxiliary is
compatible with the other ingredients of the formulation and not
substantially deleterious to the recipient thereof.
[0291] The frequency of administration and the number of dosages
can be depend on the half-life of the exogenous donor nucleic
acids, guide RNAs, or Cas proteins (or nucleic acids encoding the
guide RNAs or Cas proteins) and the route of administration among
other factors. The introduction of nucleic acids or proteins into
the cell or non-human animal can be performed one time or multiple
times over a period of time. For example, the introduction can be
performed at least two times over a period of time, at least three
times over a period of time, at least four times over a period of
time, at least five times over a period of time, at least six times
over a period of time, at least seven times over a period of time,
at least eight times over a period of time, at least nine times
over a period of times, at least ten times over a period of time,
at least eleven times, at least twelve times over a period of time,
at least thirteen times over a period of time, at least fourteen
times over a period of time, at least fifteen times over a period
of time, at least sixteen times over a period of time, at least
seventeen times over a period of time, at least eighteen times over
a period of time, at least nineteen times over a period of time, or
at least twenty times over a period of time.
[0292] E. Measuring Delivery, Activity, or Efficacy of
Human-TTR-Targeting Reagents In Vivo or Ex Vivo
[0293] The methods disclosed herein can further comprise detecting
or measuring activity of human-TTR-targeting reagents. For example,
if the human-TTR-targeting reagent is a genome editing reagent
(e.g., CRISPR/Cas designed to target the human TTR locus), the
measuring can comprise assessing the humanized TTR locus for
modifications.
[0294] Various methods can be used to identify cells having a
targeted genetic modification. The screening can comprise a
quantitative assay for assessing modification of allele (MOA) of a
parental chromosome. For example, the quantitative assay can be
carried out via a quantitative PCR, such as a real-time PCR (qPCR).
The real-time PCR can utilize a first primer set that recognizes
the target locus and a second primer set that recognizes a
non-targeted reference locus. The primer set can comprise a
fluorescent probe that recognizes the amplified sequence. Other
examples of suitable quantitative assays include
fluorescence-mediated in situ hybridization (FISH), comparative
genomic hybridization, isothermic DNA amplification, quantitative
hybridization to an immobilized probe(s), INVADER.RTM. Probes,
TAQMAN.RTM. Molecular Beacon probes, or ECLIPSE.TM. probe
technology (see, e.g., US 2005/0144655, herein incorporated by
reference in its entirety for all purposes).
[0295] Next-generation sequencing (NGS) can also be used for
screening. Next-generation sequencing can also be referred to as
"NGS" or "massively parallel sequencing" or "high throughput
sequencing." NGS can be used as a screening tool in addition to the
MOA assays to define the exact nature of the targeted genetic
modification and whether it is consistent across cell types or
tissue types or organ types.
[0296] Assessing modification of the humanized TTR locus in a
non-human animal can be in any cell type from any tissue or organ.
For example, the assessment can be in multiple cell types from the
same tissue or organ or in cells from multiple locations within the
tissue or organ. This can provide information about which cell
types within a target tissue or organ are being targeted or which
sections of a tissue or organ are being reached by the
human-TTR-targeting reagent. As another example, the assessment can
be in multiple types of tissue or in multiple organs. In methods in
which a particular tissue, organ, or cell type is being targeted,
this can provide information about how effectively that tissue or
organ is being targeted and whether there are off-target effects in
other tissues or organs.
[0297] If the reagent is designed to inactivate the humanized TTR
locus, affect expression of the humanized TTR locus, prevent
translation of the humanized TTR mRNA, or clear the humanized TTR
protein, the measuring can comprise assessing humanized TTR mRNA or
protein expression. This measuring can be within the liver or
particular cell types or regions within the liver, or it can
involve measuring serum levels of secreted humanized TTR
protein.
[0298] Production and secretion of the humanized TTR protein can be
assessed by any known means. For example, expression can be
assessed by measuring levels of the encoded mRNA in the liver of
the non-human animal or levels of the encoded protein in the liver
of the non-human animal using known assays. Secretion of the
humanized TTR protein can be assessed by measuring or plasma levels
or serum levels of the encoded humanized TTR protein in the
non-human animal using known assays.
IV. Methods of Making Non-Human Animals Comprising a Humanized TTR
Locus
[0299] Various methods are provided for making a non-human animal
comprising a humanized TTR locus as disclosed elsewhere herein. Any
convenient method or protocol for producing a genetically modified
organism is suitable for producing such a genetically modified
non-human animal. See, e.g., Cho et al. (2009) Current Protocols in
Cell Biology 42:19.11:19.11.1-19.11.22 and Gama Sosa et al. (2010)
Brain Struct. Funct. 214(2-3):91-109, each of which is herein
incorporated by reference in its entirety for all purposes. Such
genetically modified non-human animals can be generated, for
example, through gene knock-in at a targeted Ttr locus.
[0300] For example, the method of producing a non-human animal
comprising a humanized TTR locus can comprise: (1) modifying the
genome of a pluripotent cell to comprise the humanized TTR locus;
(2) identifying or selecting the genetically modified pluripotent
cell comprising the humanized TTR locus; (3) introducing the
genetically modified pluripotent cell into a non-human animal host
embryo; and (4) implanting and gestating the host embryo in a
surrogate mother. Optionally, the host embryo comprising modified
pluripotent cell (e.g., a non-human ES cell) can be incubated until
the blastocyst stage before being implanted into and gestated in
the surrogate mother to produce an F0 non-human animal. The
surrogate mother can then produce an F0 generation non-human animal
comprising the humanized TTR locus.
[0301] The methods can further comprise identifying a cell or
animal having a modified target genomic locus (i.e., a humanized
TTR locus). Various methods can be used to identify cells and
animals having a targeted genetic modification.
[0302] The screening step can comprise, for example, a quantitative
assay for assessing modification of allele (MOA) of a parental
chromosome. For example, the quantitative assay can be carried out
via a quantitative PCR, such as a real-time PCR (qPCR). The
real-time PCR can utilize a first primer set that recognizes the
target locus and a second primer set that recognizes a non-targeted
reference locus. The primer set can comprise a fluorescent probe
that recognizes the amplified sequence.
[0303] Other examples of suitable quantitative assays include
fluorescence-mediated in situ hybridization (FISH), comparative
genomic hybridization, isothermic DNA amplification, quantitative
hybridization to an immobilized probe(s), INVADER.RTM. Probes,
TAQMAN.RTM. Molecular Beacon probes, or ECLIPSE.TM. probe
technology (see, e.g., US 2005/0144655, incorporated herein by
reference in its entirety for all purposes).
[0304] An example of a suitable pluripotent cell is an embryonic
stem (ES) cell (e.g., a mouse ES cell or a rat ES cell). The
modified pluripotent cell can be generated, for example, through
recombination by (a) introducing into the cell one or more
targeting vectors comprising an insert nucleic acid flanked by 5'
and 3' homology arms corresponding to 5' and 3' target sites,
wherein the insert nucleic acid comprises a humanized TTR locus;
and (b) identifying at least one cell comprising in its genome the
insert nucleic acid integrated at the endogenous Ttr locus.
Alternatively, the modified pluripotent cell can be generated by
(a) introducing into the cell: (i) a nuclease agent, wherein the
nuclease agent induces a nick or double-strand break at a target
sequence within the endogenous Ttr locus; and (ii) one or more
targeting vectors comprising an insert nucleic acid flanked by 5'
and 3' homology arms corresponding to 5' and 3' target sites
located in sufficient proximity to the target sequence, wherein the
insert nucleic acid comprises the humanized TTR locus; and (c)
identifying at least one cell comprising a modification (e.g.,
integration of the insert nucleic acid) at the endogenous Ttr
locus. Any nuclease agent that induces a nick or double-strand
break into a desired target sequence can be used. Examples of
suitable nucleases include a Transcription Activator-Like Effector
Nuclease (TALEN), a zinc-finger nuclease (ZFN), a meganuclease, and
Clustered Regularly Interspersed Short Palindromic Repeats
(CRISPR)/CRISPR-associated (Cas) systems or components of such
systems (e.g., CRISPR/Cas9). See, e.g., US 2013/0309670 and US
2015/0159175, each of which is herein incorporated by reference in
its entirety for all purposes.
[0305] In a specific example, a method of making a non-human animal
comprising a humanized TTR locus can comprise: (a) introducing into
a non-human animal embryonic stem (ES) cell: (i) a nuclease agent
that targets a target sequence in the endogenous Ttr locus; and
(ii) a targeting vector comprising a nucleic acid insert comprising
the human TTR sequence flanked by a 5' homology arm corresponding
to a 5' target sequence in the endogenous Ttr locus and a 3'
homology arm corresponding to a 3' target sequence in the
endogenous Ttr locus, wherein the targeting vector recombines with
the endogenous Ttr locus to produce a genetically modified
non-human ES cell comprising in its genome the genetically modified
endogenous Ttr locus comprising the human TTR sequence; (b)
introducing the genetically modified non-human ES cell into a
non-human animal host embryo; and (c) gestating the non-human
animal host embryo in a surrogate mother, wherein the surrogate
mother produces an F0 progeny genetically modified non-human animal
comprising in its genome the genetically modified endogenous Ttr
locus comprising the human TTR sequence.
[0306] In some such methods, the nuclease agent can comprise a Cas
protein (e.g., a Cas9 protein) and a guide RNA that targets a
target sequence in the endogenous Ttr locus, but other suitable
nuclease agents can also be used. CRISPR/Cas and CRISPR/Cas9
systems are described in more detail elsewhere herein. Optionally,
two or more (e.g., three or four) nuclease agents (e.g., guide
RNAs) can be used. The target sequence(s) can be any suitable
target sequence within the endogenous Ttr locus. For example, the
target sequence(s) can be within about 10, about 20, about 30,
about 40, about 50, about 100, about 200, about 300, about 400,
about 500, about 1000 nucleotides about 2000, about 3000, about
4000, or about 5000 nucleotides of the start codon and/or the stop
codon (e.g., one target sequence in proximity to the start codon
and one target sequence in proximity to the stop codon).
[0307] In some such methods, the targeting vector is a large
targeting vector at least 10 kb in length or in which the sum total
of the 5' and 3' homology arms is at least 10 kb in length, but
other types of exogenous donor nucleic acids can also be used and
are well-known. The 5' and 3' homology arms can correspond with 5'
and 3' target sequences, respectively, that flank the region being
replaced by the human TTR insert nucleic acid or that flank the
region into which the human TTR insert nucleic acid is to be
inserted. The exogenous donor nucleic acid or targeting vector can
recombine with the target locus via homology directed repair or can
be inserted via NHEJ-mediated insertion to generate the humanized
TTR locus.
[0308] The donor cell can be introduced into a host embryo at any
stage, such as the blastocyst stage or the pre-morula stage (i.e.,
the 4 cell stage or the 8 cell stage). Progeny that are capable of
transmitting the genetic modification though the germline are
generated. See, e.g., U.S. Pat. No. 7,294,754, herein incorporated
by reference in its entirety for all purposes.
[0309] Alternatively, the method of producing the non-human animals
described elsewhere herein can comprise: (1) modifying the genome
of a one-cell stage embryo to comprise the humanized TTR locus
using the methods described above for modifying pluripotent cells;
(2) selecting the genetically modified embryo; and (3) implanting
and gestating the genetically modified embryo into a surrogate
mother. Progeny that are capable of transmitting the genetic
modification though the germline are generated.
[0310] Nuclear transfer techniques can also be used to generate the
non-human mammalian animals. Briefly, methods for nuclear transfer
can include the steps of: (1) enucleating an oocyte or providing an
enucleated oocyte; (2) isolating or providing a donor cell or
nucleus to be combined with the enucleated oocyte; (3) inserting
the cell or nucleus into the enucleated oocyte to form a
reconstituted cell; (4) implanting the reconstituted cell into the
womb of an animal to form an embryo; and (5) allowing the embryo to
develop. In such methods, oocytes are generally retrieved from
deceased animals, although they may be isolated also from either
oviducts and/or ovaries of live animals. Oocytes can be matured in
a variety of well-known media prior to enucleation. Enucleation of
the oocyte can be performed in a number of well-known manners.
Insertion of the donor cell or nucleus into the enucleated oocyte
to form a reconstituted cell can be by microinjection of a donor
cell under the zona pellucida prior to fusion. Fusion may be
induced by application of a DC electrical pulse across the
contact/fusion plane (electrofusion), by exposure of the cells to
fusion-promoting chemicals, such as polyethylene glycol, or by way
of an inactivated virus, such as the Sendai virus. A reconstituted
cell can be activated by electrical and/or non-electrical means
before, during, and/or after fusion of the nuclear donor and
recipient oocyte. Activation methods include electric pulses,
chemically induced shock, penetration by sperm, increasing levels
of divalent cations in the oocyte, and reducing phosphorylation of
cellular proteins (as by way of kinase inhibitors) in the oocyte.
The activated reconstituted cells, or embryos, can be cultured in
well-known media and then transferred to the womb of an animal.
See, e.g., US 2008/0092249, WO 1999/005266, US 2004/0177390, WO
2008/017234, and U.S. Pat. No. 7,612,250, each of which is herein
incorporated by reference in its entirety for all purposes.
[0311] The various methods provided herein allow for the generation
of a genetically modified non-human F0 animal wherein the cells of
the genetically modified F0 animal comprise the humanized TTR
locus. Depending on the method used to generate the F0 animal, the
number of cells within the F0 animal that have the humanized TTR
locus will vary. The introduction of the donor ES cells into a
pre-morula stage embryo from a corresponding organism (e.g., an
8-cell stage mouse embryo) via for example, the VELOCIMOUSE.RTM.
method allows for a greater percentage of the cell population of
the F0 animal to comprise cells having the nucleotide sequence of
interest comprising the targeted genetic modification. For example,
at least 50%, 60%, 65%, 70%, 75%, 85%, 86%, 87%, 87%, 88%, 89%,
90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% of the
cellular contribution of the non-human F0 animal can comprise a
cell population having the targeted modification.
[0312] The cells of the genetically modified F0 animal can be
heterozygous for the humanized TTR locus or can be homozygous for
the humanized TTR locus.
[0313] All patent filings, websites, other publications, accession
numbers and the like cited above or below are incorporated by
reference in their entirety for all purposes to the same extent as
if each individual item were specifically and individually
indicated to be so incorporated by reference. If different versions
of a sequence are associated with an accession number at different
times, the version associated with the accession number at the
effective filing date of this application is meant. The effective
filing date means the earlier of the actual filing date or filing
date of a priority application referring to the accession number if
applicable. Likewise, if different versions of a publication,
website or the like are published at different times, the version
most recently published at the effective filing date of the
application is meant unless otherwise indicated. Any feature, step,
element, embodiment, or aspect of the invention can be used in
combination with any other unless specifically indicated otherwise.
Although the present invention has been described in some detail by
way of illustration and example for purposes of clarity and
understanding, it will be apparent that certain changes and
modifications may be practiced within the scope of the appended
claims.
BRIEF DESCRIPTION OF THE SEQUENCES
[0314] The nucleotide and amino acid sequences listed in the
accompanying sequence listing are shown using standard letter
abbreviations for nucleotide bases, and three-letter code for amino
acids. The nucleotide sequences follow the standard convention of
beginning at the 5' end of the sequence and proceeding forward
(i.e., from left to right in each line) to the 3' end. Only one
strand of each nucleotide sequence is shown, but the complementary
strand is understood to be included by any reference to the
displayed strand. When a nucleotide sequence encoding an amino acid
sequence is provided, it is understood that codon degenerate
variants thereof that encode the same amino acid sequence are also
provided. The amino acid sequences follow the standard convention
of beginning at the amino terminus of the sequence and proceeding
forward (i.e., from left to right in each line) to the carboxy
terminus.
TABLE-US-00002 TABLE 2 Description of Sequences. SEQ ID NO Type
Description 1 Protein Human TTR Protein NP_000362.1 and P02766.1 2
Protein Expected Chimeric Mouse/Human TTR Protein - Humanization V2
3 DNA Human TTR Gene NG_009490.1 4 DNA Human TTR mRNA NM_000371.3 5
DNA Mouse Ttr gene NC_000084.6 6 Protein Mouse TTR protein P07309.1
and NP_038725.1 7 DNA Mouse Ttr mRNA NM_013697.5 8 RNA Generic
Guide RNA Scaffold v.2 9 RNA Generic Guide RNA Scaffold v.3 10 RNA
Generic Guide RNA Scaffold v.4 11 DNA Generic Guide RNA Target
Sequence plus PAM v.1 12 DNA Generic Guide RNA Target Sequence plus
PAM v.2 13 DNA Generic Guide RNA Target Sequence plus PAM v.3 14
DNA Expected Humanization V1 - F0, with SDC Pmci2 UbiNeo cassette
15 DNA Expected Humanization V1 - F1, Cassette-Deleted 16 DNA
Expected Humanization V2 - F0, with SDC Pmci2 UbiNeo cassette 17
DNA Expected Humanization V2 - F1, Cassette-Deleted 18 DNA Human
TTR Sequence Inserted in Humanized TTR V1 19 DNA Human TTR Sequence
Inserted in Humanized TTR V2 20 DNA Mouse Ttr Locus - Start Codon
to Stop Codon 21 DNA 9090retU3 - F Primer 22 DNA 9090retU2 - F
Primer 23 DNA 9090retU - F Primer 24 DNA 9090mTGU - F Primer 25 DNA
7576mTU - F Primer 26 DNA 9090mTM - F Primer 27 DNA 7576mTD - F
Primer 28 DNA 9090mTGD - F Primer 29 DNA 9090retD - F Primer 30 DNA
9090retD2 - F Primer 31 DNA 9090retD3 - F Primer 32 DNA 7576hTU - F
Primer 33 DNA 7576hTD - F Primer 34 DNA Neo - F Primer 35 DNA
7655hTU - F Primer 36 DNA 9212mTU - F Primer 37 DNA 9212mTGD - F
Primer 38 DNA 7655mTU - F Primer 39 DNA 7655mTD - F Primer 40 DNA
9204mretD - F Primer 41 DNA 9204mretU - F Primer 42 DNA 4552mTU - F
Primer 43 DNA 9090retU3 - R Primer 44 DNA 9090retU2 - R Primer 45
DNA 9090retU - R Primer 46 DNA 9090mTGU - R Primer 47 DNA 7576mTU -
R Primer 48 DNA 9090mTM - R Primer 49 DNA 7576mTD - R Primer 50 DNA
9090mTGD - R Primer 51 DNA 9090retD - R Primer 52 DNA 9090retD2 - R
Primer 53 DNA 9090retD3 - R Primer 54 DNA 7576hTU - R Primer 55 DNA
7576hTD - R Primer 56 DNA Neo - R Primer 57 DNA 7655hTU - R Primer
58 DNA 9212mTU - R Primer 59 DNA 9212mTGD - R Primer 60 DNA 7655mTU
- R Primer 61 DNA 7655mTD - R Primer 62 DNA 9204mretD - R Primer 63
DNA 9204mretU - R Primer 64 DNA 4552mTU - R Primer 65 DNA 9090retU3
- Probe 66 DNA 9090retU2 - Probe 67 DNA 9090retU - Probe 68 DNA
9090mTGU - Probe 69 DNA 7576mTU - Probe 70 DNA 9090mTM - Probe 71
DNA 7576mTD - Probe 72 DNA 9090mTGD - Probe 73 DNA 9090retD - Probe
74 DNA 9090retD2 - Probe 75 DNA 9090retD3 - Probe 76 DNA 7576hTU -
Probe 77 DNA 7576hTD - Probe 78 DNA Neo - Probe 79 DNA 7655hTU -
Probe 80 DNA 9212mTU - Probe 81 DNA 9212mTGD - Probe 82 DNA 7655mTU
- Probe 83 DNA 7655mTD - Probe 84 DNA 9204mretD - Probe 85 DNA
9204mretU - Probe 86 DNA 4552mTU - Probe 87 RNA crRNA tail 88 RNA
tracrRNA 89 RNA Generic Guide RNA Scaffold v.1 90 DNA Humanized TTR
CDS v1.0 91 DNA Humanized TTR CDS v2.0 92 DNA Mouse TTR CDS 93 DNA
Cas9 DNA Sequence 94 Protein Cas9 Protein Sequence
EXAMPLES
Example 1. Generation of Mice Comprising a Humanized TTR Locus
[0315] One promising therapeutic approach for the TTR amyloidosis
diseases is to reduce the TTR load in the patient by inactivation
of the gene with genome editing technology, such as CRISPR/Cas9
technology. To assist in the development of CRISPR/Cas9
therapeutics, mice with targeted modifications in the Ttr gene were
developed.
[0316] The first Ttr allele made was a complete deletion of the
mouse transthyretin coding sequence and its replacement with the
orthologous part of the human TTR gene. A large targeting vector
comprising a 5' homology arm including 33.7 kb of sequence upstream
from the mouse Ttr start codon and 34.5 kb of the sequence
downstream of the mouse Ttr stop codon was generated to replace the
approximately 8.3 kb region from the mouse Ttr start codon to the
mouse Ttr stop codon with the approximately 7.1 kb orthologous
human TTR sequence from the human TTR start codon to the end of the
last human TTR exon (exon 4, including the human 3' UTR) and a
self-deleting neomycin selection cassette (SDC Neo) flanked by loxP
sites. See FIG. 3. The SDC Neo cassette includes the following
components from 5' to 3': loxP site, mouse protamine (Prm1)
promoter, Crei (Cre coding sequence optimized to include intron),
polyA, human ubiquitin promoter, neomycin phosphotransferase
(neo.sub.r) coding sequence, polyA, loxP. To generate the humanized
allele, CRISPR/Cas9 components targeting the mouse Ttr locus were
introduced into F1H4 mouse embryonic stem cells together with the
large targeting vector. Loss-of-allele assays, gain-of-allele
assays, retention assays, and CRISPR assays using primers and
probes set forth in FIG. 5A and in Table 3 were performed to
confirm the humanization of the mouse Ttr allele. Loss-of-allele,
gain-of-allele assays, and retention assays are described, for
example, in US 2014/0178879; US 2016/0145646; WO 2016/081923; and
Frendewey et al. (2010) Methods Enzymol. 476:295-307, each of which
is herein incorporated by reference in its entirety for all
purposes. CRISPR assays are TAQMAN.RTM. assays designed to cover
the region that is disrupted by the CRISPR gRNAs. When a CRISPR
gRNA cuts and creates an indel (insertion or deletion), the
TAQMAN.RTM. assay will fail to amplify and thus reports CRISPR
cleavage. Versions with the SDC Neo cassette and after excision of
the SDC Neo cassette are shown in FIG. 3. F0 mice were then
generated using the VELOCIMOUSE.RTM. method. See, e.g., U.S. Pat.
Nos. 7,576,259; 7,659,442; 7,294,754; US 2008/007800; and
Poueymirou et al. (2007) Nature Biotech. 25(1):91-99, each of which
is herein incorporated by reference in its entirety for all
purposes.
[0317] F0 generation mice (50% C57BL/6NTac and 50% 129S6/SvEvTac)
were generated from multiple humanized ES cell clones, including
clones 7576A-A5, 7576C-G7, and 7576B-F10. The sequence for the
expected humanized mouse Ttr locus in the F0 generation mice is set
forth in SEQ ID NO: 14 and includes the SDC Neo cassette. F1 and F2
generation mice (75% C57BL/6NTac and 25% 12956/SvEvTac) were then
generated by breeding. The sequence for the expected humanized
mouse Ttr locus in the F1 and F2 generation mice is set forth in
SEQ ID NO: 15 and does not include the SDC Neo cassette.
[0318] A comparison of the human and mouse transthyretin precursor
protein sequences is shown in FIG. 1A, a comparison of the human
and mouse transthyretin coding sequences is shown in FIG. 1B, and a
schematic showing the wild type mouse Ttr locus and the final
humanized mouse Ttr locus (humanized TTR version 1 with the SDC Neo
cassette deleted) is shown in FIG. 2. The endogenous mouse Ttr
locus sequence from the start codon to the stop codon is provided
in SEQ ID NO: 20. Sequences for the expected humanized mouse Ttr
locus with the SDC Neo cassette and without the SDC Neo cassette
are set forth in SEQ ID NOS: 14 and 15, respectively. The expected
transthyretin precursor protein encoded by the humanized mouse Ttr
locus is set forth in SEQ ID NO: 1. This allele provides the true
human target of human TTR CRISPR/Cas9 therapeutics, thereby
enabling testing of the efficacy and mode of action of CRISPR/Cas9
therapeutics in live animals as well as pharmacokinetic and
pharmacodynamics studies in a setting where the human protein is
the only version of TTR present.
TABLE-US-00003 TABLE 3 Primers and Probes for Loss-of-Allele
Assays, Gain-of-Allele Assays, Retention Assays, and CRISPR Assays.
Assay Forward Primer Reverse Primer Probe 9090retU3
CACAGACAATCAGACGTACCAGTA GGGACATCTCGGTTTCCTGACTT
TCATGTAATCTGGCTTCAGAGTGGGA (SEQ ID NO: 21) (SEQ ID NO: 43) (SEQ ID
NO: 65) 9090retU2 CCAGCTTTGCCAGTTTACGA TCCACACTACTGAACTCCACAA
TGGGAGGCAATTCTTAGTTTCAATGGA (SEQ ID NO: 22) (SEQ ID NO: 44) (SEQ ID
NO: 66) 9090retU TTGGACGGTTGCCCTCTT CGGAACACTCGCTCTACGAAA
TCCCAAAGGTGTCTGTCTGCACA (SEQ ID NO: 23) (SEQ ID NO: 45) (SEQ ID NO:
67) 9090mTGU GATGGCTTCCCTTCGACTCTTC GGGCCAGCTTCAGACACA
CTCCTTTGCCTCGCTGGACTGG (SEQ ID NO: 24) (SEQ ID NO: 46) (SEQ ID NO:
68) 7576TU CACTGACATTTCTCTTGTCTCCTCT CCCAGGGTGCTGGAGAATCCAA
CGGACAGCATCCAGGACTT (SEQ ID NO: 25) (SEQ ID NO: 47) (SEQ ID NO: 69)
9090TM GGGCTCACCACAGATGAGAAG GCCAAGTGTCTTCCAGTACGAT
AGAAGGAGTGTACAGAGTAGAACTGGACA (SEQ ID NO: 26) (SEQ ID NO: 48) (SEQ
ID NO: 70) 7576TD CACTGTTCGCCACAGGTCTT GTTCCCTTTCTTGGGTTCAGA
TGTTTGTGGGTGTCAGTGTTTCTACTC (SEQ ID NO: 27) (SEQ ID NO: 49) (SEQ ID
NO: 71) 9090mTGD GCTCAGCCCATACTCCTACA GATGCTACTGCTTTGGCAAGATC
CACCACGGCTGTCGTCAGCAA (SEQ ID NO: 28) (SEQ ID NO: 50) (SEQ ID NO:
72) 9090retD GCCCAGGAGGACCAGGAT CCTGAGCTGCTAACACGGTT
CTTGCCAAAGCAGTAGCATCCCA (SEQ ID NO: 29) (SEQ ID NO: 51) (SEQ ID NO:
73) 9090retD2 GGCAACTTGCTTGAGGAAGA AGCTACAGACCATGCTTAGTGTA
AGGTCAGAAAGCAGAGTGGACCA (SEQ ID NO: 30) (SEQ ID NO: 52) (SEQ ID NO:
74) 9090retD3 GCAGCAACCCAGCTTCACTT TGCCAGTTTAGGAGGAATATGTTC
CCCAGGCAATTCCTACCTTCCCA (SEQ ID NO: 31) (SEQ ID NO: 53) (SEQ ID NO:
75) 7576hTU ACTGAGCTGGGACTTGAAC CTGAGGAAACAGAGGTACCAGATAT
TCTGAGCATTCTACCTCATTGCTTTGGT (SEQ ID NO: 32) (SEQ ID NO: 54) (SEQ
ID NO: 76) 7576hTD TGCCTCACTCTGAGAACCA AGTCACACAGTTCTGTCAAATCAG
AGGCTGTCCCAGCACCTGAGTCG (SEQ ID NO: 33) (SEQ ID NO: 55) (SEQ ID NO:
77) Neo GGTGGAGAGGCTATTCGGC GAACACGGCGGCATCAG
TGGGCACAACAGACAATCGGCTG (SEQ ID NO: 34) (SEQ ID NO: 56) (SEQ ID NO:
78) 7655hTU GGCCGTGCATGTGTTCAG TCCTGTGGGAGGGTTCTTTG
AAGGCTGCTGATGACACCTGGGA (SEQ ID NO: 35) (SEQ ID NO: 57) (SEQ ID NO:
79) 9212mTU GGTTCCCATTTGCTCTTATTCGT CCCTCTCTCTGAGCCCTCTA
AGATTCAGACACACACAACTTACCAGC (SEQ ID NO: 36) (SEQ ID NO: 58) (SEQ ID
NO: 80) 9212mTGD CCCACACTGCAGAAGGAAACTTG GCTGCCTAAGTCTTTGGAGCT
AGACCTGCAATTCTCTAAGAGCTCCACA (SEQ ID NO: 37) (SEQ ID NO: 59) (SEQ
ID NO: 81) 7655mTU GGTTCCCATTTGCTCTTATTCGT CCCTCTCTCTGAGCCCTCTA
AGATTCAGACACACACAACTTACCAGC (SEQ ID NO: 38) (SEQ ID NO: 60) (SEQ ID
NO: 82) 7655TD CCAGCTTAGCATCCTGTGAACA GAGAGGAGAGACAGCTAGTTCTAAC
TTGTCTGCAGCTCCTACCTCTGGG (SEQ ID NO: 39) (SEQ ID NO: 61) (SEQ ID
NO: 83) 9204mretD GGCAACTTGCTTGAGGAAGA AGCTACAGACCATGCTTAGTGTA
AGGTCAGAAAGCAGAGTGGACCA (SEQ ID NO: 40) (SEQ ID NO: 62) (SEQ ID NO:
84) 9204mretU TGTGGAGTTCAGTAGTGTGGAG GCCCTCTTCATACAGGAATCAC
TTGACATGTGTGGGTGAGAGATTTTACTG (SEQ ID NO: 41) (SEQ ID NO: 63) (SEQ
ID NO: 85) 4552TU CACTGACATTTCTCTTGTCTCCTCT CGGACAGCATCCAGGACTT
CCCAGGGTGCTGGAGAATCCAA (SEQ ID NO: 42) (SEQ ID NO: 64) (SEQ ID NO:
86)
Example 2. Characterization of Mice Comprising a Humanized TTR
Locus
[0319] Humanized TTR mice F0 cohorts from clones 7576A-A5 and
7576C-G7 were then characterized. As shown in FIG. 6, humanized TTR
mRNA was robustly expressed in the liver of 8-week old, homozygous
F0 generation humanized TTR mice. Equal mass amounts of RNA from
each tissue were assayed by RT-qPCR. Five mice were assayed per
genotype, with four technical replicates per sample. Each tissue
had the RNA extracted. The genomic DNA was degraded so that it
would not count towards the qPCR reaction. The RNA was reverse
transcribed, and assays specific to human TTR and mouse Ttr were
used to detect human TTR transcripts and mouse Ttr transcripts,
respectively. As expected, the homozygous humanized TTR mouse
showed significant expression of human TTR in liver (ct values
below 30), while WT mice showed ct values of 30 and higher
indicating that there was no expression of human TTR. In contrast,
the wild type mouse showed significant expression of mouse Ttr in
the liver, while homozygous humanized TTR mice showed ct values of
30 and higher indicating that there is no endogenous expression of
mouse Ttr.
[0320] An ELISA assay was done to assess human TTR and mouse TTR
protein levels in serum and cerebrospinal fluid from 8-week-old,
homozygous F0 generation humanized TTR mice. A human TTR ELISA kit
(Aviva Systems Biology; Cat No.: OKIA00081; 1:250 dilution for
serum; 1:1000 dilution for CSF) was used to assess human TTR
levels. A mouse TTR ELISA kit (Aviva Systems Biology; Cat No:
OKIA00111; 1:4000 dilution for serum; 1:10000 dilution for CSF) was
used to assess mouse TTR levels. Human serum and human CSF were
used as positive controls for human TTR and negative controls for
mouse TTR, and F1H4 serum and F1H4 CSF were used as negative
controls for human TTR and positive controls for mouse TTR. As
shown in FIG. 7A, human TTR was detected in the serum from the
humanized TTR mice but not in serum from wild type (F1H4) mice. As
shown in FIG. 7B, mouse TTR was not detected in the serum from the
humanized TTR mice but was detected in wild type mouse serum. Human
and mouse TTR levels in serum were further assessed in humanized
TTR mice derived from two separate humanized mouse Ttr ES cell
clones: 7576C-G7 and 7576A-A5. As shown in FIG. 7C, human TTR was
detected in the serum of humanized TTR mice derived from clone
7576A-A5.
[0321] Human TTR protein expression was also assessed in
8-week-old, homozygous humanized TTR mice by western blot on serum
samples, liver samples, and kidney samples. The results are shown
in FIGS. 8-9. Serum samples (5 .mu.L total volume per well) were
boiled in Laemlli buffer (containing SDS and beta-mercaptoethanol)
and resolved on a 4-20% denaturing gradient gel (anti-TTR antibody:
1:1000; Abcam; ab75815). Mouse IgG (anti mouse IgG-HRP: 1:7500,
Jackson ImmunoResearch) was used as a loading control. Three mice
per group were tested for humanized mouse Ttr clones 7576C-G7 and
7576A-A5. Five mice per group were tested for wild type mouse
control (F1H4). Mouse serum and human serum were used as negative
and positive controls, respectively. As shown in FIG. 8, human TTR
was detected by western blot in serum from both humanized mouse Ttr
clones.
[0322] Liver and kidney samples (100 .mu.g total protein per well)
were boiled in Laemlli buffer (containing SDS and
beta-mercaptoethanol) and resolved on a 4-20% denaturing gradient
gel (anti-TTR antibody: 1:1000; Abcam; ab75815). GAPDH (anti-GAPDH:
1:2000, Santa Cruz) was used as a loading control. Three mice per
group were tested for humanized mouse Ttr clones 7576C-G7 and
7576A-A5. Five mice per group were tested for wild type mouse
control (F1H4). Mouse serum and human serum were used as negative
and positive controls, respectively. As shown in FIG. 9, human TTR
was detected by western blot in serum from both homozygous
humanized TTR mice generated from clone 7576A-A5.
[0323] In summary, TTR HumIn (TTR.sup.7576/7576) F0 mice were found
to have a detectable amount of circulating hTTR. In addition, mice
from clone 7576C-A5 had detectable amounts of hTTR in liver and
plasma.
[0324] We hypothesized that removal of the neomycin drug selection
cassette may increase secretion of the human TTR. Human TTR levels
were measured in plasma samples from non-terminal, submandibular
bleeds on 5-week-old mice homozygous for the fully humanized mouse
Ttr locus with the neomycin selection cassette (TTR.sup.7576/7576),
mice heterozygous for the fully humanized mouse Ttr locus with the
neomycin selection cassette (TTR.sup.7576/WT), mice heterozygous
for the fully humanized mouse Ttr locus without the neomycin
selection cassette (TTR.sup.7577/WT), and wild type mice (F1H4).
Human TTR levels were assayed with the AssayPro human TTR (hTTR)
ELISA kit (cat no.: EP3010-1; 1:40000 dilution). Mouse TTR serum
levels were assayed with the Aviva Systems Biology mouse TTR (mTTR)
ELISA kit (cat no. OKIA00111; 1:4000 dilution). The AssayPro human
TTR ELISA kit was previously determined to be specific for
detecting human TTR but not mouse TTR, and the Aviva Systems
Biology mouse TTR ELISA kit was previously determined to be
specific for detecting mouse TTR but not human TTR (data not
shown). As shown in Table 4, removal of the neomycin selection
cassette resulted in a statistically significant increase in human
TTR levels in the serum. MAID7576 refers to the humanized TTR locus
with the neomycin selection cassette. MAID7577 refers to the
humanized TTR locus with the neomycin selection cassette removed.
Enhanced human TTR mRNA expression was also observed in the liver
(data not shown). Mice heterozygous for hTTR and mTTR
(TTR-WT.sup.7576/WT and TTR-WT.sup.7577/WT) had increased
circulating hTTR, possibly due to increased stability from
heteromeric (e.g., cross-TTR species) interaction.
TABLE-US-00004 TABLE 4 Circulating Human and Mouse TTR Levels.
TTR.sup.7576/7576 TTR.sup.7576/WT TTR.sup.7577/WT F1H4 mTTR,
.mu.g/mL (SD) N.D. 207.62 (15.39) 359.9 (38.07)** 919.96 (79.73)
hTTR, .mu.g/mL (SD) 0.61 (0.43) 28.507 (5.61) 39.93 (3.70)**
N.D.
[0325] Serum and liver TTR levels were also measured in F2
generation homozygous humanized TTR mice (three per group) that
were generated from a different clone: 7576B-F10. As shown in FIG.
14 (Tris-saline sucrose (TSS) control sample), human TTR was
detected in liver samples at a level of more than 1000 ng/mL. As
shown in FIGS. 15A and 15B (TSS sample), human TTR was detected in
serum samples at a level of 80,000 ng/mL or higher.
[0326] In another experiment, blood was collected via submandibular
bleeds from TTR WT HumIn (v1.0, hTTR.sup.7577/7577, clone B-F10) F2
homozygous mice at 3 months of age. hTTR levels were determined in
plasma using species-specific ELISA kits (hTTR, Aviva, cat #
OKIA00081; mTTR, Aviva, cat # OKIA00111). As shown in FIGS. 17A and
17B and Table 5, hTTR was secreted into circulation in TTR WT HumIn
(v1.0, clone B-F10) F2 homozygous mice at 52.1+/-10.7 .mu.g/mL,
with no detectable levels of mTTR. mRNA levels of mTTR and hTTR in
liver samples from the wild type control mice (F1H4) and WT HumIn
(v1.0, hTTR.sup.7577/7577, clone B-F10) mice are shown in FIG.
17C.
TABLE-US-00005 TABLE 5 Plasma hTTR and mTTR Levels. hTTR, .mu.g/mL
(SD) mTTR, .mu.g/mL (SD) TTR.sup.WT/WT N.D. 831.5 (129.9)
TTR.sup.7577/7577 52.1 (10.7) Not detectable Human serum 234.5
(n.a.) Not detectable
Example 3. Use of Mice Comprising a Humanized TTR Locus to Test
Guide RNAs Targeting Human TTR Ex Vivo and In Vivo
[0327] F0 generation humanized TTR mice cohorts were then used to
test guide RNAs targeting human TTR ex vivo and in vivo. As a proof
of concept, human TTR guide RNAs were first tested in primary
hepatocytes isolated from F0 generation humanized TTR mice produced
from clone 7576C-G7. Livers from huTTR.sup.hI/hI mice were perfused
with 50 mL liver perfusion medium containing 1.times. PenStrep,
followed by 50 mL liver digestion medium (HBSS, 100 mM CaCl2, 500
mM HEPES, collagenase). Once livers appeared digested, they were
placed into wash medium containing 1.times. PenStrep and
L-glutamine. The livers were torn to release the hepatocytes from
the liver through gentle shaking. Once cells were released, they
were put through a 70 .mu.m mesh filter and spun at 50 g for 4
minutes at 4.degree. C. The pellets were washed 2.times. with wash
buffer. The pellets were then re-suspended in 20 mL of 38-40%
Percoll and spun at 200 g.times.10 min at 4.degree. C. The pellet
was washed 2.times. and re-suspended in plating medium (Williams E
Media, 1.times. Penstrep, 1.times. L-glutamine, 5% FBS). Cells were
plated at 300,000 cells per well in 24-well collagen-coated tissue
culture plates. After the cells were allowed to attach for 6-18
hours, the plating medium was replaced with medium without FBS.
Reagents used are shown in Table 6.
TABLE-US-00006 TABLE 6 Reagents for isolation of primary
hepatocytes. Material Catalog Number Liver Perfusion Media Gibco
[17701-038] HBSS (1x) Gibco [14175-079] Hepatocyte Wash Media Gibco
[17704-024] Williams E media Gibco [A12176-01] Penstrep (100x)
Gibco [15140163] L-glutamine (200 mM) Gibco [25030081] FBS
supplement Gibco [A13450] HEPES Gibco [15630080] Collagen Gibco
[A1048301] Acetic acid Sigma [A6283] Liberase TM Roche
[TM05401119001] Primary Hepatocyte Thawing and Gibco [CM3000]
Plating Supplements Primary Hepatocyte Maintenance Gibco [CM4000]
Supplements Percoll GE [17-0891-01]
[0328] Lipid nanoparticles (LNPs) (containing Cas9 mRNA plus a
human TTR gRNA (versions 1 and 2, each targeting human TTR exon 2))
were added to the hepatocytes 24 hours post-isolation. Briefly, for
each well, LNPs were added at a concentration of 500 ng in 500
.mu.L of hepatocyte maintenance medium containing 3% mouse serum
and were incubated for 5 minutes at 37.degree. C. Plated cells were
washed and 500 .mu.L of incubated LNPs in medium was added to each
well. After 48 hours, DNA lysates were prepared from the cells, and
next-generation sequencing was performed for each guide RNA
tested.
[0329] As shown in FIG. 10, editing in the humanized TTR gene was
seen with both guide RNAs in primary hepatocytes isolated from
humanized TTR mice. Human TTR guide RNA 1 had an editing efficiency
of 20.4%, and human TTR guide RNA 2 had an editing efficiency of
7.53%. Similar results were observed for a human TTR guide RNA
targeting exon 3 (editing efficiency of 17.37%; data not shown).
Editing efficiency refers to the total number of insertions or
deletions observed over the total number of sequences read in the
PCR reaction from a pool of lysed cells as determined by next
generation sequencing.
[0330] Next, human TTR guide RNAs 1 and 2 were tested in vivo in
humanized TTR mice. F0 generation humanized TTR mice
(Ttr.sup.hI/hI) from clone numbers 7576A-A5 and 7576C-G7 were used.
Three animal groups were targeted with fresh LNPs as shown in Table
7.
TABLE-US-00007 TABLE 7 Animal Groups for LNP Study. Group
Description 1 Ttr.sup.hI/hI 1M 1F A-A5 and 2M 1F C-G7: LNP(gRNA1)@
2 mg/kg 2 Ttr.sup.hI/hI 1M 1F A-A5 and 2M 1F C-G7: LNP(gRNA2) @ 2
mg/kg 3 Ttr.sup.hI/hI 1M A-A5 and 2M C-G7: Tris-saline sucrose
[0331] LNPs were formulated with human TTR guide RNAs and mRNA
encoding Cas9 with one NLS and no HA tag. The LNPs had a
nitrogen-to-phosphate (N/P) ratio of 4.5 and contained cationic
lipid, cholesterol, DSPC, and PEG2k-DMG in a 45:44:9:2 molar ratio.
The cationic lipid used in the in vitro and in vivo LNP experiments
described herein was
(9Z,12Z)-3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3-(diethylamino)propoxy-
)carbonyl)oxy)methyl)propyl octadeca-9,12-dienoate, also called
3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3-(diethylamino)propoxy)carbonyl-
)oxy)methyl)propyl (9Z,12Z)-octadeca-9,12-dienoate. The (guide
RNA):(Cas9 mRNA) ratio in each was 1:1 by weight. Additional LNP
formulation details are provided in Table 8.
TABLE-US-00008 TABLE 8 Human TTR LNP Formulations. Human TTR RNA
Z-avg Number Ave Guide RNA (mg/mL) Encapsulation (nm) PDI (nm) 1
0.46 96% 95.22 0.053 77.51 2 0.61 97% 94.91 0.016 76.77
[0332] Mice were weighed prior to injection, and LNPs (containing
Cas9 mRNA plus a human TTR gRNA) were prepared to dose at 2 mg/kg
by diluting in Tris-saline sucrose so that delivery volume was 200
.mu.l per mouse. Delivery was intravenous through tail vein
injection. After 8-14 days, mice were euthanized, and blood serum
was harvested along with liver tissues. The tissues were processed
into DNA lysates that were then analyzed by next-generation
sequencing (NGS).
[0333] Serum chemistry analysis for the liver enzymes ALT, AST,
triglycerides, total cholesterol, HDL, LDL, non-esterified fatty
acids (NEFA), and albumin showed no statistical difference between
various treatment groups. See FIGS. 11A-11H. Similar results were
observed for a human TTR guide RNA targeting exon 3 (data not
shown).
[0334] NGS showed significant editing in liver for human TTR gRNA 1
(average 42.8%) and human TTR gRNA 2 (average 36.0%). See FIG. 12.
Editing efficiency refers to the total number of insertions or
deletions observed over the total number of sequences read in the
PCR reaction from a pool of lysed cells. Minimal or no
statistically significant levels of gene editing were observed in
other tissues (data not shown).
[0335] Next, human TTR guide RNA 1 was tested in vivo in F2
generation, homozygous humanized TTR mice from clone number
7576B-F10. Animals were weighed pre-dose for dosing calculations
and then monitored 24 hours post-dose for welfare. The animals were
dosed intravenously at 1 mg/kg, 0.3 mg/kg, and 0.1 mg/kg with LNPs
formulated with human TTR guide RNA 1 and mRNA encoding Cas9 as
described above. Tris-saline sucrose was used as a control. Three
mice were tested per group. At necropsy (8 days post-dose), liver
and blood (for serum) was collected for analysis. The percent
editing of the humanized TTR locus observed in the liver was 50.7%
at a dose of 1 mg/kg of the LNP formulated with human TTR guide RNA
1 and mRNA encoding Cas9, 13.0% at a dose of 0.3 mg/kg, and 2.3% at
a dose of 0.1 mg/kg, with less than 0.1% editing observed in the
control mice. Human TTR levels were then measured in liver lysate
and serum from the dosed mice. Livers were lysed in RIPA and
protease inhibitors at 100 mg/mL. A human TTR ELISA kit (Aviva
Systems Biology; Cat No.: OKIA00081; 1:100 dilution for liver
lysates; 1:5000 or 1:10000 dilution for serum) was used to assess
human TTR levels. As shown in FIG. 14, a level of more than 1000
ng/mL human TTR was measured in liver lysates from control animals,
and these levels were decreased by more than 50% in animals dosed
at 1 mg/kg of the LNP formulated with human TTR guide RNA 1 and
mRNA encoding Cas9. As shown in FIGS. 15A and 15B, human TTR was
measured at levels of 80,000 ng/mL or more in serum from control
animals, and human TTR levels were reduced by 66% in animals dosed
at 1 mg/kg of the LNP formulated with human TTR guide RNA 1 and
mRNA encoding Cas9.
[0336] Next, three different human TTR guide RNAs (human TTR guide
RNAs 3, 4, and 5) were tested in vivo in homozygous humanized TTR
mice. The LNP formulations contained Cas9 mRNA in a 1:2 ratio by
weight to the guide RNA. The LNPs contained a cationic lipid
(9Z,12Z)-3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3-(diethylamino)propoxy-
)carbonyl)oxy)methyl)propyl octadeca-9,12-dienoate, also called
3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3-(diethylamino)propoxy)carbonyl-
)oxy)methyl)propyl (9Z,12Z)-octadeca-9,12-dienoate), cholesterol,
DSPC, and PEG2k-DMG in a 50:38:9:3 molar ratio, respectively, and
had an N:P ratio of 6.
[0337] First, editing at the humanized TTR locus was assessed. Mice
were weighed prior to injection, and LNPs (containing Cas9 mRNA
plus a human TTR gRNA) were prepared at doses of 1 mg/kg, 0.3
mg/kg, and 0.1 mg/kg (n=5 mice per group). Delivery was intravenous
through tail vein injection. As described above, mice were later
euthanized, and blood serum was harvested along with liver tissues.
The tissues were processed into DNA lysates that were then analyzed
by next-generation sequencing (NGS). NGS showed significant editing
in liver for each human TTR gRNA at all tested doses in a
dose-dependent manner. See FIG. 19. Liver editing results were
determined using primers designed to amplify the region of interest
for NGS analysis.
[0338] Second, serum TTR levels were assessed. Mice were weighed
pre-dose for dosing calculations. The mice were dosed intravenously
at 1 mg/kg, 0.3 mg/kg, and 0.1 mg/kg (n=5 mice per group) with LNPs
formulated with human TTR guide RNA 3, 4, or 5 and mRNA encoding
Cas9 as described above. The LNP formulations contained Cas9 mRNA
in a 1:2 ratio by weight to the guide RNA. The LNPs contained a
cationic lipid
(9Z,12Z)-3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3-(diethylamino)propoxy-
)carbonyl)oxy)methyl)propyl octadeca-9,12-dienoate, also called
3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3-(diethylamino)propoxy)carbonyl-
)oxy)methyl)propyl (9Z,12Z)-octadeca-9,12-dienoate), cholesterol,
DSPC, and PEG2k-DMG in a 50:38:9:3 molar ratio, respectively, and
had an N:P ratio of 6. Tris-saline sucrose was used as a control.
As described above, blood (for serum) was later collected for
analysis. Human TTR levels were then measured in serum from the
dosed mice. Human serum TTR levels were assessed as described
above. As shown in FIG. 20, human TTR levels were significantly
reduced in mice dosed with each guide RNA at all doses in a
dose-dependent manner.
Example 4. Generation of Mice Comprising a Humanized TTR Locus
Encoding a Chimeric Mouse/Human TTR Protein with a Mouse Signal
Sequence
[0339] We hypothesized that the mouse signal sequence of TTR may
enhance hTTR secretion to more robust levels. Hydrodynamic delivery
(HDD) plasmids were constructed containing a cDNA insert for mouse
Ttr (mTtr) signal sequence+hTTR ("m/hTTR"). HDD constructs using
the pRG977 vector with the cDNA inserts listed in Table 9 were
injected via HDD into male C57/BL6 mice, each 59 days old. ELISAs
were performed on submandibular blood on day 4 post-HDD. F1H4
plasma and human serum were included in the ELISAs as negative and
positive controls, respectively.
TABLE-US-00009 TABLE 9 Summary of HDD Experiment. HDD Construct
Number Mice Weight; g (SD) cDNA insert Nanoluc 8 21.5 (2.23)
Nanoluc Control Protein 7 22.8 (1.40) Control protein hTTR 8 23.4
(0.74) hTTR signal sequence + hTTR m/hTTR 8 22.9 (0.66) mTTR signal
sequence + hTTR
[0340] The results are shown in FIG. 13. HDD into wild type C57/BL6
mice revealed that utilizing the mouse signal sequence of TTR did
in fact increase hTTR secretion into plasma when compared to human
signal sequence TTR+hTTR ("hTTR"). This demonstrated that C57/BL6
mice can be used to predict TTR constructs that will result in
robust hTTR secretion.
[0341] Based on these results, a second humanized TTR allele was
generated comprising a deletion of the region of the mouse Ttr
locus from the start of the second exon to the stop codon and its
replacement with the orthologous part of the human TTR gene but
also including the 3' UTR of the human TTR gene. A large targeting
vector comprising a 5' homology arm including 36 kb of sequence
upstream from the second exon of the mouse Ttr gene and 34.5 kb of
the sequence downstream of the mouse Ttr stop codon was generated
to replace the approximately 7.3 kb region from the start of the
second exon in the mouse Ttr gene to the mouse Ttr stop codon with
the approximately 6.1 kb orthologous human TTR sequence from the
start of the second exon in the human TTR gene to the end of the
last human TTR exon (exon 4, including the human 3' UTR) and a
self-deleting neomycin selection cassette (SDC Neo) flanked by loxP
sites. See FIG. 4. To generate the humanized allele, CRISPR/Cas9
components targeting the mouse Ttr locus were introduced into F1H4
mouse embryonic stem cells together with the large targeting
vector. Loss-of-allele assays, gain-of-allele assays, and retention
assays using primers and probes set forth in FIG. 5B and Table 3
were performed to confirm the humanization of the mouse Ttr allele.
Versions with the SDC Neo cassette and after excision of the SDC
Neo cassette are shown in FIG. 4. F0 mice were then generated using
the VELOCIMOUSE.RTM. method.
[0342] A comparison of the human and mouse transthyretin precursor
protein sequences is shown in FIG. 1A, a comparison of the human
and mouse transthyretin coding sequences is shown in FIG. 1B, and a
schematic showing the wild type mouse Ttr locus and the final
humanized mouse Ttr locus (humanized TTR version 2 with the SDC Neo
cassette deleted) is shown in FIG. 2. Sequences for the expected
humanized mouse Ttr locus with the SDC Neo cassette and without the
SDC Neo cassette are set forth in SEQ ID NOS: 16 and 17,
respectively. MAID7655 refers to the humanized TTR locus (keeping
mouse signal sequence) with the neomycin selection cassette.
MAID7656 refers to the humanized TTR locus (keeping mouse signal
sequence) with the neomycin selection cassette removed. The
expected transthyretin precursor protein encoded by the humanized
mouse Ttr locus (a chimeric mouse/human TTR protein) is set forth
in SEQ ID NO: 2.
[0343] A human TTR ELISA kit (Aviva Systems Biology; Cat No.:
OKIA00081; 1:2000 dilution) was then used to assess blood plasma
human TTR levels in different versions of humanized TTR mice with
ages between 1-3 months. The mice included a wild type control
mouse and mice with various combinations of wild type, MAID7577,
MAID7655, and MAID7656 alleles. MAID7577 refers to the humanized
TTR locus with the neomycin selection cassette removed. MAID7655
refers to the humanized TTR locus (keeping mouse signal sequence)
with the neomycin selection cassette. MAID7656 refers to the
humanized TTR locus (keeping mouse signal sequence) with the
neomycin selection cassette removed. The data are summarized in
FIG. 16 and Table 10. As shown in FIG. 16, the hTTR.sup.7577/7577
mice (clone B-F10) had .about.55 .mu.g/mL circulating hTTR, which
is significant but lower than physiological levels in wild type
mice or human serum. Humanized TTR mice with the mouse TTR signal
sequence (hTTR.sup.7655/7655, hTTR.sup.7655/7656, and
hTTR.sup.7656/7656) did not have increased secreted TTR levels when
compared to humanized TTR mice with the human TTR signal sequence
(hTTR.sup.7577/7577).
TABLE-US-00010 TABLE 10 Plasma TTR Levels. Strain Description hTTR,
.mu.g/mL (SD) mTTR, .mu.g/mL (SD) F1H4 Wild type control mouse N.D.
920 (79.7) V1.0 hTTR.sup.7577/7577 Humanized TTR locus, cassette
deleted 54.41 (14.36) N.D. V2.0 hTTR.sup.7655/7655 Humanized TTR
locus with mouse TTR 37.42 (2.461) N.D. signal sequence, cassette
deleted V2.0 hTTR.sup.7656/7656 Humanized TTR locus with mouse TTR
34.88 (n.a.) N.D. signal sequence, cassette deleted V2.0
hTTR.sup.7655/7656 Humanized TTR locus with mouse TTR 33.86 (2.827)
N.D. signal sequence, cassette deleted in one allele but present in
other V2.0 hTTR.sup.7656/WT Heterozygous humanized TTR locus with
18.36 (1.233) 57.50 (4.264) mouse TTR signal sequence, cassette
deleted Human serum Human serum control 234.5 (n.a.) N.D.
[0344] A human TTR ELISA kit (Aviva Systems Biology; Cat No.:
OKIA00081; 1:2000 dilution) was then used to assess blood plasma
human TTR levels in different versions of humanized TTR mice with
ages between 2-3 months in another experiment. The mice included a
wild type control mouse (labeled F1H4) and mice homozygous for the
MAID7577 or MAID7656 alleles. MAID7577 refers to the humanized TTR
locus with the neomycin selection cassette removed. MAID7656 refers
to the humanized TTR locus (keeping mouse signal sequence) with the
neomycin selection cassette removed. The data are summarized in
FIG. 18 and Table 11. As shown in FIG. 18, the hTTR.sup.7577/7577
mice (hTTR v1) had .about.55 .mu.g/mL circulating hTTR, which is
significant but lower than physiological levels in wild type mice
or human serum. Humanized TTR mice with the mouse TTR signal
sequence (hTTR.sup.7656/7656; hTTRv2) had increased secreted TTR
levels when compared to humanized TTR mice with the human TTR
signal sequence (hTTR.sup.7577/7577).
TABLE-US-00011 TABLE 11 Plasma hTTR Levels. TTR Strain hTTR,
.mu.g/mL (SD) hTTR v2 88.45 (1.465) F1H4 Not detectable
Sequence CWU 1
1
941147PRTHomo sapiens 1Met Ala Ser His Arg Leu Leu Leu Leu Cys Leu
Ala Gly Leu Val Phe1 5 10 15Val Ser Glu Ala Gly Pro Thr Gly Thr Gly
Glu Ser Lys Cys Pro Leu 20 25 30Met Val Lys Val Leu Asp Ala Val Arg
Gly Ser Pro Ala Ile Asn Val 35 40 45Ala Val His Val Phe Arg Lys Ala
Ala Asp Asp Thr Trp Glu Pro Phe 50 55 60Ala Ser Gly Lys Thr Ser Glu
Ser Gly Glu Leu His Gly Leu Thr Thr65 70 75 80Glu Glu Glu Phe Val
Glu Gly Ile Tyr Lys Val Glu Ile Asp Thr Lys 85 90 95Ser Tyr Trp Lys
Ala Leu Gly Ile Ser Pro Phe His Glu His Ala Glu 100 105 110Val Val
Phe Thr Ala Asn Asp Ser Gly Pro Arg Arg Tyr Thr Ile Ala 115 120
125Ala Leu Leu Ser Pro Tyr Ser Tyr Ser Thr Thr Ala Val Val Thr Asn
130 135 140Pro Lys Glu1452147PRTArtificial SequenceSynthetic 2Met
Ala Ser Leu Arg Leu Phe Leu Leu Cys Leu Ala Gly Leu Val Phe1 5 10
15Val Ser Glu Ala Gly Pro Ala Gly Thr Gly Glu Ser Lys Cys Pro Leu
20 25 30Met Val Lys Val Leu Asp Ala Val Arg Gly Ser Pro Ala Ile Asn
Val 35 40 45Ala Val His Val Phe Arg Lys Ala Ala Asp Asp Thr Trp Glu
Pro Phe 50 55 60Ala Ser Gly Lys Thr Ser Glu Ser Gly Glu Leu His Gly
Leu Thr Thr65 70 75 80Glu Glu Glu Phe Val Glu Gly Ile Tyr Lys Val
Glu Ile Asp Thr Lys 85 90 95Ser Tyr Trp Lys Ala Leu Gly Ile Ser Pro
Phe His Glu His Ala Glu 100 105 110Val Val Phe Thr Ala Asn Asp Ser
Gly Pro Arg Arg Tyr Thr Ile Ala 115 120 125Ala Leu Leu Ser Pro Tyr
Ser Tyr Ser Thr Thr Ala Val Val Thr Asn 130 135 140Pro Lys
Glu14537258DNAHomo sapiens 3gttgactaag tcaataatca gaatcagcag
gtttgcagtc agattggcag ggataagcag 60cctagctcag gagaagtgag tataaaagcc
ccaggctggg agcagccatc acagaagtcc 120actcattctt ggcaggatgg
cttctcatcg tctgctcctc ctctgccttg ctggactggt 180atttgtgtct
gaggctggcc ctacggtgag tgtttctgtg acatcccatt cctacattta
240agattcacgc taaatgaagt agaagtgact ccttccagct ttgccaacca
gcttttatta 300ctagggcaag ggtacccagc atctattttt aatataatta
attcaaactt caaaaagaat 360gaagttccac tgagcttact gagctgggac
ttgaactctg agcattctac ctcattgctt 420tggtgcatta ggtttgtaat
atctggtacc tctgtttcct cagatagatg atagaaataa 480agatatgata
ttaaggaagc tgttaatact gaattttcag aaaagtatcc ctccataaaa
540tgtatttggg ggacaaactg caggagatta tattctggcc ctatagttat
tcaaaacgta 600tttattgatt aatctttaaa aggcttagtg aacaatattc
tagtcagata tctaattctt 660aaatcctcta gaagaattaa ctaatactat
aaaatgggtc tggatgtagt tctgacatta 720ttttataaca actggtaaga
gggagtgact atagcaacaa ctaaaatgat ctcaggaaaa 780cctgtttggc
cctatgtatg gtacattaca tcttttcagt aattccactc aaatggagac
840ttttaacaaa gcaactgttc tcaggggacc tattttctcc cttaaaattc
attatacaca 900tccctggttg atagcagtgt gtctggaggc agaaaccatt
cttgctttgg aaacaattac 960gtctgtgtta tactgagtag ggaagctcat
taattgtcga cacttacgtt cctgataatg 1020ggatcagtgt gtaattcttg
tttcgctcca gatttctaat accacaaaga ataaatcctt 1080tcactctgat
caattttgtt aacttctcac gtgtcttctc tacacccagg gcaccggtga
1140atccaagtgt cctctgatgg tcaaagttct agatgctgtc cgaggcagtc
ctgccatcaa 1200tgtggccgtg catgtgttca gaaaggctgc tgatgacacc
tgggagccat ttgcctctgg 1260gtaagttgcc aaagaaccct cccacaggac
ttggttttat cttcccgttt gcccctcact 1320tggtagagag aggctcacat
catctgctaa agaatttaca agtagattga aaaacgtagg 1380cagaggtcaa
gtatgccctc tgaaggatgc cctctttttg ttttgcttag ctaggaagtg
1440accaggaacc tgagcatcat ttaggggcag acagtagaga aaagaaggaa
tcagaactcc 1500tctcctctag ctgtggtttg caaccctttt gggtcacaga
acactttatg taggtgatga 1560aaagtaaaca ttctatgccc agaaaaaatg
cacagataca cacacataca aaatcatata 1620tgtgatttta ggagtttcac
agattccctg gtgtccctgg gtaacaccaa agctaagtgt 1680ccttgtctta
gaattttagg aaaaggtata atgtgtatta acccattaac aaaaggaaag
1740gaattcagaa atattattaa ccaggcatct gtctgtagtt aatatggatc
acccaaaacc 1800caaggctttt gcctaatgaa cactttgggg cacctactgt
gtgcaaggct gggggctgtc 1860aagctcagtt aaaaaaaaaa agatagaaga
gatggatcca tgaggcaaag tacagcccca 1920ggctaatccc acgatcaccc
gacttcatgt ccaagagtgg cttctcacct tcattagcca 1980gttcacaatt
ttcatggagt ttttctacct gcactagcaa aaacttcaag gaaaatacat
2040attaataaat ctaagcaaag tgaccagaag acagagcaat caggagaccc
tttgcatcca 2100gcagaagagg aactgctaag tatttacatc tccacagaga
agaatttctg ttgggtttta 2160attgaacccc aagaaccaca tgattcttca
accattattg ggaagatcat tttcttaggt 2220ctggttttaa ctggcttttt
atttgggaat tcatttatgt ttatataaaa tgccaagcat 2280aacatgaaaa
gtggttacag gactattcta agggagagac agaatggaca ccaaaaatat
2340tccaatgttc ttgtgaatct tttccttgca ccaggacaaa aaaaaaaaga
agtgaaaaga 2400agaaaggagg aggggcataa tcagagtcag taaagacaac
tgctattttt atctatcgta 2460gctgttgcag tcaaatggga agcaatttcc
aacattcaac tatggagctg gtacttacat 2520ggaaatagaa gttgcctagt
gtttgttgct ggcaaagagt tatcagagag gttaaatata 2580taaaagggaa
aagagtcaga tacaggttct tcttcctact ttaggttttc cactgtgtgt
2640gcaaatgata ctccctggtg gtgtgcagat gcctcaaagc tatcctcaca
ccacaaggga 2700gaggagcgag atcctgctgt cctggagaag tgcagagtta
gaacagctgt ggccacttgc 2760atccaatcat caatcttgaa tcacagggac
tctttcttaa gtaaacatta tacctggccg 2820ggcacggtgg ctcacgcctg
taatcccagc actttgggat gccaaagtgg gcatatcatc 2880tgaggtcagg
agttcaagac cagcctggcc aacatggcaa aactccgtct ttatgaaaaa
2940tacaaaaatt agccaggcat ggtggcaggc gcctgtaatc ccagctaatt
gggaggctga 3000ggctggagaa tcccttgaat ctaggaggca gaggttgcag
tgagctgaga tcgtgccatt 3060gcactccagc ctgggtgaca agagtaaaac
tctgtctcaa aaaaaaaaaa ttatacctac 3120attctcttct tatcagagaa
aaaaatctac agtgagcttt tcaaaaagtt tttacaaact 3180ttttgccatt
taatttcagt taggagtttt ccctacttct gacttagttg aggggaaatg
3240ttcataacat gtttataaca tgtttatgtg tgttagttgg tgggggtgta
ttactttgcc 3300atgccatttg tttcctccat gcgtaactta atccagactt
tcacacctta taggaaaacc 3360agtgagtctg gagagctgca tgggctcaca
actgaggagg aatttgtaga agggatatac 3420aaagtggaaa tagacaccaa
atcttactgg aaggcacttg gcatctcccc attccatgag 3480catgcagagg
tgagtataca gaccttcgag ggttgttttg gttttggttt ttgcttttgg
3540cattccagga aatgcacagt tttactcagt gtaccacaga aatgtcctaa
ggaaggtgat 3600gaatgaccaa aggttccctt tcctattata caagaaaaaa
ttcacaacac tctgagaagc 3660aaatttcttt ttgactttga tgaaaatcca
cttagtaaca tgacttgaac ttacatgaaa 3720ctactcatag tctattcatt
ccactttata tgaatattga tgtatctgct gttgaaataa 3780tagtttatga
ggcagccctc cagaccccac gtagagtgta tgtaacaaga gatgcaccat
3840tttatttctc gaaaacccgt aacattcttc attccaaaac acatctggct
tctcggaggt 3900ctggacaagt gattcttggc aacacatacc tatagagaca
ataaaatcaa agtaataatg 3960gcaacacaat agataacatt taccaagcat
acaccatgtg gcagacacaa ttataagtgt 4020tttccatatt taacctactt
aatcctcagg aataagccac tgaggtcagt cctattatta 4080tccccatctt
atagatgaag aaaatgaggc accaggaagt caaataactt gtcaaaggtc
4140acaagactag gaaatacaca agtagaaatg tttacaatta aggcccaggc
tgggtttgcc 4200ctcagttctg ctatgcctcg cattatgccc caggaaactt
tttcccttgt gaaagccaag 4260cttaaaaaaa gaaaagccac atttgtaacg
tgctctgttc ccctgcctat ggtgaggatc 4320ttcaaacagt tatacatgga
cccagtcccc ctgccttctc cttaatttct taagtcattt 4380gaaacagatg
gctgtcatgg aaatagaatc cagacatgtt ggtcagagtt aaagatcaac
4440taattccatc aaaaatagct cggcatgaaa gggaactatt ctctggctta
gtcatggatg 4500agactttcaa ttgctataaa gtggttcctt tattagacaa
tgttaccagg gaaacaacag 4560gggtttgttt gacttctggg gcccacaagt
caacaagaga gccccatcta ccaaggagca 4620tgtccctgac tacccctcag
ccagcagcaa gacatggacc ccagtcaggg caggagcagg 4680gtttcggcgg
cgcccagcac aagacattgc ccctagagtc tcagccccta ccctcgagta
4740atagatctgc ctacctgaga ctgttgtttg cccaagagct gggtctcagc
ctgatgggaa 4800ccatataaaa aggttcactg acatactgcc cacatgttgt
tctctttcat tagatcttag 4860cttccttgtc tgctcttcat tcttgcagta
ttcattcaac aaacattaaa aaaaaaaaaa 4920agcattctat gtgtggaaca
ctctgctaga tgctgtggat ttagaaatga aaatacatcc 4980cgacccttgg
aatggaaggg aaaggactga agtaagacag attaagcagg accgtcagcc
5040cagcttgaag cccagataaa tacggagaac aagagagagc gagtagtgag
agatgagtcc 5100caatgcctca ctttggtgac gggtgcgtgg tgggcttcat
gcagcttctt ctgataaatg 5160cctccttcag aactggtcaa ctctaccttg
gccagtgacc caggtggtca tagtagattt 5220accaagggaa aatggaaact
tttattagga gctcttaggc ctcttcactt catggatttt 5280tttttccttt
ttttttgaga tggagttttg ccctgtcacc caggctggaa tgcagtggtg
5340caatctcagc tcactgcaac ctccgcctcc caggttcaag caattctcct
gcctcagcct 5400cccgagtagc tgggactaca ggtgtgcgcc accacaccag
gctaattttt gtattttttg 5460taaagacagg ttttcaccac gttggccagg
ctggtctgaa ctccagacct caggtgattc 5520acctgtctca gcctcccaaa
gtgctgggat tacaggtgtg agccaccgtg cccggctact 5580tcatggattt
ttgattacag attatgcctc ttacaatttt taagaagaat caagtgggct
5640gaaggtcaat gtcaccataa gacaaaagac atttttatta gttgattcta
gggaattggc 5700cttaagggga gccctttctt cctaagagat tcttaggtga
ttctcacttc ctcttgcccc 5760agtattattt ttgtttttgg tatggctcac
tcagatcctt ttttcctcct atccctaagt 5820aatccgggtt tctttttccc
atatttagaa caaaatgtat ttatgcagag tgtgtccaaa 5880cctcaaccca
aggcctgtat acaaaataaa tcaaattaaa cacatcttta ctgtcttcta
5940cctctttcct gacctcaata tatcccaact tgcctcactc tgagaaccaa
ggctgtccca 6000gcacctgagt cgcagatatt ctactgattt gacagaactg
tgtgactatc tggaacagca 6060ttttgatcca caatttgccc agttacaaag
cttaaatgag ctctagtgca tgcatatata 6120tttcaaaatt ccaccatgat
cttccacact ctgtattgta aatagagccc tgtaatgctt 6180ttacttcgta
tttcattgct tgttatacat aaaaatatac ttttcttctt catgttagaa
6240aatgcaaaga ataggagggt gggggaatct ctgggcttgg agacaggaga
cttgccttcc 6300tactatggtt ccatcagaat gtagactggg acaatacaat
aattcaagtc tggtttgctc 6360atctgtaaat tgggaagaat gtttccagct
ccagaatgct aaatctctaa gtctgtggtt 6420ggcagccact attgcagcag
ctcttcaatg actcaatgca gttttgcatt ctccctacct 6480tttttttcta
aaaccaataa aatagataca gcctttaggc tttctgggat ttcccttagt
6540caagctaggg tcatcctgac tttcggcgtg aatttgcaaa acaagacctg
actctgtact 6600cctgctctaa ggactgtgca tggttccaaa ggcttagctt
gccagcatat ttgagctttt 6660tccttctgtt caaactgttc caaaatataa
aagaataaaa ttaattaagt tggcactgga 6720cttccggtgg tcagtcatgt
gtgtcatctg tcacgttttt cgggctctgg tggaaatgga 6780tctgtctgtc
ttctctcata ggtggtattc acagccaacg actccggccc ccgccgctac
6840accattgccg ccctgctgag cccctactcc tattccacca cggctgtcgt
caccaatccc 6900aaggaatgag ggacttctcc tccagtggac ctgaaggacg
agggatggga tttcatgtaa 6960ccaagagtat tccattttta ctaaagcagt
gttttcacct catatgctat gttagaagtc 7020caggcagaga caataaaaca
ttcctgtgaa aggcactttt cattccactt taacttgatt 7080ttttaaattc
ccttattgtc ccttccaaaa aaaagagaat caaaatttta caaagaatca
7140aaggaattct agaaagtatc tgggcagaac gctaggagag atccaaattt
ccattgtctt 7200gcaagcaaag cacgtattaa atatgatctg cagccattaa
aaagacacat tctgtaaa 72584938DNAHomo sapiens 4gttgactaag tcaataatca
gaatcagcag gtttgcagtc agattggcag ggataagcag 60cctagctcag gagaagtgag
tataaaagcc ccaggctggg agcagccatc acagaagtcc 120actcattctt
ggcaggatgg cttctcatcg tctgctcctc ctctgccttg ctggactggt
180atttgtgtct gaggctggcc ctacgggcac cggtgaatcc aagtgtcctc
tgatggtcaa 240agttctagat gctgtccgag gcagtcctgc catcaatgtg
gccgtgcatg tgttcagaaa 300ggctgctgat gacacctggg agccatttgc
ctctgggaaa accagtgagt ctggagagct 360gcatgggctc acaactgagg
aggaatttgt agaagggata tacaaagtgg aaatagacac 420caaatcttac
tggaaggcac ttggcatctc cccattccat gagcatgcag aggtggtatt
480cacagccaac gactccggcc cccgccgcta caccattgcc gccctgctga
gcccctactc 540ctattccacc acggctgtcg tcaccaatcc caaggaatga
gggacttctc ctccagtgga 600cctgaaggac gagggatggg atttcatgta
accaagagta ttccattttt actaaagcag 660tgttttcacc tcatatgcta
tgttagaagt ccaggcagag acaataaaac attcctgtga 720aaggcacttt
tcattccact ttaacttgat tttttaaatt cccttattgt cccttccaaa
780aaaaagagaa tcaaaatttt acaaagaatc aaaggaattc tagaaagtat
ctgggcagaa 840cgctaggaga gatccaaatt tccattgtct tgcaagcaaa
gcacgtatta aatatgatct 900gcagccatta aaaagacaca ttctgtaaaa aaaaaaaa
93859077DNAMus musculus 5ctaatctccc taggcaaggt tcatatttgt
gtaggttact tattctcctt ttgttgacta 60agtcaataat cagaatcagc aggtttggag
tcagcttggc agggatcagc agcctgggtt 120ggaaggaggg ggtataaaag
ccccttcacc aggagaagcc gtcacacaga tccacaagct 180cctgacagga
tggcttccct tcgactcttc ctcctttgcc tcgctggact ggtatttgtg
240tctgaagctg gccccgcggt gagtgatcct gtgagcgatc cagacatggc
agttagacct 300tagataaaga agaagtgcct tcttccagat gtgagaacta
gagtactcag actctatatt 360taccattaga ctccaaagag aagagctgga
gtgcctctgg ctcttccttc tattgcttta 420gcgcattggg tctgtagtgc
tcagtctctg gtgtccttag ataataaaga tatgagatta 480acatagaaat
aaagatataa aagggctgga tgtatagttt agtggtccag tgtatgccta
540gtatgtgaaa agccttctgt tcaacctcta gcaatagaaa aacaagatat
attctcggtg 600gggctgttaa tattgaattc tcataaaatc tttaatatat
ttagtatgcc tattatgttg 660ttatatttta gttctttagc taatcaaaat
gcattattga tctttctttg tctttttttg 720gccaacactc tattccagtc
tttgaaaaag tcctttaaaa gagttaatca gtataattaa 780atgagtcagg
aagtatgtga gggttatttt acaaccagag ggaattacta tagcaacagc
840tgattagaat gatctcaaga aaaagcccat tctgtctttt tgcaccatgc
acctttcagt 900ggctccattc agatggagag gcaaacagag caatggctct
cagagggcct attttccctt 960tgaacattca ttatccatat ccctggtgca
cagcagtgca tctgggggca gaaactgttc 1020ttgctttgga aacaatgctg
tctatgtcat actggataaa gaagctcatt aattgtcaac 1080acttatgtta
tcataatggg atcagcatgt acttttggtt ttgttccaga gtctatcacc
1140ggaaagaaca agccggttta ctctgaccca tttcactgac atttctcttg
tctcctctgt 1200gcccagggtg ctggagaatc caaatgtcct ctgatggtca
aagtcctgga tgctgtccga 1260ggcagccctg ctgtagacgt ggctgtaaaa
gtgttcaaaa agacctctga gggatcctgg 1320gagccctttg cctctgggta
agcttgtaga aagcccacca tgggaccggt tccaggttcc 1380catttgctct
tattcgtgtt agattcagac acacacaact taccagctag agggctcaga
1440gagagggctc aggggcgaag ggcacgtatt gctcttgtaa gagacacagg
tttaattcct 1500agcaccagaa tggcagctca taaccatctg aaactcacag
tcttaggaga tctgggtatc 1560tgacattctc ttctacccac catgtgtgtg
gtgcacaaat tcacatgcag gcatcaaatc 1620ttataaacaa caacaaaaaa
ccaacaaacc tggtagcaaa agaagattag aaggttaaac 1680atatgagccg
agagcttttg ttttgttttg ttttgttttg ttttgtttac atttcaaatg
1740ttatcccctt tctcggtccc cctccccaaa ccctctaccc cattctctcc
tccccttctt 1800ctatgagggt gttccccacc aacccactcc caccttcctg
ctctcgaatt cccctatact 1860gggacatcaa gccttcacag aatcaagggc
ctctcctccc attgatgccc gacaatgtca 1920tcctctgcta cctatgtggc
tggagccatg ggtcccttca tgtatcctcc ttggttggtg 1980gtttagtctc
tgggaggtct gggggatctg gttgattgat attattgttc ttcctatgag
2040attgcaaacc ccttcagctc cttcggtcct ttaactcctc cactggggac
cccgagctca 2100gtccaatggt tggctgtgag catccaccag cagaggcctt
tttttttttt tttaacaaag 2160ctgctttatt atgttgctta gagcatgacc
aggaaccaga gcacagtcca agactgaagg 2220gaggaaaagg gggggagtca
ataaccccac tgtttcatag tggtttgcaa cccttttata 2280tcacagccca
ctttaggcaa ataatgaaaa ttatagtctc cagggacaga gaagatggtg
2340caggaagtga agtgcctgct cagaaaatgg gggcttgaat gtgagttccc
agactctgtg 2400taagatgccc agcatcgaag tgcatgctta taacaccagc
ctggaggtag aagcttagaa 2460acaggggtac cctgaagttg cttgttcacc
agtgtccctg aatgggtagg tgcatgtttg 2520gtgagagacc ctgtctcaaa
aatcaaggtg taggataatt gaaaatacct agctttgagc 2580ttagatcatg
caaatgtgta cacacactca cacacaccac acacacaaaa aaatgcagag
2640acagagagat acagagagac agagagatac agagacagag acagagagaa
aaggagaaag 2700taaaaaacaa ataatttaaa gacccatggc cacaaagagg
ctcaaagaca agcacgtata 2760aaaccataca catgtaattt taggagtttt
cagattccct ggtacccgtg ggtgatgcac 2820aagctttgaa tcccagtctt
aaaatcttac gaagaacgtg ttcgtgtgtg ctaatttatt 2880gatgagagga
aaggaattga caaagtgccc ttccggagct tcctgcatta cccagactca
2940gggttttttt aaatgtacac tcagaacaga gtagctctgt gcaagggtag
caaccacgaa 3000gcttaataag aaacatatcg tgagagatct gcaaggcaaa
tctaggggct gaccaatctc 3060acagtcaccc actagcatgt caacacaact
tcccacctgt gctagccact tagcaatttt 3120gtgttgttct gttttgtttt
tgtttttaac aaagcaattt caaagagatt tctaattcat 3180ctaaacaaac
aaaccaaaag gaaaacagca aagacgccct gagcacttag cagagcagct
3240atgcagttat gactcctggg tggagacttt atatcaggct tcaactgaat
acctagaacc 3300tactagtgct cttcatcaat ccttgggaag gtcattttct
tttggtgctg ttttgagttt 3360ctatttgtta atgtcttcat aattatacac
gtgttgagca cagcatgcaa agtgattagg 3420ggaatctagt tggagtggaa
tggataccca aatattcaga ctttcttgtg actcttcttt 3480cttgtaccca
catcaaaaaa aaaaaaaatg gagatgagac atggtcagag tcactaaaac
3540cagctgctac ttttaattac gtggggagca gtttctaaca ttgccattat
tgaactgatg 3600ctgcctgggt ggaaatggaa atcacttagt atttcttgtt
ggcaaagaat tactgaatgg 3660attaaatttc caaagggaga agtcagttac
aagtcttttc tttgtttatt aggctttctg 3720ctatgataaa ttacactact
tccagaagtt acccttaggc catgggacac tggactatca 3780ctctgctgtc
acaagagatt acagagttag tcaaggcagc ttgtgacacc ttcagggact
3840gtcataaact tccagcaagt cattaatcct gaatgcaata ctgtgtgtgt
gtgtctatgt 3900gtgtttgtat gtctgtgtgt gtcttatgtc tgtgtctctg
tgtgtgtgtg tgtttgtgtg 3960tgtgtgtgta tgtatgcctg tgtgtgtctt
atgtctgtgt ttgtgtgtct gtgtgtgtct 4020tatgtctgtg tttgtatgtc
tgtgtgtgtc tgtgtgtgtc ttatgtctgt gtctctgtgt 4080gtgtgtgtgt
gtatgtatgt atgtatgtat gtatgtgtat gtgtttgcat ctctctgtgt
4140gtctgcgctt atatatttgt gtatgtgttt atgtgttcgc ctttgtgcgt
tgttggggat 4200tgaatccagg ggaatacaaa tgttaagaaa gaacgttacc
actaagcttc acctgtaggc 4260cttaaagctt ttctttcttt taaaaattgt
aattaattca ttttcagtca ggatctccac 4320acctcgtccc tgctgctcta
gaactcacta tttaaacaca atcgccctca aacctgcagc 4380aaccctcccg
cctctaccct gcgagcacta gaataataac aggtgacccc acacgcctag
4440attaagacct ttaaggtaaa cattttacta tattttagtc tcataagaca
agatgctaca 4500ataaagctgt acataaagtt ccctcgaatt tcttgctatt
ttaactcaaa cataaggatt 4560tcctcctttt tgattcaggt aacagaaaaa
atacacaggt acatacatgt acacacatga 4620acacacacgc atcacaacca
catatgcgca cgcttgtgtg atctatcatt taccatgcca 4680ctgaactctt
ctttccccat aaattcctct ggacttgtgt gccctccagg aagaccgcgg
4740agtctggaga gctgcacggg ctcaccacag atgagaagtt tgtagaagga
gtgtacagag 4800tagaactgga caccaaatcg tactggaaga cacttggcat
ttccccgttc catgaattcg 4860cggatgtaag tggacacacc aagttgtttg
gattttgttt ttagtctcag gaaattccct 4920tcgctcttgc tgtacgatgg
gcatgagtgg aaagtagatt ccacagccag
aatccacagt 4980gctgggaaag caagccttct gaatttttct aaaactcatt
tagcaacatg gcctgaacct 5040gttcacactg cttatggtca gctaactata
tttatgtaaa tattcatttc tctgttgagg 5100aaatgttagt atttgctttt
gaggcaacct ccagatacca tggagggcat gtcatagtca 5160aagagagggc
tccctatggt atttctctaa attctggcat ttcctttatt ccaaagcaca
5220tctagtgtcc ccagaagttt gggtagacaa ttcttggcaa cacagagaat
tacaacatgt 5280tcaaaaccca acagcttaat atctaaatca tcaagcaaac
atcacatggc aaagggattt 5340ctgaatcaaa actgtttcat ccttatgatc
aacctatgga ggtctagcct cgacttacac 5400ccattttacc aataagctaa
gagaagctaa gttcctcatc aaggacacaa ggctagcatg 5460tgtgagcaag
tgacagagtt gccctctatg ttggttagtg tgccttagcc agtgtctcag
5520taagaaatgg agctaaatca aaacccaagg ccaacagcca aaggcacatg
agtaaccttt 5580gcttggcact gggctcagtt tccctggctc ctctcagtcc
tcagttcaca gaggcagctg 5640tcatgcaaat agaatccaag cttgttggtc
agacctggag ataacaaatt ccatcaaaaa 5700tagctcctca tgtgacctag
tttgctgtct gttgctatga tacacaccat gaccgaaaag 5760caaccctggg
gagagaaggg tttatttcat cttacagctt acagttcacc atggaggaaa
5820gccaggtggg aacctggaag tggaaattga agcagagacc agaaaggaat
gctgtttact 5880ggctggctta gctccttttc ttatacagct taggtctatg
tgcccagggg atggtactgc 5940cgagcatagg ctgagcccgc ctacatcaac
cattagtcaa aaaaaggtcc atagacttgc 6000ctacaggcca atctcatgga
ggcaataccc cagtggaggg tccctcttcg caggttactc 6060tagtttgtgt
caagttgaca aaacctaacc acaaagcaca aacagggtct gcccttgtgg
6120cttagccatg gatgacactc tcagatgatg gtgttaccag acaaaccaga
ggggctcacc 6180aagagtctgc cacctaccaa ggtagtactc tactcctcac
tgggcaccaa cacccatatt 6240agctgggcca gtacaggacc cttgctgttt
cctgcatgaa ttgtccatag accctgggtc 6300tcagcctgcc gggagtacct
gtaagtagtc gcctcaaaca cattattcct gttggaagac 6360ttgtctgatt
ctcttttaga actcaatcaa caaacgtttt tattttgttt tggctttttg
6420gagacaagat ctctcatagg ccagcctgac ttgaatgtag ctgaggatga
cctgtgctgc 6480taatcttctc gcctcttcct cccaagtggt aggataatag
gcataagaca ccacagcagt 6540tttactccat accagggctc tgaacccaga
ctttaaacac tctatcaact gattcacatt 6600cccaccccat cattcaacaa
acatttgaaa aataaaaccc ttctgccttg agcactctgc 6660taaatacagc
ctttgagtgc ggagtatttc ctcacaacca gggtccaaga tgaccccatc
6720atacatacca cggaaaatta ggagatgttt ttaggtctct ttgcttgggg
taatttttat 6780gtgtgtgtgt acacagccct gtgcgtgtgt gtgtgtgtgt
gtgtgtgtgt gtacaggcac 6840acacgtgtat gcatgtagag gctacataaa
aaccttaggt gtcattctca ggcactctgt 6900tcaccccttc acacagcccg
aacacacaaa atttgaggca ttagcctgga gctcaccagt 6960taggctagac
tgacttgcca gcagacccca ggctgtctcc atctccccag ctctgggatt
7020acaaactcta tcataccaga catttttata catattctga gcataaaatt
catgtcttca 7080ggctaacaag tcaagagctt aaatgactga gctctcttac
gtggtggatt ttttttaaaa 7140ctacataata tctttttttt ttttttcact
tctggggaag aaacaaatga gcctgagtga 7200caatgcgaca gaaaagaaat
tttgaggagt gtgtgtgtct gtgtgtgtgg tggcacatgc 7260ctctcatcta
atgctagagg ctacagtaga atgctcctga attagtggcc agccaaggcc
7320aagggctagg gttgtaactc agtggcagag ggcttgccta gcattcgcag
gatttgatcc 7380atagcgctat aaataataat aaataaatac aacagtctaa
gatgattctc cctttcattt 7440atctggatgt tatttttgtg ttagttttac
tctgtcatcc aatcattgtt tgccctatat 7500ttggacattt aaaaaaaatc
tttattccaa gtgtgttcaa agctgtatcc aaaacctgtc 7560caccaaatga
gtccaatgac atacatcttc tatattacca tctgttccag atttggctga
7620ctcccggcac ctgggctgtt gctgcaccca tgtctcagat agtctagtga
tttgagaagt 7680gactagtaat tgcaaaatcc agactttgtc cagaaacttc
tatgagctcc aaaactttca 7740tttacatttc tgccagccac aaaccgcttg
tgttgtggag agaaccctgt gatgtcttcc 7800cacagcatct cagccttgtt
tcttccctta aaatattcat cttttcacat tagaacatgc 7860aaagggacag
tgggagcgaa acccctggac tgggacgcac gaagccttcc tttctggtca
7920ggctctcact gtagaaactt aggccggttt cagcatgcag tctgctggag
aatggctcct 7980gccaacattc caggtctgga agtttgtagt ggagttgttg
ataaccactg ttcgccacag 8040gtcttttgtt tgtgggtgtc agtgtttcta
ctctcctgac ttttatctga acccaagaaa 8100gggaacaata gccttcaagc
tctctgtgac tctgatctga ccagggccac ccacactgca 8160gaaggaaact
tgcaaagaga gacctgcaat tctctaagag ctccacacag ctccaaagac
8220ttaggcagca tattttaatc taattattcg tcccccaacc ccaccccaga
ggacagttag 8280acaataaaag gaagattacc agcttagcat cctgtgaaca
ctttgtctgc agctcctacc 8340tctgggctct gttagaacta gctgtctctc
ctctctccta ggtggttttc acagccaacg 8400actctggcca tcgccactac
accatcgcag ccctgctcag cccatactcc tacagcacca 8460cggctgtcgt
cagcaacccc cagaattgag agactcagcc caggaggacc aggatcttgc
8520caaagcagta gcatcccatt tgtaccaaaa cagtgttctt gctctataaa
ccgtgttagc 8580agctcaggaa gatgccgtga agcattctta ttaaaccacc
tgctatttca ttcaaactgt 8640gtttcttttt tatttcctca tttttctccc
ctgctcctaa aacccaaaat cttctaaaga 8700attctagaag gtatgcgatc
aaacttttta aagaaagaaa atactttttg actcatggtt 8760taaaggcatc
ctttccatct tggggaggtc atgggtgctc ctggcaactt gcttgaggaa
8820gataggtcag aaagcagagt ggaccaaccg ttcaatgttt tacaagcaaa
acatacacta 8880agcatggtct gtagctatta aaagcacaca atctgaaggg
ctgtagatgc acagtagtgt 8940tttcccagag catgttcaaa agccctgggt
tcaatcacaa tactgaaaag taggccaaaa 9000aacattctga aaatgaaata
tttgggtttt tttttataac ctttagtgac taaataaaga 9060caaatctaag agactaa
90776147PRTMus musculus 6Met Ala Ser Leu Arg Leu Phe Leu Leu Cys
Leu Ala Gly Leu Val Phe1 5 10 15Val Ser Glu Ala Gly Pro Ala Gly Ala
Gly Glu Ser Lys Cys Pro Leu 20 25 30Met Val Lys Val Leu Asp Ala Val
Arg Gly Ser Pro Ala Val Asp Val 35 40 45Ala Val Lys Val Phe Lys Lys
Thr Ser Glu Gly Ser Trp Glu Pro Phe 50 55 60Ala Ser Gly Lys Thr Ala
Glu Ser Gly Glu Leu His Gly Leu Thr Thr65 70 75 80Asp Glu Lys Phe
Val Glu Gly Val Tyr Arg Val Glu Leu Asp Thr Lys 85 90 95Ser Tyr Trp
Lys Thr Leu Gly Ile Ser Pro Phe His Glu Phe Ala Asp 100 105 110Val
Val Phe Thr Ala Asn Asp Ser Gly His Arg His Tyr Thr Ile Ala 115 120
125Ala Leu Leu Ser Pro Tyr Ser Tyr Ser Thr Thr Ala Val Val Ser Asn
130 135 140Pro Gln Asn14571237DNAMus musculus 7ctaatctccc
taggcaaggt tcatatttgt gtaggttact tattctcctt ttgttgacta 60agtcaataat
cagaatcagc aggtttggag tcagcttggc agggatcagc agcctgggtt
120ggaaggaggg ggtataaaag ccccttcacc aggagaagcc gtcacacaga
tccacaagct 180cctgacagga tggcttccct tcgactcttc ctcctttgcc
tcgctggact ggtatttgtg 240tctgaagctg gccccgcggg tgctggagaa
tccaaatgtc ctctgatggt caaagtcctg 300gatgctgtcc gaggcagccc
tgctgtagac gtggctgtaa aagtgttcaa aaagacctct 360gagggatcct
gggagccctt tgcctctggg aagaccgcgg agtctggaga gctgcacggg
420ctcaccacag atgagaagtt tgtagaagga gtgtacagag tagaactgga
caccaaatcg 480tactggaaga cacttggcat ttccccgttc catgaattcg
cggatgtggt tttcacagcc 540aacgactctg gccatcgcca ctacaccatc
gcagccctgc tcagcccata ctcctacagc 600accacggctg tcgtcagcaa
cccccagaat tgagagactc agcccaggag gaccaggatc 660ttgccaaagc
agtagcatcc catttgtacc aaaacagtgt tcttgctcta taaaccgtgt
720tagcagctca ggaagatgcc gtgaagcatt cttattaaac cacctgctat
ttcattcaaa 780ctgtgtttct tttttatttc ctcatttttc tcccctgctc
ctaaaaccca aaatcttcta 840aagaattcta gaaggtatgc gatcaaactt
tttaaagaaa gaaaatactt tttgactcat 900ggtttaaagg catcctttcc
atcttgggga ggtcatgggt gctcctggca acttgcttga 960ggaagatagg
tcagaaagca gagtggacca accgttcaat gttttacaag caaaacatac
1020actaagcatg gtctgtagct attaaaagca cacaatctga agggctgtag
atgcacagta 1080gtgttttccc agagcatgtt caaaagccct gggttcaatc
acaatactga aaagtaggcc 1140aaaaaacatt ctgaaaatga aatatttggg
ttttttttta taacctttag tgactaaata 1200aagacaaatc taagagacta
aaaaaaaaaa aaaaaaa 1237882RNAArtificial SequenceSynthetic
8guuggaacca uucaaaacag cauagcaagu uaaaauaagg cuaguccguu aucaacuuga
60aaaaguggca ccgagucggu gc 82976RNAArtificial SequenceSynthetic
9guuuuagagc uagaaauagc aaguuaaaau aaggcuaguc cguuaucaac uugaaaaagu
60ggcaccgagu cggugc 761086RNAArtificial SequenceSynthetic
10guuuaagagc uaugcuggaa acagcauagc aaguuuaaau aaggcuaguc cguuaucaac
60uugaaaaagu ggcaccgagu cggugc 861123DNAArtificial
SequenceSyntheticmisc_feature(2)..(21)n = A, T, C, or G
11gnnnnnnnnn nnnnnnnnnn ngg 231223DNAArtificial
SequenceSyntheticmisc_feature(1)..(21)n = A, T, C, or G
12nnnnnnnnnn nnnnnnnnnn ngg 231325DNAArtificial
SequenceSyntheticmisc_feature(3)..(23)n = A, T, C, or G
13ggnnnnnnnn nnnnnnnnnn nnngg 251412208DNAArtificial
SequenceSyntheticmisc_feature(1)..(97)Mouse
Sequencemisc_feature(98)..(7298)Human
Sequencemisc_feature(7299)..(12108)SDC Neo
Cassettemisc_feature(12109)..(12208)Mouse Sequence 14agcttggcag
ggatcagcag cctgggttgg aaggaggggg tataaaagcc ccttcaccag 60gagaagccgt
cacacagatc cacaagctcc tgacaggatg gcttctcatc gtctgctcct
120cctctgcctt gctggactgg tatttgtgtc tgaggctggc cctacggtga
gtgtttctgt 180gacatcccat tcctacattt aagattcacg ctaaatgaag
tagaagtgac tccttccagc 240tttgccaacc agcttttatt actagggcaa
gggtacccag catctatttt taatataatt 300aattcaaact tcaaaaagaa
tgaagttcca ctgagcttac tgagctggga cttgaactct 360gagcattcta
cctcattgct ttggtgcatt aggtttgtaa tatctggtac ctctgtttcc
420tcagatagat gatagaaata aagatatgat attaaggaag ctgttaatac
tgaattttca 480gaaaagtatc cctccataaa atgtatttgg gggacaaact
gcaggagatt atattctggc 540cctatagtta ttcaaaacgt atttattgat
taatctttaa aaggcttagt gaacaatatt 600ctagtcagat atctaattct
taaatcctct agaagaatta actaatacta taaaatgggt 660ctggatgtag
ttctgacatt attttataac aactggtaag agggagtgac tatagcaaca
720actaaaatga tctcaggaaa acctgtttgg ccctatgtat ggtacattac
atcttttcag 780taattccact caaatggaga cttttaacaa agcaactgtt
ctcaggggac ctattttctc 840ccttaaaatt cattatacac atccctggtt
gatagcagtg tgtctggagg cagaaaccat 900tcttgctttg gaaacaatta
cgtctgtgtt atactgagta gggaagctca ttaattgtcg 960acacttacgt
tcctgataat gggatcagtg tgtaattctt gtttcgctcc agatttctaa
1020taccacaaag aataaatcct ttcactctga tcaattttgt taacttctca
cgtgtcttct 1080ctacacccag ggcaccggtg aatccaagtg tcctctgatg
gtcaaagttc tagatgctgt 1140ccgaggcagt cctgccatca atgtggccgt
gcatgtgttc agaaaggctg ctgatgacac 1200ctgggagcca tttgcctctg
ggtaagttgc caaagaaccc tcccacagga cttggtttta 1260tcttcccgtt
tgcccctcac ttggtagaga gaggctcaca tcatctgcta aagaatttac
1320aagtagattg aaaaacgtag gcagaggtca agtatgccct ctgaaggatg
ccctcttttt 1380gttttgctta gctaggaagt gaccaggaac ctgagcatca
tttaggggca gacagtagag 1440aaaagaagga atcagaactc ctctcctcta
gctgtggttt gcaacccttt tgggtcacag 1500aacactttat gtaggtgatg
aaaagtaaac attctatgcc cagaaaaaat gcacagatac 1560acacacatac
aaaatcatat atgtgatttt aggagtttca cagattccct ggtgtccctg
1620ggtaacacca aagctaagtg tccttgtctt agaattttag gaaaaggtat
aatgtgtatt 1680aacccattaa caaaaggaaa ggaattcaga aatattatta
accaggcatc tgtctgtagt 1740taatatggat cacccaaaac ccaaggcttt
tgcctaatga acactttggg gcacctactg 1800tgtgcaaggc tgggggctgt
caagctcagt taaaaaaaaa aagatagaag agatggatcc 1860atgaggcaaa
gtacagcccc aggctaatcc cacgatcacc cgacttcatg tccaagagtg
1920gcttctcacc ttcattagcc agttcacaat tttcatggag tttttctacc
tgcactagca 1980aaaacttcaa ggaaaataca tattaataaa tctaagcaaa
gtgaccagaa gacagagcaa 2040tcaggagacc ctttgcatcc agcagaagag
gaactgctaa gtatttacat ctccacagag 2100aagaatttct gttgggtttt
aattgaaccc caagaaccac atgattcttc aaccattatt 2160gggaagatca
ttttcttagg tctggtttta actggctttt tatttgggaa ttcatttatg
2220tttatataaa atgccaagca taacatgaaa agtggttaca ggactattct
aagggagaga 2280cagaatggac accaaaaata ttccaatgtt cttgtgaatc
ttttccttgc accaggacaa 2340aaaaaaaaag aagtgaaaag aagaaaggag
gaggggcata atcagagtca gtaaagacaa 2400ctgctatttt tatctatcgt
agctgttgca gtcaaatggg aagcaatttc caacattcaa 2460ctatggagct
ggtacttaca tggaaataga agttgcctag tgtttgttgc tggcaaagag
2520ttatcagaga ggttaaatat ataaaaggga aaagagtcag atacaggttc
ttcttcctac 2580tttaggtttt ccactgtgtg tgcaaatgat actccctggt
ggtgtgcaga tgcctcaaag 2640ctatcctcac accacaaggg agaggagcga
gatcctgctg tcctggagaa gtgcagagtt 2700agaacagctg tggccacttg
catccaatca tcaatcttga atcacaggga ctctttctta 2760agtaaacatt
atacctggcc gggcacggtg gctcacgcct gtaatcccag cactttggga
2820tgccaaagtg ggcatatcat ctgaggtcag gagttcaaga ccagcctggc
caacatggca 2880aaactccgtc tttatgaaaa atacaaaaat tagccaggca
tggtggcagg cgcctgtaat 2940cccagctaat tgggaggctg aggctggaga
atcccttgaa tctaggaggc agaggttgca 3000gtgagctgag atcgtgccat
tgcactccag cctgggtgac aagagtaaaa ctctgtctca 3060aaaaaaaaaa
attataccta cattctcttc ttatcagaga aaaaaatcta cagtgagctt
3120ttcaaaaagt ttttacaaac tttttgccat ttaatttcag ttaggagttt
tccctacttc 3180tgacttagtt gaggggaaat gttcataaca tgtttataac
atgtttatgt gtgttagttg 3240gtgggggtgt attactttgc catgccattt
gtttcctcca tgcgtaactt aatccagact 3300ttcacacctt ataggaaaac
cagtgagtct ggagagctgc atgggctcac aactgaggag 3360gaatttgtag
aagggatata caaagtggaa atagacacca aatcttactg gaaggcactt
3420ggcatctccc cattccatga gcatgcagag gtgagtatac agaccttcga
gggttgtttt 3480ggttttggtt tttgcttttg gcattccagg aaatgcacag
ttttactcag tgtaccacag 3540aaatgtccta aggaaggtga tgaatgacca
aaggttccct ttcctattat acaagaaaaa 3600attcacaaca ctctgagaag
caaatttctt tttgactttg atgaaaatcc acttagtaac 3660atgacttgaa
cttacatgaa actactcata gtctattcat tccactttat atgaatattg
3720atgtatctgc tgttgaaata atagtttatg aggcagccct ccagacccca
cgtagagtgt 3780atgtaacaag agatgcacca ttttatttct cgaaaacccg
taacattctt cattccaaaa 3840cacatctggc ttctcggagg tctggacaag
tgattcttgg caacacatac ctatagagac 3900aataaaatca aagtaataat
ggcaacacaa tagataacat ttaccaagca tacaccatgt 3960ggcagacaca
attataagtg ttttccatat ttaacctact taatcctcag gaataagcca
4020ctgaggtcag tcctattatt atccccatct tatagatgaa gaaaatgagg
caccaggaag 4080tcaaataact tgtcaaaggt cacaagacta ggaaatacac
aagtagaaat gtttacaatt 4140aaggcccagg ctgggtttgc cctcagttct
gctatgcctc gcattatgcc ccaggaaact 4200ttttcccttg tgaaagccaa
gcttaaaaaa agaaaagcca catttgtaac gtgctctgtt 4260cccctgccta
tggtgaggat cttcaaacag ttatacatgg acccagtccc cctgccttct
4320ccttaatttc ttaagtcatt tgaaacagat ggctgtcatg gaaatagaat
ccagacatgt 4380tggtcagagt taaagatcaa ctaattccat caaaaatagc
tcggcatgaa agggaactat 4440tctctggctt agtcatggat gagactttca
attgctataa agtggttcct ttattagaca 4500atgttaccag ggaaacaaca
ggggtttgtt tgacttctgg ggcccacaag tcaacaagag 4560agccccatct
accaaggagc atgtccctga ctacccctca gccagcagca agacatggac
4620cccagtcagg gcaggagcag ggtttcggcg gcgcccagca caagacattg
cccctagagt 4680ctcagcccct accctcgagt aatagatctg cctacctgag
actgttgttt gcccaagagc 4740tgggtctcag cctgatggga accatataaa
aaggttcact gacatactgc ccacatgttg 4800ttctctttca ttagatctta
gcttccttgt ctgctcttca ttcttgcagt attcattcaa 4860caaacattaa
aaaaaaaaaa aagcattcta tgtgtggaac actctgctag atgctgtgga
4920tttagaaatg aaaatacatc ccgacccttg gaatggaagg gaaaggactg
aagtaagaca 4980gattaagcag gaccgtcagc ccagcttgaa gcccagataa
atacggagaa caagagagag 5040cgagtagtga gagatgagtc ccaatgcctc
actttggtga cgggtgcgtg gtgggcttca 5100tgcagcttct tctgataaat
gcctccttca gaactggtca actctacctt ggccagtgac 5160ccaggtggtc
atagtagatt taccaaggga aaatggaaac ttttattagg agctcttagg
5220cctcttcact tcatggattt ttttttcctt tttttttgag atggagtttt
gccctgtcac 5280ccaggctgga atgcagtggt gcaatctcag ctcactgcaa
cctccgcctc ccaggttcaa 5340gcaattctcc tgcctcagcc tcccgagtag
ctgggactac aggtgtgcgc caccacacca 5400ggctaatttt tgtatttttt
gtaaagacag gttttcacca cgttggccag gctggtctga 5460actccagacc
tcaggtgatt cacctgtctc agcctcccaa agtgctggga ttacaggtgt
5520gagccaccgt gcccggctac ttcatggatt tttgattaca gattatgcct
cttacaattt 5580ttaagaagaa tcaagtgggc tgaaggtcaa tgtcaccata
agacaaaaga catttttatt 5640agttgattct agggaattgg ccttaagggg
agccctttct tcctaagaga ttcttaggtg 5700attctcactt cctcttgccc
cagtattatt tttgtttttg gtatggctca ctcagatcct 5760tttttcctcc
tatccctaag taatccgggt ttctttttcc catatttaga acaaaatgta
5820tttatgcaga gtgtgtccaa acctcaaccc aaggcctgta tacaaaataa
atcaaattaa 5880acacatcttt actgtcttct acctctttcc tgacctcaat
atatcccaac ttgcctcact 5940ctgagaacca aggctgtccc agcacctgag
tcgcagatat tctactgatt tgacagaact 6000gtgtgactat ctggaacagc
attttgatcc acaatttgcc cagttacaaa gcttaaatga 6060gctctagtgc
atgcatatat atttcaaaat tccaccatga tcttccacac tctgtattgt
6120aaatagagcc ctgtaatgct tttacttcgt atttcattgc ttgttataca
taaaaatata 6180cttttcttct tcatgttaga aaatgcaaag aataggaggg
tgggggaatc tctgggcttg 6240gagacaggag acttgccttc ctactatggt
tccatcagaa tgtagactgg gacaatacaa 6300taattcaagt ctggtttgct
catctgtaaa ttgggaagaa tgtttccagc tccagaatgc 6360taaatctcta
agtctgtggt tggcagccac tattgcagca gctcttcaat gactcaatgc
6420agttttgcat tctccctacc ttttttttct aaaaccaata aaatagatac
agcctttagg 6480ctttctggga tttcccttag tcaagctagg gtcatcctga
ctttcggcgt gaatttgcaa 6540aacaagacct gactctgtac tcctgctcta
aggactgtgc atggttccaa aggcttagct 6600tgccagcata tttgagcttt
ttccttctgt tcaaactgtt ccaaaatata aaagaataaa 6660attaattaag
ttggcactgg acttccggtg gtcagtcatg tgtgtcatct gtcacgtttt
6720tcgggctctg gtggaaatgg atctgtctgt cttctctcat aggtggtatt
cacagccaac 6780gactccggcc cccgccgcta caccattgcc gccctgctga
gcccctactc ctattccacc 6840acggctgtcg tcaccaatcc caaggaatga
gggacttctc ctccagtgga cctgaaggac 6900gagggatggg atttcatgta
accaagagta ttccattttt actaaagcag tgttttcacc 6960tcatatgcta
tgttagaagt ccaggcagag acaataaaac attcctgtga aaggcacttt
7020tcattccact ttaacttgat tttttaaatt cccttattgt cccttccaaa
aaaaagagaa 7080tcaaaatttt acaaagaatc aaaggaattc tagaaagtat
ctgggcagaa cgctaggaga 7140gatccaaatt tccattgtct tgcaagcaaa
gcacgtatta aatatgatct gcagccatta 7200aaaagacaca ttctgtaaat
gagagagcct tattttcctg taaccttcag caaatagcaa 7260aagacacatt
ccaagggccc acttctttac tgtgggcact cgagataact tcgtataatg
7320tatgctatac gaagttatat gcatgccagt agcagcaccc acgtccacct
tctgtctagt 7380aatgtccaac acctccctca gtccaaacac tgctctgcat
ccatgtggct cccatttata 7440cctgaagcac ttgatggggc ctcaatgttt
tactagagcc cacccccctg caactctgag 7500accctctgga tttgtctgtc
agtgcctcac tggggcgttg gataatttct taaaaggtca 7560agttccctca
gcagcattct ctgagcagtc tgaagatgtg tgcttttcac agttcaaatc
7620catgtggctg tttcacccac ctgcctggcc ttgggttatc tatcaggacc
tagcctagaa 7680gcaggtgtgt
ggcacttaac acctaagctg agtgactaac tgaacactca agtggatgcc
7740atctttgtca cttcttgact gtgacacaag caactcctga tgccaaagcc
ctgcccaccc 7800ctctcatgcc catatttgga catggtacag gtcctcactg
gccatggtct gtgaggtcct 7860ggtcctcttt gacttcataa ttcctagggg
ccactagtat ctataagagg aagagggtgc 7920tggctcccag gccacagccc
acaaaattcc acctgctcac aggttggctg gctcgaccca 7980ggtggtgtcc
cctgctctga gccagctccc ggccaagcca gcaccatggg aacccccaag
8040aagaagagga aggtgcgtac cgatttaaat tccaatttac tgaccgtaca
ccaaaatttg 8100cctgcattac cggtcgatgc aacgagtgat gaggttcgca
agaacctgat ggacatgttc 8160agggatcgcc aggcgttttc tgagcatacc
tggaaaatgc ttctgtccgt ttgccggtcg 8220tgggcggcat ggtgcaagtt
gaataaccgg aaatggtttc ccgcagaacc tgaagatgtt 8280cgcgattatc
ttctatatct tcaggcgcgc ggtctggcag taaaaactat ccagcaacat
8340ttgggccagc taaacatgct tcatcgtcgg tccgggctgc cacgaccaag
tgacagcaat 8400gctgtttcac tggttatgcg gcggatccga aaagaaaacg
ttgatgccgg tgaacgtgca 8460aaacaggtaa atataaaatt tttaagtgta
taatgatgtt aaactactga ttctaattgt 8520ttgtgtattt taggctctag
cgttcgaacg cactgatttc gaccaggttc gttcactcat 8580ggaaaatagc
gatcgctgcc aggatatacg taatctggca tttctgggga ttgcttataa
8640caccctgtta cgtatagccg aaattgccag gatcagggtt aaagatatct
cacgtactga 8700cggtgggaga atgttaatcc atattggcag aacgaaaacg
ctggttagca ccgcaggtgt 8760agagaaggca cttagcctgg gggtaactaa
actggtcgag cgatggattt ccgtctctgg 8820tgtagctgat gatccgaata
actacctgtt ttgccgggtc agaaaaaatg gtgttgccgc 8880gccatctgcc
accagccagc tatcaactcg cgccctggaa gggatttttg aagcaactca
8940tcgattgatt tacggcgcta aggatgactc tggtcagaga tacctggcct
ggtctggaca 9000cagtgcccgt gtcggagccg cgcgagatat ggcccgcgct
ggagtttcaa taccggagat 9060catgcaagct ggtggctgga ccaatgtaaa
tattgtcatg aactatatcc gtaacctgga 9120tagtgaaaca ggggcaatgg
tgcgcctgct ggaagatggc gattaggcgg ccggccgcta 9180atcagccata
ccacatttgt agaggtttta cttgctttaa aaaacctccc acacctcccc
9240ctgaacctga aacataaaat gaatgcaatt gttgttgtta acttgtttat
tgcagcttat 9300aatggttaca aataaagcaa tagcatcaca aatttcacaa
ataaagcatt tttttcactg 9360cattctagtt gtggtttgtc caaactcatc
aatgtatctt atcatgtctg gatcccccgg 9420ctagagttta aacactagaa
ctagtggatc ccccgggatc atggcctccg cgccgggttt 9480tggcgcctcc
cgcgggcgcc cccctcctca cggcgagcgc tgccacgtca gacgaagggc
9540gcagcgagcg tcctgatcct tccgcccgga cgctcaggac agcggcccgc
tgctcataag 9600actcggcctt agaaccccag tatcagcaga aggacatttt
aggacgggac ttgggtgact 9660ctagggcact ggttttcttt ccagagagcg
gaacaggcga ggaaaagtag tcccttctcg 9720gcgattctgc ggagggatct
ccgtggggcg gtgaacgccg atgattatat aaggacgcgc 9780cgggtgtggc
acagctagtt ccgtcgcagc cgggatttgg gtcgcggttc ttgtttgtgg
9840atcgctgtga tcgtcacttg gtgagtagcg ggctgctggg ctggccgggg
ctttcgtggc 9900cgccgggccg ctcggtggga cggaagcgtg tggagagacc
gccaagggct gtagtctggg 9960tccgcgagca aggttgccct gaactggggg
ttggggggag cgcagcaaaa tggcggctgt 10020tcccgagtct tgaatggaag
acgcttgtga ggcgggctgt gaggtcgttg aaacaaggtg 10080gggggcatgg
tgggcggcaa gaacccaagg tcttgaggcc ttcgctaatg cgggaaagct
10140cttattcggg tgagatgggc tggggcacca tctggggacc ctgacgtgaa
gtttgtcact 10200gactggagaa ctcggtttgt cgtctgttgc gggggcggca
gttatggcgg tgccgttggg 10260cagtgcaccc gtacctttgg gagcgcgcgc
cctcgtcgtg tcgtgacgtc acccgttctg 10320ttggcttata atgcagggtg
gggccacctg ccggtaggtg tgcggtaggc ttttctccgt 10380cgcaggacgc
agggttcggg cctagggtag gctctcctga atcgacaggc gccggacctc
10440tggtgagggg agggataagt gaggcgtcag tttctttggt cggttttatg
tacctatctt 10500cttaagtagc tgaagctccg gttttgaact atgcgctcgg
ggttggcgag tgtgttttgt 10560gaagtttttt aggcaccttt tgaaatgtaa
tcatttgggt caatatgtaa ttttcagtgt 10620tagactagta aattgtccgc
taaattctgg ccgtttttgg cttttttgtt agacgtgttg 10680acaattaatc
atcggcatag tatatcggca tagtataata cgacaaggtg aggaactaaa
10740ccatgggatc ggccattgaa caagatggat tgcacgcagg ttctccggcc
gcttgggtgg 10800agaggctatt cggctatgac tgggcacaac agacaatcgg
ctgctctgat gccgccgtgt 10860tccggctgtc agcgcagggg cgcccggttc
tttttgtcaa gaccgacctg tccggtgccc 10920tgaatgaact gcaggacgag
gcagcgcggc tatcgtggct ggccacgacg ggcgttcctt 10980gcgcagctgt
gctcgacgtt gtcactgaag cgggaaggga ctggctgcta ttgggcgaag
11040tgccggggca ggatctcctg tcatctcacc ttgctcctgc cgagaaagta
tccatcatgg 11100ctgatgcaat gcggcggctg catacgcttg atccggctac
ctgcccattc gaccaccaag 11160cgaaacatcg catcgagcga gcacgtactc
ggatggaagc cggtcttgtc gatcaggatg 11220atctggacga agagcatcag
gggctcgcgc cagccgaact gttcgccagg ctcaaggcgc 11280gcatgcccga
cggcgatgat ctcgtcgtga cccatggcga tgcctgcttg ccgaatatca
11340tggtggaaaa tggccgcttt tctggattca tcgactgtgg ccggctgggt
gtggcggacc 11400gctatcagga catagcgttg gctacccgtg atattgctga
agagcttggc ggcgaatggg 11460ctgaccgctt cctcgtgctt tacggtatcg
ccgctcccga ttcgcagcgc atcgccttct 11520atcgccttct tgacgagttc
ttctgagggg atccgctgta agtctgcaga aattgatgat 11580ctattaaaca
ataaagatgt ccactaaaat ggaagttttt cctgtcatac tttgttaaga
11640agggtgagaa cagagtacct acattttgaa tggaaggatt ggagctacgg
gggtgggggt 11700ggggtgggat tagataaatg cctgctcttt actgaaggct
ctttactatt gctttatgat 11760aatgtttcat agttggatat cataatttaa
acaagcaaaa ccaaattaag ggccagctca 11820ttcctcccac tcatgatcta
tagatctata gatctctcgt gggatcattg tttttctctt 11880gattcccact
ttgtggttct aagtactgtg gtttccaaat gtgtcagttt catagcctga
11940agaacgagat cagcagcctc tgttccacat acacttcatt ctcagtattg
ttttgccaag 12000ttctaattcc atcagacctc gacctgcagc ccctagataa
cttcgtataa tgtatgctat 12060acgaagttat gctaggtaac tataacggtc
ctaaggtagc gagctagcga gactcagccc 12120aggaggacca ggatcttgcc
aaagcagtag catcccattt gtaccaaaac agtgttcttg 12180ctctataaac
cgtgttagca gctcagga 12208157476DNAArtificial
SequenceSyntheticmisc_feature(1)..(97)Mouse
Sequencemisc_feature(98)..(7298)Human
Sequencemisc_feature(7299)..(7376)Cassette LoxP
Scarmisc_feature(7377)..(7476)Mouse Sequence 15agcttggcag
ggatcagcag cctgggttgg aaggaggggg tataaaagcc ccttcaccag 60gagaagccgt
cacacagatc cacaagctcc tgacaggatg gcttctcatc gtctgctcct
120cctctgcctt gctggactgg tatttgtgtc tgaggctggc cctacggtga
gtgtttctgt 180gacatcccat tcctacattt aagattcacg ctaaatgaag
tagaagtgac tccttccagc 240tttgccaacc agcttttatt actagggcaa
gggtacccag catctatttt taatataatt 300aattcaaact tcaaaaagaa
tgaagttcca ctgagcttac tgagctggga cttgaactct 360gagcattcta
cctcattgct ttggtgcatt aggtttgtaa tatctggtac ctctgtttcc
420tcagatagat gatagaaata aagatatgat attaaggaag ctgttaatac
tgaattttca 480gaaaagtatc cctccataaa atgtatttgg gggacaaact
gcaggagatt atattctggc 540cctatagtta ttcaaaacgt atttattgat
taatctttaa aaggcttagt gaacaatatt 600ctagtcagat atctaattct
taaatcctct agaagaatta actaatacta taaaatgggt 660ctggatgtag
ttctgacatt attttataac aactggtaag agggagtgac tatagcaaca
720actaaaatga tctcaggaaa acctgtttgg ccctatgtat ggtacattac
atcttttcag 780taattccact caaatggaga cttttaacaa agcaactgtt
ctcaggggac ctattttctc 840ccttaaaatt cattatacac atccctggtt
gatagcagtg tgtctggagg cagaaaccat 900tcttgctttg gaaacaatta
cgtctgtgtt atactgagta gggaagctca ttaattgtcg 960acacttacgt
tcctgataat gggatcagtg tgtaattctt gtttcgctcc agatttctaa
1020taccacaaag aataaatcct ttcactctga tcaattttgt taacttctca
cgtgtcttct 1080ctacacccag ggcaccggtg aatccaagtg tcctctgatg
gtcaaagttc tagatgctgt 1140ccgaggcagt cctgccatca atgtggccgt
gcatgtgttc agaaaggctg ctgatgacac 1200ctgggagcca tttgcctctg
ggtaagttgc caaagaaccc tcccacagga cttggtttta 1260tcttcccgtt
tgcccctcac ttggtagaga gaggctcaca tcatctgcta aagaatttac
1320aagtagattg aaaaacgtag gcagaggtca agtatgccct ctgaaggatg
ccctcttttt 1380gttttgctta gctaggaagt gaccaggaac ctgagcatca
tttaggggca gacagtagag 1440aaaagaagga atcagaactc ctctcctcta
gctgtggttt gcaacccttt tgggtcacag 1500aacactttat gtaggtgatg
aaaagtaaac attctatgcc cagaaaaaat gcacagatac 1560acacacatac
aaaatcatat atgtgatttt aggagtttca cagattccct ggtgtccctg
1620ggtaacacca aagctaagtg tccttgtctt agaattttag gaaaaggtat
aatgtgtatt 1680aacccattaa caaaaggaaa ggaattcaga aatattatta
accaggcatc tgtctgtagt 1740taatatggat cacccaaaac ccaaggcttt
tgcctaatga acactttggg gcacctactg 1800tgtgcaaggc tgggggctgt
caagctcagt taaaaaaaaa aagatagaag agatggatcc 1860atgaggcaaa
gtacagcccc aggctaatcc cacgatcacc cgacttcatg tccaagagtg
1920gcttctcacc ttcattagcc agttcacaat tttcatggag tttttctacc
tgcactagca 1980aaaacttcaa ggaaaataca tattaataaa tctaagcaaa
gtgaccagaa gacagagcaa 2040tcaggagacc ctttgcatcc agcagaagag
gaactgctaa gtatttacat ctccacagag 2100aagaatttct gttgggtttt
aattgaaccc caagaaccac atgattcttc aaccattatt 2160gggaagatca
ttttcttagg tctggtttta actggctttt tatttgggaa ttcatttatg
2220tttatataaa atgccaagca taacatgaaa agtggttaca ggactattct
aagggagaga 2280cagaatggac accaaaaata ttccaatgtt cttgtgaatc
ttttccttgc accaggacaa 2340aaaaaaaaag aagtgaaaag aagaaaggag
gaggggcata atcagagtca gtaaagacaa 2400ctgctatttt tatctatcgt
agctgttgca gtcaaatggg aagcaatttc caacattcaa 2460ctatggagct
ggtacttaca tggaaataga agttgcctag tgtttgttgc tggcaaagag
2520ttatcagaga ggttaaatat ataaaaggga aaagagtcag atacaggttc
ttcttcctac 2580tttaggtttt ccactgtgtg tgcaaatgat actccctggt
ggtgtgcaga tgcctcaaag 2640ctatcctcac accacaaggg agaggagcga
gatcctgctg tcctggagaa gtgcagagtt 2700agaacagctg tggccacttg
catccaatca tcaatcttga atcacaggga ctctttctta 2760agtaaacatt
atacctggcc gggcacggtg gctcacgcct gtaatcccag cactttggga
2820tgccaaagtg ggcatatcat ctgaggtcag gagttcaaga ccagcctggc
caacatggca 2880aaactccgtc tttatgaaaa atacaaaaat tagccaggca
tggtggcagg cgcctgtaat 2940cccagctaat tgggaggctg aggctggaga
atcccttgaa tctaggaggc agaggttgca 3000gtgagctgag atcgtgccat
tgcactccag cctgggtgac aagagtaaaa ctctgtctca 3060aaaaaaaaaa
attataccta cattctcttc ttatcagaga aaaaaatcta cagtgagctt
3120ttcaaaaagt ttttacaaac tttttgccat ttaatttcag ttaggagttt
tccctacttc 3180tgacttagtt gaggggaaat gttcataaca tgtttataac
atgtttatgt gtgttagttg 3240gtgggggtgt attactttgc catgccattt
gtttcctcca tgcgtaactt aatccagact 3300ttcacacctt ataggaaaac
cagtgagtct ggagagctgc atgggctcac aactgaggag 3360gaatttgtag
aagggatata caaagtggaa atagacacca aatcttactg gaaggcactt
3420ggcatctccc cattccatga gcatgcagag gtgagtatac agaccttcga
gggttgtttt 3480ggttttggtt tttgcttttg gcattccagg aaatgcacag
ttttactcag tgtaccacag 3540aaatgtccta aggaaggtga tgaatgacca
aaggttccct ttcctattat acaagaaaaa 3600attcacaaca ctctgagaag
caaatttctt tttgactttg atgaaaatcc acttagtaac 3660atgacttgaa
cttacatgaa actactcata gtctattcat tccactttat atgaatattg
3720atgtatctgc tgttgaaata atagtttatg aggcagccct ccagacccca
cgtagagtgt 3780atgtaacaag agatgcacca ttttatttct cgaaaacccg
taacattctt cattccaaaa 3840cacatctggc ttctcggagg tctggacaag
tgattcttgg caacacatac ctatagagac 3900aataaaatca aagtaataat
ggcaacacaa tagataacat ttaccaagca tacaccatgt 3960ggcagacaca
attataagtg ttttccatat ttaacctact taatcctcag gaataagcca
4020ctgaggtcag tcctattatt atccccatct tatagatgaa gaaaatgagg
caccaggaag 4080tcaaataact tgtcaaaggt cacaagacta ggaaatacac
aagtagaaat gtttacaatt 4140aaggcccagg ctgggtttgc cctcagttct
gctatgcctc gcattatgcc ccaggaaact 4200ttttcccttg tgaaagccaa
gcttaaaaaa agaaaagcca catttgtaac gtgctctgtt 4260cccctgccta
tggtgaggat cttcaaacag ttatacatgg acccagtccc cctgccttct
4320ccttaatttc ttaagtcatt tgaaacagat ggctgtcatg gaaatagaat
ccagacatgt 4380tggtcagagt taaagatcaa ctaattccat caaaaatagc
tcggcatgaa agggaactat 4440tctctggctt agtcatggat gagactttca
attgctataa agtggttcct ttattagaca 4500atgttaccag ggaaacaaca
ggggtttgtt tgacttctgg ggcccacaag tcaacaagag 4560agccccatct
accaaggagc atgtccctga ctacccctca gccagcagca agacatggac
4620cccagtcagg gcaggagcag ggtttcggcg gcgcccagca caagacattg
cccctagagt 4680ctcagcccct accctcgagt aatagatctg cctacctgag
actgttgttt gcccaagagc 4740tgggtctcag cctgatggga accatataaa
aaggttcact gacatactgc ccacatgttg 4800ttctctttca ttagatctta
gcttccttgt ctgctcttca ttcttgcagt attcattcaa 4860caaacattaa
aaaaaaaaaa aagcattcta tgtgtggaac actctgctag atgctgtgga
4920tttagaaatg aaaatacatc ccgacccttg gaatggaagg gaaaggactg
aagtaagaca 4980gattaagcag gaccgtcagc ccagcttgaa gcccagataa
atacggagaa caagagagag 5040cgagtagtga gagatgagtc ccaatgcctc
actttggtga cgggtgcgtg gtgggcttca 5100tgcagcttct tctgataaat
gcctccttca gaactggtca actctacctt ggccagtgac 5160ccaggtggtc
atagtagatt taccaaggga aaatggaaac ttttattagg agctcttagg
5220cctcttcact tcatggattt ttttttcctt tttttttgag atggagtttt
gccctgtcac 5280ccaggctgga atgcagtggt gcaatctcag ctcactgcaa
cctccgcctc ccaggttcaa 5340gcaattctcc tgcctcagcc tcccgagtag
ctgggactac aggtgtgcgc caccacacca 5400ggctaatttt tgtatttttt
gtaaagacag gttttcacca cgttggccag gctggtctga 5460actccagacc
tcaggtgatt cacctgtctc agcctcccaa agtgctggga ttacaggtgt
5520gagccaccgt gcccggctac ttcatggatt tttgattaca gattatgcct
cttacaattt 5580ttaagaagaa tcaagtgggc tgaaggtcaa tgtcaccata
agacaaaaga catttttatt 5640agttgattct agggaattgg ccttaagggg
agccctttct tcctaagaga ttcttaggtg 5700attctcactt cctcttgccc
cagtattatt tttgtttttg gtatggctca ctcagatcct 5760tttttcctcc
tatccctaag taatccgggt ttctttttcc catatttaga acaaaatgta
5820tttatgcaga gtgtgtccaa acctcaaccc aaggcctgta tacaaaataa
atcaaattaa 5880acacatcttt actgtcttct acctctttcc tgacctcaat
atatcccaac ttgcctcact 5940ctgagaacca aggctgtccc agcacctgag
tcgcagatat tctactgatt tgacagaact 6000gtgtgactat ctggaacagc
attttgatcc acaatttgcc cagttacaaa gcttaaatga 6060gctctagtgc
atgcatatat atttcaaaat tccaccatga tcttccacac tctgtattgt
6120aaatagagcc ctgtaatgct tttacttcgt atttcattgc ttgttataca
taaaaatata 6180cttttcttct tcatgttaga aaatgcaaag aataggaggg
tgggggaatc tctgggcttg 6240gagacaggag acttgccttc ctactatggt
tccatcagaa tgtagactgg gacaatacaa 6300taattcaagt ctggtttgct
catctgtaaa ttgggaagaa tgtttccagc tccagaatgc 6360taaatctcta
agtctgtggt tggcagccac tattgcagca gctcttcaat gactcaatgc
6420agttttgcat tctccctacc ttttttttct aaaaccaata aaatagatac
agcctttagg 6480ctttctggga tttcccttag tcaagctagg gtcatcctga
ctttcggcgt gaatttgcaa 6540aacaagacct gactctgtac tcctgctcta
aggactgtgc atggttccaa aggcttagct 6600tgccagcata tttgagcttt
ttccttctgt tcaaactgtt ccaaaatata aaagaataaa 6660attaattaag
ttggcactgg acttccggtg gtcagtcatg tgtgtcatct gtcacgtttt
6720tcgggctctg gtggaaatgg atctgtctgt cttctctcat aggtggtatt
cacagccaac 6780gactccggcc cccgccgcta caccattgcc gccctgctga
gcccctactc ctattccacc 6840acggctgtcg tcaccaatcc caaggaatga
gggacttctc ctccagtgga cctgaaggac 6900gagggatggg atttcatgta
accaagagta ttccattttt actaaagcag tgttttcacc 6960tcatatgcta
tgttagaagt ccaggcagag acaataaaac attcctgtga aaggcacttt
7020tcattccact ttaacttgat tttttaaatt cccttattgt cccttccaaa
aaaaagagaa 7080tcaaaatttt acaaagaatc aaaggaattc tagaaagtat
ctgggcagaa cgctaggaga 7140gatccaaatt tccattgtct tgcaagcaaa
gcacgtatta aatatgatct gcagccatta 7200aaaagacaca ttctgtaaat
gagagagcct tattttcctg taaccttcag caaatagcaa 7260aagacacatt
ccaagggccc acttctttac tgtgggcact cgagataact tcgtataatg
7320tatgctatac gaagttatgc taggtaacta taacggtcct aaggtagcga
gctagcgaga 7380ctcagcccag gaggaccagg atcttgccaa agcagtagca
tcccatttgt accaaaacag 7440tgttcttgct ctataaaccg tgttagcagc tcagga
74761611218DNAArtificial
SequenceSyntheticmisc_feature(1)..(100)Mouse
Sequencemisc_feature(101)..(6308)Human
Sequencemisc_feature(6309)..(11118)SDC Neo
Cassettemisc_feature(11119)..(11218)Mouse Sequence 16atgtactttt
ggttttgttc cagagtctat caccggaaag aacaagccgg tttactctga 60cccatttcac
tgacatttct cttgtctcct ctgtgcccag ggcaccggtg aatccaagtg
120tcctctgatg gtcaaagttc tagatgctgt ccgaggcagt cctgccatca
atgtggccgt 180gcatgtgttc agaaaggctg ctgatgacac ctgggagcca
tttgcctctg ggtaagttgc 240caaagaaccc tcccacagga cttggtttta
tcttcccgtt tgcccctcac ttggtagaga 300gaggctcaca tcatctgcta
aagaatttac aagtagattg aaaaacgtag gcagaggtca 360agtatgccct
ctgaaggatg ccctcttttt gttttgctta gctaggaagt gaccaggaac
420ctgagcatca tttaggggca gacagtagag aaaagaagga atcagaactc
ctctcctcta 480gctgtggttt gcaacccttt tgggtcacag aacactttat
gtaggtgatg aaaagtaaac 540attctatgcc cagaaaaaat gcacagatac
acacacatac aaaatcatat atgtgatttt 600aggagtttca cagattccct
ggtgtccctg ggtaacacca aagctaagtg tccttgtctt 660agaattttag
gaaaaggtat aatgtgtatt aacccattaa caaaaggaaa ggaattcaga
720aatattatta accaggcatc tgtctgtagt taatatggat cacccaaaac
ccaaggcttt 780tgcctaatga acactttggg gcacctactg tgtgcaaggc
tgggggctgt caagctcagt 840taaaaaaaaa aagatagaag agatggatcc
atgaggcaaa gtacagcccc aggctaatcc 900cacgatcacc cgacttcatg
tccaagagtg gcttctcacc ttcattagcc agttcacaat 960tttcatggag
tttttctacc tgcactagca aaaacttcaa ggaaaataca tattaataaa
1020tctaagcaaa gtgaccagaa gacagagcaa tcaggagacc ctttgcatcc
agcagaagag 1080gaactgctaa gtatttacat ctccacagag aagaatttct
gttgggtttt aattgaaccc 1140caagaaccac atgattcttc aaccattatt
gggaagatca ttttcttagg tctggtttta 1200actggctttt tatttgggaa
ttcatttatg tttatataaa atgccaagca taacatgaaa 1260agtggttaca
ggactattct aagggagaga cagaatggac accaaaaata ttccaatgtt
1320cttgtgaatc ttttccttgc accaggacaa aaaaaaaaag aagtgaaaag
aagaaaggag 1380gaggggcata atcagagtca gtaaagacaa ctgctatttt
tatctatcgt agctgttgca 1440gtcaaatggg aagcaatttc caacattcaa
ctatggagct ggtacttaca tggaaataga 1500agttgcctag tgtttgttgc
tggcaaagag ttatcagaga ggttaaatat ataaaaggga 1560aaagagtcag
atacaggttc ttcttcctac tttaggtttt ccactgtgtg tgcaaatgat
1620actccctggt ggtgtgcaga tgcctcaaag ctatcctcac accacaaggg
agaggagcga 1680gatcctgctg tcctggagaa gtgcagagtt agaacagctg
tggccacttg catccaatca 1740tcaatcttga atcacaggga ctctttctta
agtaaacatt atacctggcc gggcacggtg 1800gctcacgcct gtaatcccag
cactttggga tgccaaagtg ggcatatcat ctgaggtcag 1860gagttcaaga
ccagcctggc caacatggca aaactccgtc tttatgaaaa atacaaaaat
1920tagccaggca tggtggcagg cgcctgtaat cccagctaat tgggaggctg
aggctggaga 1980atcccttgaa tctaggaggc agaggttgca gtgagctgag
atcgtgccat tgcactccag 2040cctgggtgac aagagtaaaa ctctgtctca
aaaaaaaaaa attataccta cattctcttc 2100ttatcagaga aaaaaatcta
cagtgagctt ttcaaaaagt ttttacaaac tttttgccat 2160ttaatttcag
ttaggagttt tccctacttc tgacttagtt gaggggaaat gttcataaca
2220tgtttataac atgtttatgt gtgttagttg gtgggggtgt attactttgc
catgccattt 2280gtttcctcca tgcgtaactt aatccagact ttcacacctt
ataggaaaac cagtgagtct 2340ggagagctgc atgggctcac aactgaggag
gaatttgtag aagggatata caaagtggaa 2400atagacacca aatcttactg
gaaggcactt ggcatctccc cattccatga gcatgcagag 2460gtgagtatac
agaccttcga gggttgtttt ggttttggtt tttgcttttg gcattccagg
2520aaatgcacag
ttttactcag tgtaccacag aaatgtccta aggaaggtga tgaatgacca
2580aaggttccct ttcctattat acaagaaaaa attcacaaca ctctgagaag
caaatttctt 2640tttgactttg atgaaaatcc acttagtaac atgacttgaa
cttacatgaa actactcata 2700gtctattcat tccactttat atgaatattg
atgtatctgc tgttgaaata atagtttatg 2760aggcagccct ccagacccca
cgtagagtgt atgtaacaag agatgcacca ttttatttct 2820cgaaaacccg
taacattctt cattccaaaa cacatctggc ttctcggagg tctggacaag
2880tgattcttgg caacacatac ctatagagac aataaaatca aagtaataat
ggcaacacaa 2940tagataacat ttaccaagca tacaccatgt ggcagacaca
attataagtg ttttccatat 3000ttaacctact taatcctcag gaataagcca
ctgaggtcag tcctattatt atccccatct 3060tatagatgaa gaaaatgagg
caccaggaag tcaaataact tgtcaaaggt cacaagacta 3120ggaaatacac
aagtagaaat gtttacaatt aaggcccagg ctgggtttgc cctcagttct
3180gctatgcctc gcattatgcc ccaggaaact ttttcccttg tgaaagccaa
gcttaaaaaa 3240agaaaagcca catttgtaac gtgctctgtt cccctgccta
tggtgaggat cttcaaacag 3300ttatacatgg acccagtccc cctgccttct
ccttaatttc ttaagtcatt tgaaacagat 3360ggctgtcatg gaaatagaat
ccagacatgt tggtcagagt taaagatcaa ctaattccat 3420caaaaatagc
tcggcatgaa agggaactat tctctggctt agtcatggat gagactttca
3480attgctataa agtggttcct ttattagaca atgttaccag ggaaacaaca
ggggtttgtt 3540tgacttctgg ggcccacaag tcaacaagag agccccatct
accaaggagc atgtccctga 3600ctacccctca gccagcagca agacatggac
cccagtcagg gcaggagcag ggtttcggcg 3660gcgcccagca caagacattg
cccctagagt ctcagcccct accctcgagt aatagatctg 3720cctacctgag
actgttgttt gcccaagagc tgggtctcag cctgatggga accatataaa
3780aaggttcact gacatactgc ccacatgttg ttctctttca ttagatctta
gcttccttgt 3840ctgctcttca ttcttgcagt attcattcaa caaacattaa
aaaaaaaaaa aagcattcta 3900tgtgtggaac actctgctag atgctgtgga
tttagaaatg aaaatacatc ccgacccttg 3960gaatggaagg gaaaggactg
aagtaagaca gattaagcag gaccgtcagc ccagcttgaa 4020gcccagataa
atacggagaa caagagagag cgagtagtga gagatgagtc ccaatgcctc
4080actttggtga cgggtgcgtg gtgggcttca tgcagcttct tctgataaat
gcctccttca 4140gaactggtca actctacctt ggccagtgac ccaggtggtc
atagtagatt taccaaggga 4200aaatggaaac ttttattagg agctcttagg
cctcttcact tcatggattt ttttttcctt 4260tttttttgag atggagtttt
gccctgtcac ccaggctgga atgcagtggt gcaatctcag 4320ctcactgcaa
cctccgcctc ccaggttcaa gcaattctcc tgcctcagcc tcccgagtag
4380ctgggactac aggtgtgcgc caccacacca ggctaatttt tgtatttttt
gtaaagacag 4440gttttcacca cgttggccag gctggtctga actccagacc
tcaggtgatt cacctgtctc 4500agcctcccaa agtgctggga ttacaggtgt
gagccaccgt gcccggctac ttcatggatt 4560tttgattaca gattatgcct
cttacaattt ttaagaagaa tcaagtgggc tgaaggtcaa 4620tgtcaccata
agacaaaaga catttttatt agttgattct agggaattgg ccttaagggg
4680agccctttct tcctaagaga ttcttaggtg attctcactt cctcttgccc
cagtattatt 4740tttgtttttg gtatggctca ctcagatcct tttttcctcc
tatccctaag taatccgggt 4800ttctttttcc catatttaga acaaaatgta
tttatgcaga gtgtgtccaa acctcaaccc 4860aaggcctgta tacaaaataa
atcaaattaa acacatcttt actgtcttct acctctttcc 4920tgacctcaat
atatcccaac ttgcctcact ctgagaacca aggctgtccc agcacctgag
4980tcgcagatat tctactgatt tgacagaact gtgtgactat ctggaacagc
attttgatcc 5040acaatttgcc cagttacaaa gcttaaatga gctctagtgc
atgcatatat atttcaaaat 5100tccaccatga tcttccacac tctgtattgt
aaatagagcc ctgtaatgct tttacttcgt 5160atttcattgc ttgttataca
taaaaatata cttttcttct tcatgttaga aaatgcaaag 5220aataggaggg
tgggggaatc tctgggcttg gagacaggag acttgccttc ctactatggt
5280tccatcagaa tgtagactgg gacaatacaa taattcaagt ctggtttgct
catctgtaaa 5340ttgggaagaa tgtttccagc tccagaatgc taaatctcta
agtctgtggt tggcagccac 5400tattgcagca gctcttcaat gactcaatgc
agttttgcat tctccctacc ttttttttct 5460aaaaccaata aaatagatac
agcctttagg ctttctggga tttcccttag tcaagctagg 5520gtcatcctga
ctttcggcgt gaatttgcaa aacaagacct gactctgtac tcctgctcta
5580aggactgtgc atggttccaa aggcttagct tgccagcata tttgagcttt
ttccttctgt 5640tcaaactgtt ccaaaatata aaagaataaa attaattaag
ttggcactgg acttccggtg 5700gtcagtcatg tgtgtcatct gtcacgtttt
tcgggctctg gtggaaatgg atctgtctgt 5760cttctctcat aggtggtatt
cacagccaac gactccggcc cccgccgcta caccattgcc 5820gccctgctga
gcccctactc ctattccacc acggctgtcg tcaccaatcc caaggaatga
5880gggacttctc ctccagtgga cctgaaggac gagggatggg atttcatgta
accaagagta 5940ttccattttt actaaagcag tgttttcacc tcatatgcta
tgttagaagt ccaggcagag 6000acaataaaac attcctgtga aaggcacttt
tcattccact ttaacttgat tttttaaatt 6060cccttattgt cccttccaaa
aaaaagagaa tcaaaatttt acaaagaatc aaaggaattc 6120tagaaagtat
ctgggcagaa cgctaggaga gatccaaatt tccattgtct tgcaagcaaa
6180gcacgtatta aatatgatct gcagccatta aaaagacaca ttctgtaaat
gagagagcct 6240tattttcctg taaccttcag caaatagcaa aagacacatt
ccaagggccc acttctttac 6300tgtgggcact cgagataact tcgtataatg
tatgctatac gaagttatat gcatgccagt 6360agcagcaccc acgtccacct
tctgtctagt aatgtccaac acctccctca gtccaaacac 6420tgctctgcat
ccatgtggct cccatttata cctgaagcac ttgatggggc ctcaatgttt
6480tactagagcc cacccccctg caactctgag accctctgga tttgtctgtc
agtgcctcac 6540tggggcgttg gataatttct taaaaggtca agttccctca
gcagcattct ctgagcagtc 6600tgaagatgtg tgcttttcac agttcaaatc
catgtggctg tttcacccac ctgcctggcc 6660ttgggttatc tatcaggacc
tagcctagaa gcaggtgtgt ggcacttaac acctaagctg 6720agtgactaac
tgaacactca agtggatgcc atctttgtca cttcttgact gtgacacaag
6780caactcctga tgccaaagcc ctgcccaccc ctctcatgcc catatttgga
catggtacag 6840gtcctcactg gccatggtct gtgaggtcct ggtcctcttt
gacttcataa ttcctagggg 6900ccactagtat ctataagagg aagagggtgc
tggctcccag gccacagccc acaaaattcc 6960acctgctcac aggttggctg
gctcgaccca ggtggtgtcc cctgctctga gccagctccc 7020ggccaagcca
gcaccatggg aacccccaag aagaagagga aggtgcgtac cgatttaaat
7080tccaatttac tgaccgtaca ccaaaatttg cctgcattac cggtcgatgc
aacgagtgat 7140gaggttcgca agaacctgat ggacatgttc agggatcgcc
aggcgttttc tgagcatacc 7200tggaaaatgc ttctgtccgt ttgccggtcg
tgggcggcat ggtgcaagtt gaataaccgg 7260aaatggtttc ccgcagaacc
tgaagatgtt cgcgattatc ttctatatct tcaggcgcgc 7320ggtctggcag
taaaaactat ccagcaacat ttgggccagc taaacatgct tcatcgtcgg
7380tccgggctgc cacgaccaag tgacagcaat gctgtttcac tggttatgcg
gcggatccga 7440aaagaaaacg ttgatgccgg tgaacgtgca aaacaggtaa
atataaaatt tttaagtgta 7500taatgatgtt aaactactga ttctaattgt
ttgtgtattt taggctctag cgttcgaacg 7560cactgatttc gaccaggttc
gttcactcat ggaaaatagc gatcgctgcc aggatatacg 7620taatctggca
tttctgggga ttgcttataa caccctgtta cgtatagccg aaattgccag
7680gatcagggtt aaagatatct cacgtactga cggtgggaga atgttaatcc
atattggcag 7740aacgaaaacg ctggttagca ccgcaggtgt agagaaggca
cttagcctgg gggtaactaa 7800actggtcgag cgatggattt ccgtctctgg
tgtagctgat gatccgaata actacctgtt 7860ttgccgggtc agaaaaaatg
gtgttgccgc gccatctgcc accagccagc tatcaactcg 7920cgccctggaa
gggatttttg aagcaactca tcgattgatt tacggcgcta aggatgactc
7980tggtcagaga tacctggcct ggtctggaca cagtgcccgt gtcggagccg
cgcgagatat 8040ggcccgcgct ggagtttcaa taccggagat catgcaagct
ggtggctgga ccaatgtaaa 8100tattgtcatg aactatatcc gtaacctgga
tagtgaaaca ggggcaatgg tgcgcctgct 8160ggaagatggc gattaggcgg
ccggccgcta atcagccata ccacatttgt agaggtttta 8220cttgctttaa
aaaacctccc acacctcccc ctgaacctga aacataaaat gaatgcaatt
8280gttgttgtta acttgtttat tgcagcttat aatggttaca aataaagcaa
tagcatcaca 8340aatttcacaa ataaagcatt tttttcactg cattctagtt
gtggtttgtc caaactcatc 8400aatgtatctt atcatgtctg gatcccccgg
ctagagttta aacactagaa ctagtggatc 8460ccccgggatc atggcctccg
cgccgggttt tggcgcctcc cgcgggcgcc cccctcctca 8520cggcgagcgc
tgccacgtca gacgaagggc gcagcgagcg tcctgatcct tccgcccgga
8580cgctcaggac agcggcccgc tgctcataag actcggcctt agaaccccag
tatcagcaga 8640aggacatttt aggacgggac ttgggtgact ctagggcact
ggttttcttt ccagagagcg 8700gaacaggcga ggaaaagtag tcccttctcg
gcgattctgc ggagggatct ccgtggggcg 8760gtgaacgccg atgattatat
aaggacgcgc cgggtgtggc acagctagtt ccgtcgcagc 8820cgggatttgg
gtcgcggttc ttgtttgtgg atcgctgtga tcgtcacttg gtgagtagcg
8880ggctgctggg ctggccgggg ctttcgtggc cgccgggccg ctcggtggga
cggaagcgtg 8940tggagagacc gccaagggct gtagtctggg tccgcgagca
aggttgccct gaactggggg 9000ttggggggag cgcagcaaaa tggcggctgt
tcccgagtct tgaatggaag acgcttgtga 9060ggcgggctgt gaggtcgttg
aaacaaggtg gggggcatgg tgggcggcaa gaacccaagg 9120tcttgaggcc
ttcgctaatg cgggaaagct cttattcggg tgagatgggc tggggcacca
9180tctggggacc ctgacgtgaa gtttgtcact gactggagaa ctcggtttgt
cgtctgttgc 9240gggggcggca gttatggcgg tgccgttggg cagtgcaccc
gtacctttgg gagcgcgcgc 9300cctcgtcgtg tcgtgacgtc acccgttctg
ttggcttata atgcagggtg gggccacctg 9360ccggtaggtg tgcggtaggc
ttttctccgt cgcaggacgc agggttcggg cctagggtag 9420gctctcctga
atcgacaggc gccggacctc tggtgagggg agggataagt gaggcgtcag
9480tttctttggt cggttttatg tacctatctt cttaagtagc tgaagctccg
gttttgaact 9540atgcgctcgg ggttggcgag tgtgttttgt gaagtttttt
aggcaccttt tgaaatgtaa 9600tcatttgggt caatatgtaa ttttcagtgt
tagactagta aattgtccgc taaattctgg 9660ccgtttttgg cttttttgtt
agacgtgttg acaattaatc atcggcatag tatatcggca 9720tagtataata
cgacaaggtg aggaactaaa ccatgggatc ggccattgaa caagatggat
9780tgcacgcagg ttctccggcc gcttgggtgg agaggctatt cggctatgac
tgggcacaac 9840agacaatcgg ctgctctgat gccgccgtgt tccggctgtc
agcgcagggg cgcccggttc 9900tttttgtcaa gaccgacctg tccggtgccc
tgaatgaact gcaggacgag gcagcgcggc 9960tatcgtggct ggccacgacg
ggcgttcctt gcgcagctgt gctcgacgtt gtcactgaag 10020cgggaaggga
ctggctgcta ttgggcgaag tgccggggca ggatctcctg tcatctcacc
10080ttgctcctgc cgagaaagta tccatcatgg ctgatgcaat gcggcggctg
catacgcttg 10140atccggctac ctgcccattc gaccaccaag cgaaacatcg
catcgagcga gcacgtactc 10200ggatggaagc cggtcttgtc gatcaggatg
atctggacga agagcatcag gggctcgcgc 10260cagccgaact gttcgccagg
ctcaaggcgc gcatgcccga cggcgatgat ctcgtcgtga 10320cccatggcga
tgcctgcttg ccgaatatca tggtggaaaa tggccgcttt tctggattca
10380tcgactgtgg ccggctgggt gtggcggacc gctatcagga catagcgttg
gctacccgtg 10440atattgctga agagcttggc ggcgaatggg ctgaccgctt
cctcgtgctt tacggtatcg 10500ccgctcccga ttcgcagcgc atcgccttct
atcgccttct tgacgagttc ttctgagggg 10560atccgctgta agtctgcaga
aattgatgat ctattaaaca ataaagatgt ccactaaaat 10620ggaagttttt
cctgtcatac tttgttaaga agggtgagaa cagagtacct acattttgaa
10680tggaaggatt ggagctacgg gggtgggggt ggggtgggat tagataaatg
cctgctcttt 10740actgaaggct ctttactatt gctttatgat aatgtttcat
agttggatat cataatttaa 10800acaagcaaaa ccaaattaag ggccagctca
ttcctcccac tcatgatcta tagatctata 10860gatctctcgt gggatcattg
tttttctctt gattcccact ttgtggttct aagtactgtg 10920gtttccaaat
gtgtcagttt catagcctga agaacgagat cagcagcctc tgttccacat
10980acacttcatt ctcagtattg ttttgccaag ttctaattcc atcagacctc
gacctgcagc 11040ccctagataa cttcgtataa tgtatgctat acgaagttat
gctaggtaac tataacggtc 11100ctaaggtagc gagctagcga gactcagccc
aggaggacca ggatcttgcc aaagcagtag 11160catcccattt gtaccaaaac
agtgttcttg ctctataaac cgtgttagca gctcagga 11218176486DNAArtificial
SequenceSyntheticmisc_feature(1)..(100)Mouse
Sequencemisc_feature(101)..(6308)Human
Sequencemisc_feature(6309)..(6386)Cassette LoxP
Scarmisc_feature(6387)..(6486)Mouse Sequence 17atgtactttt
ggttttgttc cagagtctat caccggaaag aacaagccgg tttactctga 60cccatttcac
tgacatttct cttgtctcct ctgtgcccag ggcaccggtg aatccaagtg
120tcctctgatg gtcaaagttc tagatgctgt ccgaggcagt cctgccatca
atgtggccgt 180gcatgtgttc agaaaggctg ctgatgacac ctgggagcca
tttgcctctg ggtaagttgc 240caaagaaccc tcccacagga cttggtttta
tcttcccgtt tgcccctcac ttggtagaga 300gaggctcaca tcatctgcta
aagaatttac aagtagattg aaaaacgtag gcagaggtca 360agtatgccct
ctgaaggatg ccctcttttt gttttgctta gctaggaagt gaccaggaac
420ctgagcatca tttaggggca gacagtagag aaaagaagga atcagaactc
ctctcctcta 480gctgtggttt gcaacccttt tgggtcacag aacactttat
gtaggtgatg aaaagtaaac 540attctatgcc cagaaaaaat gcacagatac
acacacatac aaaatcatat atgtgatttt 600aggagtttca cagattccct
ggtgtccctg ggtaacacca aagctaagtg tccttgtctt 660agaattttag
gaaaaggtat aatgtgtatt aacccattaa caaaaggaaa ggaattcaga
720aatattatta accaggcatc tgtctgtagt taatatggat cacccaaaac
ccaaggcttt 780tgcctaatga acactttggg gcacctactg tgtgcaaggc
tgggggctgt caagctcagt 840taaaaaaaaa aagatagaag agatggatcc
atgaggcaaa gtacagcccc aggctaatcc 900cacgatcacc cgacttcatg
tccaagagtg gcttctcacc ttcattagcc agttcacaat 960tttcatggag
tttttctacc tgcactagca aaaacttcaa ggaaaataca tattaataaa
1020tctaagcaaa gtgaccagaa gacagagcaa tcaggagacc ctttgcatcc
agcagaagag 1080gaactgctaa gtatttacat ctccacagag aagaatttct
gttgggtttt aattgaaccc 1140caagaaccac atgattcttc aaccattatt
gggaagatca ttttcttagg tctggtttta 1200actggctttt tatttgggaa
ttcatttatg tttatataaa atgccaagca taacatgaaa 1260agtggttaca
ggactattct aagggagaga cagaatggac accaaaaata ttccaatgtt
1320cttgtgaatc ttttccttgc accaggacaa aaaaaaaaag aagtgaaaag
aagaaaggag 1380gaggggcata atcagagtca gtaaagacaa ctgctatttt
tatctatcgt agctgttgca 1440gtcaaatggg aagcaatttc caacattcaa
ctatggagct ggtacttaca tggaaataga 1500agttgcctag tgtttgttgc
tggcaaagag ttatcagaga ggttaaatat ataaaaggga 1560aaagagtcag
atacaggttc ttcttcctac tttaggtttt ccactgtgtg tgcaaatgat
1620actccctggt ggtgtgcaga tgcctcaaag ctatcctcac accacaaggg
agaggagcga 1680gatcctgctg tcctggagaa gtgcagagtt agaacagctg
tggccacttg catccaatca 1740tcaatcttga atcacaggga ctctttctta
agtaaacatt atacctggcc gggcacggtg 1800gctcacgcct gtaatcccag
cactttggga tgccaaagtg ggcatatcat ctgaggtcag 1860gagttcaaga
ccagcctggc caacatggca aaactccgtc tttatgaaaa atacaaaaat
1920tagccaggca tggtggcagg cgcctgtaat cccagctaat tgggaggctg
aggctggaga 1980atcccttgaa tctaggaggc agaggttgca gtgagctgag
atcgtgccat tgcactccag 2040cctgggtgac aagagtaaaa ctctgtctca
aaaaaaaaaa attataccta cattctcttc 2100ttatcagaga aaaaaatcta
cagtgagctt ttcaaaaagt ttttacaaac tttttgccat 2160ttaatttcag
ttaggagttt tccctacttc tgacttagtt gaggggaaat gttcataaca
2220tgtttataac atgtttatgt gtgttagttg gtgggggtgt attactttgc
catgccattt 2280gtttcctcca tgcgtaactt aatccagact ttcacacctt
ataggaaaac cagtgagtct 2340ggagagctgc atgggctcac aactgaggag
gaatttgtag aagggatata caaagtggaa 2400atagacacca aatcttactg
gaaggcactt ggcatctccc cattccatga gcatgcagag 2460gtgagtatac
agaccttcga gggttgtttt ggttttggtt tttgcttttg gcattccagg
2520aaatgcacag ttttactcag tgtaccacag aaatgtccta aggaaggtga
tgaatgacca 2580aaggttccct ttcctattat acaagaaaaa attcacaaca
ctctgagaag caaatttctt 2640tttgactttg atgaaaatcc acttagtaac
atgacttgaa cttacatgaa actactcata 2700gtctattcat tccactttat
atgaatattg atgtatctgc tgttgaaata atagtttatg 2760aggcagccct
ccagacccca cgtagagtgt atgtaacaag agatgcacca ttttatttct
2820cgaaaacccg taacattctt cattccaaaa cacatctggc ttctcggagg
tctggacaag 2880tgattcttgg caacacatac ctatagagac aataaaatca
aagtaataat ggcaacacaa 2940tagataacat ttaccaagca tacaccatgt
ggcagacaca attataagtg ttttccatat 3000ttaacctact taatcctcag
gaataagcca ctgaggtcag tcctattatt atccccatct 3060tatagatgaa
gaaaatgagg caccaggaag tcaaataact tgtcaaaggt cacaagacta
3120ggaaatacac aagtagaaat gtttacaatt aaggcccagg ctgggtttgc
cctcagttct 3180gctatgcctc gcattatgcc ccaggaaact ttttcccttg
tgaaagccaa gcttaaaaaa 3240agaaaagcca catttgtaac gtgctctgtt
cccctgccta tggtgaggat cttcaaacag 3300ttatacatgg acccagtccc
cctgccttct ccttaatttc ttaagtcatt tgaaacagat 3360ggctgtcatg
gaaatagaat ccagacatgt tggtcagagt taaagatcaa ctaattccat
3420caaaaatagc tcggcatgaa agggaactat tctctggctt agtcatggat
gagactttca 3480attgctataa agtggttcct ttattagaca atgttaccag
ggaaacaaca ggggtttgtt 3540tgacttctgg ggcccacaag tcaacaagag
agccccatct accaaggagc atgtccctga 3600ctacccctca gccagcagca
agacatggac cccagtcagg gcaggagcag ggtttcggcg 3660gcgcccagca
caagacattg cccctagagt ctcagcccct accctcgagt aatagatctg
3720cctacctgag actgttgttt gcccaagagc tgggtctcag cctgatggga
accatataaa 3780aaggttcact gacatactgc ccacatgttg ttctctttca
ttagatctta gcttccttgt 3840ctgctcttca ttcttgcagt attcattcaa
caaacattaa aaaaaaaaaa aagcattcta 3900tgtgtggaac actctgctag
atgctgtgga tttagaaatg aaaatacatc ccgacccttg 3960gaatggaagg
gaaaggactg aagtaagaca gattaagcag gaccgtcagc ccagcttgaa
4020gcccagataa atacggagaa caagagagag cgagtagtga gagatgagtc
ccaatgcctc 4080actttggtga cgggtgcgtg gtgggcttca tgcagcttct
tctgataaat gcctccttca 4140gaactggtca actctacctt ggccagtgac
ccaggtggtc atagtagatt taccaaggga 4200aaatggaaac ttttattagg
agctcttagg cctcttcact tcatggattt ttttttcctt 4260tttttttgag
atggagtttt gccctgtcac ccaggctgga atgcagtggt gcaatctcag
4320ctcactgcaa cctccgcctc ccaggttcaa gcaattctcc tgcctcagcc
tcccgagtag 4380ctgggactac aggtgtgcgc caccacacca ggctaatttt
tgtatttttt gtaaagacag 4440gttttcacca cgttggccag gctggtctga
actccagacc tcaggtgatt cacctgtctc 4500agcctcccaa agtgctggga
ttacaggtgt gagccaccgt gcccggctac ttcatggatt 4560tttgattaca
gattatgcct cttacaattt ttaagaagaa tcaagtgggc tgaaggtcaa
4620tgtcaccata agacaaaaga catttttatt agttgattct agggaattgg
ccttaagggg 4680agccctttct tcctaagaga ttcttaggtg attctcactt
cctcttgccc cagtattatt 4740tttgtttttg gtatggctca ctcagatcct
tttttcctcc tatccctaag taatccgggt 4800ttctttttcc catatttaga
acaaaatgta tttatgcaga gtgtgtccaa acctcaaccc 4860aaggcctgta
tacaaaataa atcaaattaa acacatcttt actgtcttct acctctttcc
4920tgacctcaat atatcccaac ttgcctcact ctgagaacca aggctgtccc
agcacctgag 4980tcgcagatat tctactgatt tgacagaact gtgtgactat
ctggaacagc attttgatcc 5040acaatttgcc cagttacaaa gcttaaatga
gctctagtgc atgcatatat atttcaaaat 5100tccaccatga tcttccacac
tctgtattgt aaatagagcc ctgtaatgct tttacttcgt 5160atttcattgc
ttgttataca taaaaatata cttttcttct tcatgttaga aaatgcaaag
5220aataggaggg tgggggaatc tctgggcttg gagacaggag acttgccttc
ctactatggt 5280tccatcagaa tgtagactgg gacaatacaa taattcaagt
ctggtttgct catctgtaaa 5340ttgggaagaa tgtttccagc tccagaatgc
taaatctcta agtctgtggt tggcagccac 5400tattgcagca gctcttcaat
gactcaatgc agttttgcat tctccctacc ttttttttct 5460aaaaccaata
aaatagatac agcctttagg ctttctggga tttcccttag tcaagctagg
5520gtcatcctga ctttcggcgt gaatttgcaa aacaagacct gactctgtac
tcctgctcta 5580aggactgtgc atggttccaa aggcttagct tgccagcata
tttgagcttt ttccttctgt 5640tcaaactgtt ccaaaatata aaagaataaa
attaattaag ttggcactgg acttccggtg 5700gtcagtcatg tgtgtcatct
gtcacgtttt tcgggctctg gtggaaatgg atctgtctgt 5760cttctctcat
aggtggtatt cacagccaac gactccggcc cccgccgcta caccattgcc
5820gccctgctga gcccctactc ctattccacc acggctgtcg tcaccaatcc
caaggaatga 5880gggacttctc ctccagtgga cctgaaggac gagggatggg
atttcatgta accaagagta 5940ttccattttt actaaagcag tgttttcacc
tcatatgcta tgttagaagt ccaggcagag 6000acaataaaac attcctgtga
aaggcacttt tcattccact ttaacttgat tttttaaatt 6060cccttattgt
cccttccaaa aaaaagagaa tcaaaatttt acaaagaatc aaaggaattc
6120tagaaagtat ctgggcagaa
cgctaggaga gatccaaatt tccattgtct tgcaagcaaa 6180gcacgtatta
aatatgatct gcagccatta aaaagacaca ttctgtaaat gagagagcct
6240tattttcctg taaccttcag caaatagcaa aagacacatt ccaagggccc
acttctttac 6300tgtgggcact cgagataact tcgtataatg tatgctatac
gaagttatgc taggtaacta 6360taacggtcct aaggtagcga gctagcgaga
ctcagcccag gaggaccagg atcttgccaa 6420agcagtagca tcccatttgt
accaaaacag tgttcttgct ctataaaccg tgttagcagc 6480tcagga
6486187201DNAHomo sapiens 18atggcttctc atcgtctgct cctcctctgc
cttgctggac tggtatttgt gtctgaggct 60ggccctacgg tgagtgtttc tgtgacatcc
cattcctaca tttaagattc acgctaaatg 120aagtagaagt gactccttcc
agctttgcca accagctttt attactaggg caagggtacc 180cagcatctat
ttttaatata attaattcaa acttcaaaaa gaatgaagtt ccactgagct
240tactgagctg ggacttgaac tctgagcatt ctacctcatt gctttggtgc
attaggtttg 300taatatctgg tacctctgtt tcctcagata gatgatagaa
ataaagatat gatattaagg 360aagctgttaa tactgaattt tcagaaaagt
atccctccat aaaatgtatt tgggggacaa 420actgcaggag attatattct
ggccctatag ttattcaaaa cgtatttatt gattaatctt 480taaaaggctt
agtgaacaat attctagtca gatatctaat tcttaaatcc tctagaagaa
540ttaactaata ctataaaatg ggtctggatg tagttctgac attattttat
aacaactggt 600aagagggagt gactatagca acaactaaaa tgatctcagg
aaaacctgtt tggccctatg 660tatggtacat tacatctttt cagtaattcc
actcaaatgg agacttttaa caaagcaact 720gttctcaggg gacctatttt
ctcccttaaa attcattata cacatccctg gttgatagca 780gtgtgtctgg
aggcagaaac cattcttgct ttggaaacaa ttacgtctgt gttatactga
840gtagggaagc tcattaattg tcgacactta cgttcctgat aatgggatca
gtgtgtaatt 900cttgtttcgc tccagatttc taataccaca aagaataaat
cctttcactc tgatcaattt 960tgttaacttc tcacgtgtct tctctacacc
cagggcaccg gtgaatccaa gtgtcctctg 1020atggtcaaag ttctagatgc
tgtccgaggc agtcctgcca tcaatgtggc cgtgcatgtg 1080ttcagaaagg
ctgctgatga cacctgggag ccatttgcct ctgggtaagt tgccaaagaa
1140ccctcccaca ggacttggtt ttatcttccc gtttgcccct cacttggtag
agagaggctc 1200acatcatctg ctaaagaatt tacaagtaga ttgaaaaacg
taggcagagg tcaagtatgc 1260cctctgaagg atgccctctt tttgttttgc
ttagctagga agtgaccagg aacctgagca 1320tcatttaggg gcagacagta
gagaaaagaa ggaatcagaa ctcctctcct ctagctgtgg 1380tttgcaaccc
ttttgggtca cagaacactt tatgtaggtg atgaaaagta aacattctat
1440gcccagaaaa aatgcacaga tacacacaca tacaaaatca tatatgtgat
tttaggagtt 1500tcacagattc cctggtgtcc ctgggtaaca ccaaagctaa
gtgtccttgt cttagaattt 1560taggaaaagg tataatgtgt attaacccat
taacaaaagg aaaggaattc agaaatatta 1620ttaaccaggc atctgtctgt
agttaatatg gatcacccaa aacccaaggc ttttgcctaa 1680tgaacacttt
ggggcaccta ctgtgtgcaa ggctgggggc tgtcaagctc agttaaaaaa
1740aaaaagatag aagagatgga tccatgaggc aaagtacagc cccaggctaa
tcccacgatc 1800acccgacttc atgtccaaga gtggcttctc accttcatta
gccagttcac aattttcatg 1860gagtttttct acctgcacta gcaaaaactt
caaggaaaat acatattaat aaatctaagc 1920aaagtgacca gaagacagag
caatcaggag accctttgca tccagcagaa gaggaactgc 1980taagtattta
catctccaca gagaagaatt tctgttgggt tttaattgaa ccccaagaac
2040cacatgattc ttcaaccatt attgggaaga tcattttctt aggtctggtt
ttaactggct 2100ttttatttgg gaattcattt atgtttatat aaaatgccaa
gcataacatg aaaagtggtt 2160acaggactat tctaagggag agacagaatg
gacaccaaaa atattccaat gttcttgtga 2220atcttttcct tgcaccagga
caaaaaaaaa aagaagtgaa aagaagaaag gaggaggggc 2280ataatcagag
tcagtaaaga caactgctat ttttatctat cgtagctgtt gcagtcaaat
2340gggaagcaat ttccaacatt caactatgga gctggtactt acatggaaat
agaagttgcc 2400tagtgtttgt tgctggcaaa gagttatcag agaggttaaa
tatataaaag ggaaaagagt 2460cagatacagg ttcttcttcc tactttaggt
tttccactgt gtgtgcaaat gatactccct 2520ggtggtgtgc agatgcctca
aagctatcct cacaccacaa gggagaggag cgagatcctg 2580ctgtcctgga
gaagtgcaga gttagaacag ctgtggccac ttgcatccaa tcatcaatct
2640tgaatcacag ggactctttc ttaagtaaac attatacctg gccgggcacg
gtggctcacg 2700cctgtaatcc cagcactttg ggatgccaaa gtgggcatat
catctgaggt caggagttca 2760agaccagcct ggccaacatg gcaaaactcc
gtctttatga aaaatacaaa aattagccag 2820gcatggtggc aggcgcctgt
aatcccagct aattgggagg ctgaggctgg agaatccctt 2880gaatctagga
ggcagaggtt gcagtgagct gagatcgtgc cattgcactc cagcctgggt
2940gacaagagta aaactctgtc tcaaaaaaaa aaaattatac ctacattctc
ttcttatcag 3000agaaaaaaat ctacagtgag cttttcaaaa agtttttaca
aactttttgc catttaattt 3060cagttaggag ttttccctac ttctgactta
gttgagggga aatgttcata acatgtttat 3120aacatgttta tgtgtgttag
ttggtggggg tgtattactt tgccatgcca tttgtttcct 3180ccatgcgtaa
cttaatccag actttcacac cttataggaa aaccagtgag tctggagagc
3240tgcatgggct cacaactgag gaggaatttg tagaagggat atacaaagtg
gaaatagaca 3300ccaaatctta ctggaaggca cttggcatct ccccattcca
tgagcatgca gaggtgagta 3360tacagacctt cgagggttgt tttggttttg
gtttttgctt ttggcattcc aggaaatgca 3420cagttttact cagtgtacca
cagaaatgtc ctaaggaagg tgatgaatga ccaaaggttc 3480cctttcctat
tatacaagaa aaaattcaca acactctgag aagcaaattt ctttttgact
3540ttgatgaaaa tccacttagt aacatgactt gaacttacat gaaactactc
atagtctatt 3600cattccactt tatatgaata ttgatgtatc tgctgttgaa
ataatagttt atgaggcagc 3660cctccagacc ccacgtagag tgtatgtaac
aagagatgca ccattttatt tctcgaaaac 3720ccgtaacatt cttcattcca
aaacacatct ggcttctcgg aggtctggac aagtgattct 3780tggcaacaca
tacctataga gacaataaaa tcaaagtaat aatggcaaca caatagataa
3840catttaccaa gcatacacca tgtggcagac acaattataa gtgttttcca
tatttaacct 3900acttaatcct caggaataag ccactgaggt cagtcctatt
attatcccca tcttatagat 3960gaagaaaatg aggcaccagg aagtcaaata
acttgtcaaa ggtcacaaga ctaggaaata 4020cacaagtaga aatgtttaca
attaaggccc aggctgggtt tgccctcagt tctgctatgc 4080ctcgcattat
gccccaggaa actttttccc ttgtgaaagc caagcttaaa aaaagaaaag
4140ccacatttgt aacgtgctct gttcccctgc ctatggtgag gatcttcaaa
cagttataca 4200tggacccagt ccccctgcct tctccttaat ttcttaagtc
atttgaaaca gatggctgtc 4260atggaaatag aatccagaca tgttggtcag
agttaaagat caactaattc catcaaaaat 4320agctcggcat gaaagggaac
tattctctgg cttagtcatg gatgagactt tcaattgcta 4380taaagtggtt
cctttattag acaatgttac cagggaaaca acaggggttt gtttgacttc
4440tggggcccac aagtcaacaa gagagcccca tctaccaagg agcatgtccc
tgactacccc 4500tcagccagca gcaagacatg gaccccagtc agggcaggag
cagggtttcg gcggcgccca 4560gcacaagaca ttgcccctag agtctcagcc
cctaccctcg agtaatagat ctgcctacct 4620gagactgttg tttgcccaag
agctgggtct cagcctgatg ggaaccatat aaaaaggttc 4680actgacatac
tgcccacatg ttgttctctt tcattagatc ttagcttcct tgtctgctct
4740tcattcttgc agtattcatt caacaaacat taaaaaaaaa aaaaagcatt
ctatgtgtgg 4800aacactctgc tagatgctgt ggatttagaa atgaaaatac
atcccgaccc ttggaatgga 4860agggaaagga ctgaagtaag acagattaag
caggaccgtc agcccagctt gaagcccaga 4920taaatacgga gaacaagaga
gagcgagtag tgagagatga gtcccaatgc ctcactttgg 4980tgacgggtgc
gtggtgggct tcatgcagct tcttctgata aatgcctcct tcagaactgg
5040tcaactctac cttggccagt gacccaggtg gtcatagtag atttaccaag
ggaaaatgga 5100aacttttatt aggagctctt aggcctcttc acttcatgga
tttttttttc cttttttttt 5160gagatggagt tttgccctgt cacccaggct
ggaatgcagt ggtgcaatct cagctcactg 5220caacctccgc ctcccaggtt
caagcaattc tcctgcctca gcctcccgag tagctgggac 5280tacaggtgtg
cgccaccaca ccaggctaat ttttgtattt tttgtaaaga caggttttca
5340ccacgttggc caggctggtc tgaactccag acctcaggtg attcacctgt
ctcagcctcc 5400caaagtgctg ggattacagg tgtgagccac cgtgcccggc
tacttcatgg atttttgatt 5460acagattatg cctcttacaa tttttaagaa
gaatcaagtg ggctgaaggt caatgtcacc 5520ataagacaaa agacattttt
attagttgat tctagggaat tggccttaag gggagccctt 5580tcttcctaag
agattcttag gtgattctca cttcctcttg ccccagtatt atttttgttt
5640ttggtatggc tcactcagat ccttttttcc tcctatccct aagtaatccg
ggtttctttt 5700tcccatattt agaacaaaat gtatttatgc agagtgtgtc
caaacctcaa cccaaggcct 5760gtatacaaaa taaatcaaat taaacacatc
tttactgtct tctacctctt tcctgacctc 5820aatatatccc aacttgcctc
actctgagaa ccaaggctgt cccagcacct gagtcgcaga 5880tattctactg
atttgacaga actgtgtgac tatctggaac agcattttga tccacaattt
5940gcccagttac aaagcttaaa tgagctctag tgcatgcata tatatttcaa
aattccacca 6000tgatcttcca cactctgtat tgtaaataga gccctgtaat
gcttttactt cgtatttcat 6060tgcttgttat acataaaaat atacttttct
tcttcatgtt agaaaatgca aagaatagga 6120gggtggggga atctctgggc
ttggagacag gagacttgcc ttcctactat ggttccatca 6180gaatgtagac
tgggacaata caataattca agtctggttt gctcatctgt aaattgggaa
6240gaatgtttcc agctccagaa tgctaaatct ctaagtctgt ggttggcagc
cactattgca 6300gcagctcttc aatgactcaa tgcagttttg cattctccct
accttttttt tctaaaacca 6360ataaaataga tacagccttt aggctttctg
ggatttccct tagtcaagct agggtcatcc 6420tgactttcgg cgtgaatttg
caaaacaaga cctgactctg tactcctgct ctaaggactg 6480tgcatggttc
caaaggctta gcttgccagc atatttgagc tttttccttc tgttcaaact
6540gttccaaaat ataaaagaat aaaattaatt aagttggcac tggacttccg
gtggtcagtc 6600atgtgtgtca tctgtcacgt ttttcgggct ctggtggaaa
tggatctgtc tgtcttctct 6660cataggtggt attcacagcc aacgactccg
gcccccgccg ctacaccatt gccgccctgc 6720tgagccccta ctcctattcc
accacggctg tcgtcaccaa tcccaaggaa tgagggactt 6780ctcctccagt
ggacctgaag gacgagggat gggatttcat gtaaccaaga gtattccatt
6840tttactaaag cagtgttttc acctcatatg ctatgttaga agtccaggca
gagacaataa 6900aacattcctg tgaaaggcac ttttcattcc actttaactt
gattttttaa attcccttat 6960tgtcccttcc aaaaaaaaga gaatcaaaat
tttacaaaga atcaaaggaa ttctagaaag 7020tatctgggca gaacgctagg
agagatccaa atttccattg tcttgcaagc aaagcacgta 7080ttaaatatga
tctgcagcca ttaaaaagac acattctgta aatgagagag ccttattttc
7140ctgtaacctt cagcaaatag caaaagacac attccaaggg cccacttctt
tactgtgggc 7200a 7201196208DNAHomo sapiens 19ggcaccggtg aatccaagtg
tcctctgatg gtcaaagttc tagatgctgt ccgaggcagt 60cctgccatca atgtggccgt
gcatgtgttc agaaaggctg ctgatgacac ctgggagcca 120tttgcctctg
ggtaagttgc caaagaaccc tcccacagga cttggtttta tcttcccgtt
180tgcccctcac ttggtagaga gaggctcaca tcatctgcta aagaatttac
aagtagattg 240aaaaacgtag gcagaggtca agtatgccct ctgaaggatg
ccctcttttt gttttgctta 300gctaggaagt gaccaggaac ctgagcatca
tttaggggca gacagtagag aaaagaagga 360atcagaactc ctctcctcta
gctgtggttt gcaacccttt tgggtcacag aacactttat 420gtaggtgatg
aaaagtaaac attctatgcc cagaaaaaat gcacagatac acacacatac
480aaaatcatat atgtgatttt aggagtttca cagattccct ggtgtccctg
ggtaacacca 540aagctaagtg tccttgtctt agaattttag gaaaaggtat
aatgtgtatt aacccattaa 600caaaaggaaa ggaattcaga aatattatta
accaggcatc tgtctgtagt taatatggat 660cacccaaaac ccaaggcttt
tgcctaatga acactttggg gcacctactg tgtgcaaggc 720tgggggctgt
caagctcagt taaaaaaaaa aagatagaag agatggatcc atgaggcaaa
780gtacagcccc aggctaatcc cacgatcacc cgacttcatg tccaagagtg
gcttctcacc 840ttcattagcc agttcacaat tttcatggag tttttctacc
tgcactagca aaaacttcaa 900ggaaaataca tattaataaa tctaagcaaa
gtgaccagaa gacagagcaa tcaggagacc 960ctttgcatcc agcagaagag
gaactgctaa gtatttacat ctccacagag aagaatttct 1020gttgggtttt
aattgaaccc caagaaccac atgattcttc aaccattatt gggaagatca
1080ttttcttagg tctggtttta actggctttt tatttgggaa ttcatttatg
tttatataaa 1140atgccaagca taacatgaaa agtggttaca ggactattct
aagggagaga cagaatggac 1200accaaaaata ttccaatgtt cttgtgaatc
ttttccttgc accaggacaa aaaaaaaaag 1260aagtgaaaag aagaaaggag
gaggggcata atcagagtca gtaaagacaa ctgctatttt 1320tatctatcgt
agctgttgca gtcaaatggg aagcaatttc caacattcaa ctatggagct
1380ggtacttaca tggaaataga agttgcctag tgtttgttgc tggcaaagag
ttatcagaga 1440ggttaaatat ataaaaggga aaagagtcag atacaggttc
ttcttcctac tttaggtttt 1500ccactgtgtg tgcaaatgat actccctggt
ggtgtgcaga tgcctcaaag ctatcctcac 1560accacaaggg agaggagcga
gatcctgctg tcctggagaa gtgcagagtt agaacagctg 1620tggccacttg
catccaatca tcaatcttga atcacaggga ctctttctta agtaaacatt
1680atacctggcc gggcacggtg gctcacgcct gtaatcccag cactttggga
tgccaaagtg 1740ggcatatcat ctgaggtcag gagttcaaga ccagcctggc
caacatggca aaactccgtc 1800tttatgaaaa atacaaaaat tagccaggca
tggtggcagg cgcctgtaat cccagctaat 1860tgggaggctg aggctggaga
atcccttgaa tctaggaggc agaggttgca gtgagctgag 1920atcgtgccat
tgcactccag cctgggtgac aagagtaaaa ctctgtctca aaaaaaaaaa
1980attataccta cattctcttc ttatcagaga aaaaaatcta cagtgagctt
ttcaaaaagt 2040ttttacaaac tttttgccat ttaatttcag ttaggagttt
tccctacttc tgacttagtt 2100gaggggaaat gttcataaca tgtttataac
atgtttatgt gtgttagttg gtgggggtgt 2160attactttgc catgccattt
gtttcctcca tgcgtaactt aatccagact ttcacacctt 2220ataggaaaac
cagtgagtct ggagagctgc atgggctcac aactgaggag gaatttgtag
2280aagggatata caaagtggaa atagacacca aatcttactg gaaggcactt
ggcatctccc 2340cattccatga gcatgcagag gtgagtatac agaccttcga
gggttgtttt ggttttggtt 2400tttgcttttg gcattccagg aaatgcacag
ttttactcag tgtaccacag aaatgtccta 2460aggaaggtga tgaatgacca
aaggttccct ttcctattat acaagaaaaa attcacaaca 2520ctctgagaag
caaatttctt tttgactttg atgaaaatcc acttagtaac atgacttgaa
2580cttacatgaa actactcata gtctattcat tccactttat atgaatattg
atgtatctgc 2640tgttgaaata atagtttatg aggcagccct ccagacccca
cgtagagtgt atgtaacaag 2700agatgcacca ttttatttct cgaaaacccg
taacattctt cattccaaaa cacatctggc 2760ttctcggagg tctggacaag
tgattcttgg caacacatac ctatagagac aataaaatca 2820aagtaataat
ggcaacacaa tagataacat ttaccaagca tacaccatgt ggcagacaca
2880attataagtg ttttccatat ttaacctact taatcctcag gaataagcca
ctgaggtcag 2940tcctattatt atccccatct tatagatgaa gaaaatgagg
caccaggaag tcaaataact 3000tgtcaaaggt cacaagacta ggaaatacac
aagtagaaat gtttacaatt aaggcccagg 3060ctgggtttgc cctcagttct
gctatgcctc gcattatgcc ccaggaaact ttttcccttg 3120tgaaagccaa
gcttaaaaaa agaaaagcca catttgtaac gtgctctgtt cccctgccta
3180tggtgaggat cttcaaacag ttatacatgg acccagtccc cctgccttct
ccttaatttc 3240ttaagtcatt tgaaacagat ggctgtcatg gaaatagaat
ccagacatgt tggtcagagt 3300taaagatcaa ctaattccat caaaaatagc
tcggcatgaa agggaactat tctctggctt 3360agtcatggat gagactttca
attgctataa agtggttcct ttattagaca atgttaccag 3420ggaaacaaca
ggggtttgtt tgacttctgg ggcccacaag tcaacaagag agccccatct
3480accaaggagc atgtccctga ctacccctca gccagcagca agacatggac
cccagtcagg 3540gcaggagcag ggtttcggcg gcgcccagca caagacattg
cccctagagt ctcagcccct 3600accctcgagt aatagatctg cctacctgag
actgttgttt gcccaagagc tgggtctcag 3660cctgatggga accatataaa
aaggttcact gacatactgc ccacatgttg ttctctttca 3720ttagatctta
gcttccttgt ctgctcttca ttcttgcagt attcattcaa caaacattaa
3780aaaaaaaaaa aagcattcta tgtgtggaac actctgctag atgctgtgga
tttagaaatg 3840aaaatacatc ccgacccttg gaatggaagg gaaaggactg
aagtaagaca gattaagcag 3900gaccgtcagc ccagcttgaa gcccagataa
atacggagaa caagagagag cgagtagtga 3960gagatgagtc ccaatgcctc
actttggtga cgggtgcgtg gtgggcttca tgcagcttct 4020tctgataaat
gcctccttca gaactggtca actctacctt ggccagtgac ccaggtggtc
4080atagtagatt taccaaggga aaatggaaac ttttattagg agctcttagg
cctcttcact 4140tcatggattt ttttttcctt tttttttgag atggagtttt
gccctgtcac ccaggctgga 4200atgcagtggt gcaatctcag ctcactgcaa
cctccgcctc ccaggttcaa gcaattctcc 4260tgcctcagcc tcccgagtag
ctgggactac aggtgtgcgc caccacacca ggctaatttt 4320tgtatttttt
gtaaagacag gttttcacca cgttggccag gctggtctga actccagacc
4380tcaggtgatt cacctgtctc agcctcccaa agtgctggga ttacaggtgt
gagccaccgt 4440gcccggctac ttcatggatt tttgattaca gattatgcct
cttacaattt ttaagaagaa 4500tcaagtgggc tgaaggtcaa tgtcaccata
agacaaaaga catttttatt agttgattct 4560agggaattgg ccttaagggg
agccctttct tcctaagaga ttcttaggtg attctcactt 4620cctcttgccc
cagtattatt tttgtttttg gtatggctca ctcagatcct tttttcctcc
4680tatccctaag taatccgggt ttctttttcc catatttaga acaaaatgta
tttatgcaga 4740gtgtgtccaa acctcaaccc aaggcctgta tacaaaataa
atcaaattaa acacatcttt 4800actgtcttct acctctttcc tgacctcaat
atatcccaac ttgcctcact ctgagaacca 4860aggctgtccc agcacctgag
tcgcagatat tctactgatt tgacagaact gtgtgactat 4920ctggaacagc
attttgatcc acaatttgcc cagttacaaa gcttaaatga gctctagtgc
4980atgcatatat atttcaaaat tccaccatga tcttccacac tctgtattgt
aaatagagcc 5040ctgtaatgct tttacttcgt atttcattgc ttgttataca
taaaaatata cttttcttct 5100tcatgttaga aaatgcaaag aataggaggg
tgggggaatc tctgggcttg gagacaggag 5160acttgccttc ctactatggt
tccatcagaa tgtagactgg gacaatacaa taattcaagt 5220ctggtttgct
catctgtaaa ttgggaagaa tgtttccagc tccagaatgc taaatctcta
5280agtctgtggt tggcagccac tattgcagca gctcttcaat gactcaatgc
agttttgcat 5340tctccctacc ttttttttct aaaaccaata aaatagatac
agcctttagg ctttctggga 5400tttcccttag tcaagctagg gtcatcctga
ctttcggcgt gaatttgcaa aacaagacct 5460gactctgtac tcctgctcta
aggactgtgc atggttccaa aggcttagct tgccagcata 5520tttgagcttt
ttccttctgt tcaaactgtt ccaaaatata aaagaataaa attaattaag
5580ttggcactgg acttccggtg gtcagtcatg tgtgtcatct gtcacgtttt
tcgggctctg 5640gtggaaatgg atctgtctgt cttctctcat aggtggtatt
cacagccaac gactccggcc 5700cccgccgcta caccattgcc gccctgctga
gcccctactc ctattccacc acggctgtcg 5760tcaccaatcc caaggaatga
gggacttctc ctccagtgga cctgaaggac gagggatggg 5820atttcatgta
accaagagta ttccattttt actaaagcag tgttttcacc tcatatgcta
5880tgttagaagt ccaggcagag acaataaaac attcctgtga aaggcacttt
tcattccact 5940ttaacttgat tttttaaatt cccttattgt cccttccaaa
aaaaagagaa tcaaaatttt 6000acaaagaatc aaaggaattc tagaaagtat
ctgggcagaa cgctaggaga gatccaaatt 6060tccattgtct tgcaagcaaa
gcacgtatta aatatgatct gcagccatta aaaagacaca 6120ttctgtaaat
gagagagcct tattttcctg taaccttcag caaatagcaa aagacacatt
6180ccaagggccc acttctttac tgtgggca 6208208300DNAMus musculus
20atggcttccc ttcgactctt cctcctttgc ctcgctggac tggtatttgt gtctgaagct
60ggccccgcgg tgagtgatcc tgtgagcgat ccagacatgg cagttagacc ttagataaag
120aagaagtgcc ttcttccaga tgtgagaact agagtactca gactctatat
ttaccattag 180actccaaaga gaagagctgg agtgcctctg gctcttcctt
ctattgcttt agcgcattgg 240gtctgtagtg ctcagtctct ggtgtcctta
gataataaag atatgagatt aacatagaaa 300taaagatata aaagggctgg
atgtatagtt tagtggtcca gtgtatgcct agtatgtgaa 360aagccttctg
ttcaacctct agcaatagaa aaacaagata tattctcggt ggggctgtta
420atattgaatt ctcataaaat ctttaatata tttagtatgc ctattatgtt
gttatatttt 480agttctttag ctaatcaaaa tgcattattg atctttcttt
gtcttttttt ggccaacact 540ctattccagt ctttgaaaaa gtcctttaaa
agagttaatc agtataatta aatgagtcag 600gaagtatgtg agggttattt
tacaaccaga gggaattact atagcaacag ctgattagaa 660tgatctcaag
aaaaagccca ttctgtcttt ttgcaccatg cacctttcag tggctccatt
720cagatggaga ggcaaacaga gcaatggctc tcagagggcc tattttccct
ttgaacattc 780attatccata tccctggtgc acagcagtgc atctgggggc
agaaactgtt cttgctttgg 840aaacaatgct gtctatgtca tactggataa
agaagctcat taattgtcaa cacttatgtt 900atcataatgg gatcagcatg
tacttttggt tttgttccag agtctatcac cggaaagaac 960aagccggttt
actctgaccc atttcactga catttctctt gtctcctctg tgcccagggt
1020gctggagaat ccaaatgtcc tctgatggtc aaagtcctgg atgctgtccg
aggcagccct 1080gctgtagacg tggctgtaaa
agtgttcaaa aagacctctg agggatcctg ggagcccttt 1140gcctctgggt
aagcttgtag aaagcccacc atgggaccgg ttccaggttc ccatttgctc
1200ttattcgtgt tagattcaga cacacacaac ttaccagcta gagggctcag
agagagggct 1260caggggcgaa gggcacgtat tgctcttgta agagacacag
gtttaattcc tagcaccaga 1320atggcagctc ataaccatct gaaactcaca
gtcttaggag atctgggtat ctgacattct 1380cttctaccca ccatgtgtgt
ggtgcacaaa ttcacatgca ggcatcaaat cttataaaca 1440acaacaaaaa
accaacaaac ctggtagcaa aagaagatta gaaggttaaa catatgagcc
1500gagagctttt gttttgtttt gttttgtttt gttttgttta catttcaaat
gttatcccct 1560ttctcggtcc ccctccccaa accctctacc ccattctctc
ctccccttct tctatgaggg 1620tgttccccac caacccactc ccaccttcct
gctctcgaat tcccctatac tgggacatca 1680agccttcaca gaatcaaggg
cctctcctcc cattgatgcc cgacaatgtc atcctctgct 1740acctatgtgg
ctggagccat gggtcccttc atgtatcctc cttggttggt ggtttagtct
1800ctgggaggtc tgggggatct ggttgattga tattattgtt cttcctatga
gattgcaaac 1860cccttcagct ccttcggtcc tttaactcct ccactgggga
ccccgagctc agtccaatgg 1920ttggctgtga gcatccacca gcagaggcct
tttttttttt ttttaacaaa gctgctttat 1980tatgttgctt agagcatgac
caggaaccag agcacagtcc aagactgaag ggaggaaaag 2040ggggggagtc
aataacccca ctgtttcata gtggtttgca acccttttat atcacagccc
2100actttaggca aataatgaaa attatagtct ccagggacag agaagatggt
gcaggaagtg 2160aagtgcctgc tcagaaaatg ggggcttgaa tgtgagttcc
cagactctgt gtaagatgcc 2220cagcatcgaa gtgcatgctt ataacaccag
cctggaggta gaagcttaga aacaggggta 2280ccctgaagtt gcttgttcac
cagtgtccct gaatgggtag gtgcatgttt ggtgagagac 2340cctgtctcaa
aaatcaaggt gtaggataat tgaaaatacc tagctttgag cttagatcat
2400gcaaatgtgt acacacactc acacacacca cacacacaaa aaaatgcaga
gacagagaga 2460tacagagaga cagagagata cagagacaga gacagagaga
aaaggagaaa gtaaaaaaca 2520aataatttaa agacccatgg ccacaaagag
gctcaaagac aagcacgtat aaaaccatac 2580acatgtaatt ttaggagttt
tcagattccc tggtacccgt gggtgatgca caagctttga 2640atcccagtct
taaaatctta cgaagaacgt gttcgtgtgt gctaatttat tgatgagagg
2700aaaggaattg acaaagtgcc cttccggagc ttcctgcatt acccagactc
agggtttttt 2760taaatgtaca ctcagaacag agtagctctg tgcaagggta
gcaaccacga agcttaataa 2820gaaacatatc gtgagagatc tgcaaggcaa
atctaggggc tgaccaatct cacagtcacc 2880cactagcatg tcaacacaac
ttcccacctg tgctagccac ttagcaattt tgtgttgttc 2940tgttttgttt
ttgtttttaa caaagcaatt tcaaagagat ttctaattca tctaaacaaa
3000caaaccaaaa ggaaaacagc aaagacgccc tgagcactta gcagagcagc
tatgcagtta 3060tgactcctgg gtggagactt tatatcaggc ttcaactgaa
tacctagaac ctactagtgc 3120tcttcatcaa tccttgggaa ggtcattttc
ttttggtgct gttttgagtt tctatttgtt 3180aatgtcttca taattataca
cgtgttgagc acagcatgca aagtgattag gggaatctag 3240ttggagtgga
atggataccc aaatattcag actttcttgt gactcttctt tcttgtaccc
3300acatcaaaaa aaaaaaaaat ggagatgaga catggtcaga gtcactaaaa
ccagctgcta 3360cttttaatta cgtggggagc agtttctaac attgccatta
ttgaactgat gctgcctggg 3420tggaaatgga aatcacttag tatttcttgt
tggcaaagaa ttactgaatg gattaaattt 3480ccaaagggag aagtcagtta
caagtctttt ctttgtttat taggctttct gctatgataa 3540attacactac
ttccagaagt tacccttagg ccatgggaca ctggactatc actctgctgt
3600cacaagagat tacagagtta gtcaaggcag cttgtgacac cttcagggac
tgtcataaac 3660ttccagcaag tcattaatcc tgaatgcaat actgtgtgtg
tgtgtctatg tgtgtttgta 3720tgtctgtgtg tgtcttatgt ctgtgtctct
gtgtgtgtgt gtgtttgtgt gtgtgtgtgt 3780atgtatgcct gtgtgtgtct
tatgtctgtg tttgtgtgtc tgtgtgtgtc ttatgtctgt 3840gtttgtatgt
ctgtgtgtgt ctgtgtgtgt cttatgtctg tgtctctgtg tgtgtgtgtg
3900tgtatgtatg tatgtatgta tgtatgtgta tgtgtttgca tctctctgtg
tgtctgcgct 3960tatatatttg tgtatgtgtt tatgtgttcg cctttgtgcg
ttgttgggga ttgaatccag 4020gggaatacaa atgttaagaa agaacgttac
cactaagctt cacctgtagg ccttaaagct 4080tttctttctt ttaaaaattg
taattaattc attttcagtc aggatctcca cacctcgtcc 4140ctgctgctct
agaactcact atttaaacac aatcgccctc aaacctgcag caaccctccc
4200gcctctaccc tgcgagcact agaataataa caggtgaccc cacacgccta
gattaagacc 4260tttaaggtaa acattttact atattttagt ctcataagac
aagatgctac aataaagctg 4320tacataaagt tccctcgaat ttcttgctat
tttaactcaa acataaggat ttcctccttt 4380ttgattcagg taacagaaaa
aatacacagg tacatacatg tacacacatg aacacacacg 4440catcacaacc
acatatgcgc acgcttgtgt gatctatcat ttaccatgcc actgaactct
4500tctttcccca taaattcctc tggacttgtg tgccctccag gaagaccgcg
gagtctggag 4560agctgcacgg gctcaccaca gatgagaagt ttgtagaagg
agtgtacaga gtagaactgg 4620acaccaaatc gtactggaag acacttggca
tttccccgtt ccatgaattc gcggatgtaa 4680gtggacacac caagttgttt
ggattttgtt tttagtctca ggaaattccc ttcgctcttg 4740ctgtacgatg
ggcatgagtg gaaagtagat tccacagcca gaatccacag tgctgggaaa
4800gcaagccttc tgaatttttc taaaactcat ttagcaacat ggcctgaacc
tgttcacact 4860gcttatggtc agctaactat atttatgtaa atattcattt
ctctgttgag gaaatgttag 4920tatttgcttt tgaggcaacc tccagatacc
atggagggca tgtcatagtc aaagagaggg 4980ctccctatgg tatttctcta
aattctggca tttcctttat tccaaagcac atctagtgtc 5040cccagaagtt
tgggtagaca attcttggca acacagagaa ttacaacatg ttcaaaaccc
5100aacagcttaa tatctaaatc atcaagcaaa catcacatgg caaagggatt
tctgaatcaa 5160aactgtttca tccttatgat caacctatgg aggtctagcc
tcgacttaca cccattttac 5220caataagcta agagaagcta agttcctcat
caaggacaca aggctagcat gtgtgagcaa 5280gtgacagagt tgccctctat
gttggttagt gtgccttagc cagtgtctca gtaagaaatg 5340gagctaaatc
aaaacccaag gccaacagcc aaaggcacat gagtaacctt tgcttggcac
5400tgggctcagt ttccctggct cctctcagtc ctcagttcac agaggcagct
gtcatgcaaa 5460tagaatccaa gcttgttggt cagacctgga gataacaaat
tccatcaaaa atagctcctc 5520atgtgaccta gtttgctgtc tgttgctatg
atacacacca tgaccgaaaa gcaaccctgg 5580ggagagaagg gtttatttca
tcttacagct tacagttcac catggaggaa agccaggtgg 5640gaacctggaa
gtggaaattg aagcagagac cagaaaggaa tgctgtttac tggctggctt
5700agctcctttt cttatacagc ttaggtctat gtgcccaggg gatggtactg
ccgagcatag 5760gctgagcccg cctacatcaa ccattagtca aaaaaaggtc
catagacttg cctacaggcc 5820aatctcatgg aggcaatacc ccagtggagg
gtccctcttc gcaggttact ctagtttgtg 5880tcaagttgac aaaacctaac
cacaaagcac aaacagggtc tgcccttgtg gcttagccat 5940ggatgacact
ctcagatgat ggtgttacca gacaaaccag aggggctcac caagagtctg
6000ccacctacca aggtagtact ctactcctca ctgggcacca acacccatat
tagctgggcc 6060agtacaggac ccttgctgtt tcctgcatga attgtccata
gaccctgggt ctcagcctgc 6120cgggagtacc tgtaagtagt cgcctcaaac
acattattcc tgttggaaga cttgtctgat 6180tctcttttag aactcaatca
acaaacgttt ttattttgtt ttggcttttt ggagacaaga 6240tctctcatag
gccagcctga cttgaatgta gctgaggatg acctgtgctg ctaatcttct
6300cgcctcttcc tcccaagtgg taggataata ggcataagac accacagcag
ttttactcca 6360taccagggct ctgaacccag actttaaaca ctctatcaac
tgattcacat tcccacccca 6420tcattcaaca aacatttgaa aaataaaacc
cttctgcctt gagcactctg ctaaatacag 6480cctttgagtg cggagtattt
cctcacaacc agggtccaag atgaccccat catacatacc 6540acggaaaatt
aggagatgtt tttaggtctc tttgcttggg gtaattttta tgtgtgtgtg
6600tacacagccc tgtgcgtgtg tgtgtgtgtg tgtgtgtgtg tgtacaggca
cacacgtgta 6660tgcatgtaga ggctacataa aaaccttagg tgtcattctc
aggcactctg ttcacccctt 6720cacacagccc gaacacacaa aatttgaggc
attagcctgg agctcaccag ttaggctaga 6780ctgacttgcc agcagacccc
aggctgtctc catctcccca gctctgggat tacaaactct 6840atcataccag
acatttttat acatattctg agcataaaat tcatgtcttc aggctaacaa
6900gtcaagagct taaatgactg agctctctta cgtggtggat tttttttaaa
actacataat 6960atcttttttt tttttttcac ttctggggaa gaaacaaatg
agcctgagtg acaatgcgac 7020agaaaagaaa ttttgaggag tgtgtgtgtc
tgtgtgtgtg gtggcacatg cctctcatct 7080aatgctagag gctacagtag
aatgctcctg aattagtggc cagccaaggc caagggctag 7140ggttgtaact
cagtggcaga gggcttgcct agcattcgca ggatttgatc catagcgcta
7200taaataataa taaataaata caacagtcta agatgattct ccctttcatt
tatctggatg 7260ttatttttgt gttagtttta ctctgtcatc caatcattgt
ttgccctata tttggacatt 7320taaaaaaaat ctttattcca agtgtgttca
aagctgtatc caaaacctgt ccaccaaatg 7380agtccaatga catacatctt
ctatattacc atctgttcca gatttggctg actcccggca 7440cctgggctgt
tgctgcaccc atgtctcaga tagtctagtg atttgagaag tgactagtaa
7500ttgcaaaatc cagactttgt ccagaaactt ctatgagctc caaaactttc
atttacattt 7560ctgccagcca caaaccgctt gtgttgtgga gagaaccctg
tgatgtcttc ccacagcatc 7620tcagccttgt ttcttccctt aaaatattca
tcttttcaca ttagaacatg caaagggaca 7680gtgggagcga aacccctgga
ctgggacgca cgaagccttc ctttctggtc aggctctcac 7740tgtagaaact
taggccggtt tcagcatgca gtctgctgga gaatggctcc tgccaacatt
7800ccaggtctgg aagtttgtag tggagttgtt gataaccact gttcgccaca
ggtcttttgt 7860ttgtgggtgt cagtgtttct actctcctga cttttatctg
aacccaagaa agggaacaat 7920agccttcaag ctctctgtga ctctgatctg
accagggcca cccacactgc agaaggaaac 7980ttgcaaagag agacctgcaa
ttctctaaga gctccacaca gctccaaaga cttaggcagc 8040atattttaat
ctaattattc gtcccccaac cccaccccag aggacagtta gacaataaaa
8100ggaagattac cagcttagca tcctgtgaac actttgtctg cagctcctac
ctctgggctc 8160tgttagaact agctgtctct cctctctcct aggtggtttt
cacagccaac gactctggcc 8220atcgccacta caccatcgca gccctgctca
gcccatactc ctacagcacc acggctgtcg 8280tcagcaaccc ccagaattga
83002124DNAArtificial SequenceSynthetic 21cacagacaat cagacgtacc
agta 242220DNAArtificial SequenceSynthetic 22ccagctttgc cagtttacga
202318DNAArtificial SequenceSynthetic 23ttggacggtt gccctctt
182422DNAArtificial SequenceSynthetic 24gatggcttcc cttcgactct tc
222525DNAArtificial SequenceSynthetic 25cactgacatt tctcttgtct cctct
252621DNAArtificial SequenceSynthetic 26gggctcacca cagatgagaa g
212720DNAArtificial SequenceSynthetic 27cactgttcgc cacaggtctt
202820DNAArtificial SequenceSynthetic 28gctcagccca tactcctaca
202918DNAArtificial SequenceSynthetic 29gcccaggagg accaggat
183020DNAArtificial SequenceSynthetic 30ggcaacttgc ttgaggaaga
203120DNAArtificial SequenceSynthetic 31gcagcaaccc agcttcactt
203219DNAArtificial SequenceSynthetic 32actgagctgg gacttgaac
193319DNAArtificial SequenceSynthetic 33tgcctcactc tgagaacca
193419DNAArtificial SequenceSynthetic 34ggtggagagg ctattcggc
193518DNAArtificial SequenceSynthetic 35ggccgtgcat gtgttcag
183623DNAArtificial SequenceSynthetic 36ggttcccatt tgctcttatt cgt
233723DNAArtificial SequenceSynthetic 37cccacactgc agaaggaaac ttg
233823DNAArtificial SequenceSynthetic 38ggttcccatt tgctcttatt cgt
233922DNAArtificial SequenceSynthetic 39ccagcttagc atcctgtgaa ca
224020DNAArtificial SequenceSynthetic 40ggcaacttgc ttgaggaaga
204122DNAArtificial SequenceSynthetic 41tgtggagttc agtagtgtgg ag
224225DNAArtificial SequenceSynthetic 42cactgacatt tctcttgtct cctct
254323DNAArtificial SequenceSynthetic 43gggacatctc ggtttcctga ctt
234422DNAArtificial SequenceSynthetic 44tccacactac tgaactccac aa
224521DNAArtificial SequenceSynthetic 45cggaacactc gctctacgaa a
214618DNAArtificial SequenceSynthetic 46gggccagctt cagacaca
184722DNAArtificial SequenceSynthetic 47cccagggtgc tggagaatcc aa
224822DNAArtificial SequenceSynthetic 48gccaagtgtc ttccagtacg at
224921DNAArtificial SequenceSynthetic 49gttccctttc ttgggttcag a
215023DNAArtificial SequenceSynthetic 50gatgctactg ctttggcaag atc
235120DNAArtificial SequenceSynthetic 51cctgagctgc taacacggtt
205223DNAArtificial SequenceSynthetic 52agctacagac catgcttagt gta
235324DNAArtificial SequenceSynthetic 53tgccagttta ggaggaatat gttc
245425DNAArtificial SequenceSynthetic 54ctgaggaaac agaggtacca gatat
255524DNAArtificial SequenceSynthetic 55agtcacacag ttctgtcaaa tcag
245617DNAArtificial SequenceSynthetic 56gaacacggcg gcatcag
175720DNAArtificial SequenceSynthetic 57tcctgtggga gggttctttg
205820DNAArtificial SequenceSynthetic 58ccctctctct gagccctcta
205921DNAArtificial SequenceSynthetic 59gctgcctaag tctttggagc t
216020DNAArtificial SequenceSynthetic 60ccctctctct gagccctcta
206125DNAArtificial SequenceSynthetic 61gagaggagag acagctagtt ctaac
256223DNAArtificial SequenceSynthetic 62agctacagac catgcttagt gta
236322DNAArtificial SequenceSynthetic 63gccctcttca tacaggaatc ac
226419DNAArtificial SequenceSynthetic 64cggacagcat ccaggactt
196526DNAArtificial SequenceSynthetic 65tcatgtaatc tggcttcaga
gtggga 266627DNAArtificial SequenceSynthetic 66tgggaggcaa
ttcttagttt caatgga 276723DNAArtificial SequenceSynthetic
67tcccaaaggt gtctgtctgc aca 236822DNAArtificial SequenceSynthetic
68ctcctttgcc tcgctggact gg 226919DNAArtificial SequenceSynthetic
69cggacagcat ccaggactt 197029DNAArtificial SequenceSynthetic
70agaaggagtg tacagagtag aactggaca 297127DNAArtificial
SequenceSynthetic 71tgtttgtggg tgtcagtgtt tctactc
277221DNAArtificial SequenceSynthetic 72caccacggct gtcgtcagca a
217323DNAArtificial SequenceSynthetic 73cttgccaaag cagtagcatc cca
237423DNAArtificial SequenceSynthetic 74aggtcagaaa gcagagtgga cca
237523DNAArtificial SequenceSynthetic 75cccaggcaat tcctaccttc cca
237628DNAArtificial SequenceSynthetic 76tctgagcatt ctacctcatt
gctttggt 287723DNAArtificial SequenceSynthetic 77aggctgtccc
agcacctgag tcg 237823DNAArtificial SequenceSynthetic 78tgggcacaac
agacaatcgg ctg 237923DNAArtificial SequenceSynthetic 79aaggctgctg
atgacacctg gga 238027DNAArtificial SequenceSynthetic 80agattcagac
acacacaact taccagc 278128DNAArtificial SequenceSynthetic
81agacctgcaa ttctctaaga gctccaca 288227DNAArtificial
SequenceSynthetic 82agattcagac acacacaact taccagc
278324DNAArtificial SequenceSynthetic 83ttgtctgcag ctcctacctc tggg
248423DNAArtificial SequenceSynthetic 84aggtcagaaa gcagagtgga cca
238529DNAArtificial SequenceSynthetic 85ttgacatgtg tgggtgagag
attttactg 298622DNAArtificial SequenceSynthetic 86cccagggtgc
tggagaatcc aa 228716RNAArtificial SequenceSynthetic 87guuuuagagc
uaugcu 168867RNAArtificial SequenceSynthetic 88agcauagcaa
guuaaaauaa ggcuaguccg uuaucaacuu gaaaaagugg caccgagucg 60gugcuuu
678977RNAArtificial SequenceSynthetic 89guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc cguuaucaac uugaaaaagu 60ggcaccgagu cggugcu
7790444DNAArtificial SequenceSynthetic 90atggcttctc atcgtctgct
cctcctctgc cttgctggac tggtatttgt gtctgaggct 60ggccctacgg gcaccggtga
atccaagtgt cctctgatgg tcaaagttct agatgctgtc 120cgaggcagtc
ctgccatcaa tgtggccgtg catgtgttca gaaaggctgc tgatgacacc
180tgggagccat ttgcctctgg gaaaaccagt gagtctggag agctgcatgg
gctcacaact 240gaggaggaat ttgtagaagg gatatacaaa gtggaaatag
acaccaaatc ttactggaag 300gcacttggca tctccccatt ccatgagcat
gcagaggtgg tattcacagc caacgactcc 360ggcccccgcc gctacaccat
tgccgccctg ctgagcccct actcctattc caccacggct 420gtcgtcacca
atcccaagga atga 44491444DNAArtificial SequenceSynthetic
91atggcttccc ttcgactctt cctcctttgc ctcgctggac tggtatttgt gtctgaagct
60ggccccgcgg gcaccggtga atccaagtgt cctctgatgg tcaaagttct agatgctgtc
120cgaggcagtc ctgccatcaa tgtggccgtg catgtgttca gaaaggctgc
tgatgacacc 180tgggagccat ttgcctctgg gaaaaccagt gagtctggag
agctgcatgg gctcacaact 240gaggaggaat ttgtagaagg gatatacaaa
gtggaaatag acaccaaatc ttactggaag 300gcacttggca tctccccatt
ccatgagcat gcagaggtgg tattcacagc caacgactcc 360ggcccccgcc
gctacaccat tgccgccctg ctgagcccct actcctattc caccacggct
420gtcgtcacca atcccaagga atga 44492444DNAArtificial
SequenceSynthetic 92atggcttccc ttcgactctt cctcctttgc ctcgctggac
tggtatttgt gtctgaagct 60ggccccgcgg gtgctggaga atccaaatgt cctctgatgg
tcaaagtcct ggatgctgtc 120cgaggcagcc ctgctgtaga cgtggctgta
aaagtgttca aaaagacctc tgagggatcc 180tgggagccct ttgcctctgg
gaagaccgcg gagtctggag agctgcacgg gctcaccaca 240gatgagaagt
ttgtagaagg agtgtacaga gtagaactgg acaccaaatc gtactggaag
300acacttggca tttccccgtt ccatgaattc gcggatgtgg ttttcacagc
caacgactct 360ggccatcgcc actacaccat cgcagccctg ctcagcccat
actcctacag caccacggct 420gtcgtcagca acccccagaa ttga
444934176DNAArtificial SequenceSyntheticmisc_feature(1)..(3)Start
Codonmisc_feature(10)..(30)5' NLSmisc_feature(4126)..(4173)3'
NLSmisc_feature(4174)..(4176)Stop Codon 93atggacaagc ccaagaaaaa
gcggaaagtg aagtacagca tcggcctgga catcggcacc 60aactctgtgg gctgggccgt
gatcaccgac gagtacaagg tgcccagcaa gaaattcaag 120gtgctgggca
acaccgacag gcacagcatc aagaagaacc tgatcggcgc cctgctgttc
180gacagcggcg aaacagccga ggccaccaga ctgaagagaa ccgccagaag
aagatacacc 240aggcggaaga acaggatctg ctatctgcaa gagatcttca
gcaacgagat ggccaaggtg 300gacgacagct tcttccacag actggaagag
tccttcctgg tggaagagga caagaagcac 360gagagacacc ccatcttcgg
caacatcgtg gacgaggtgg cctaccacga gaagtacccc 420accatctacc
acctgagaaa gaaactggtg gacagcaccg acaaggccga cctgagactg
480atctacctgg ccctggccca catgatcaag ttcagaggcc acttcctgat
cgagggcgac 540ctgaaccccg acaacagcga cgtggacaag ctgttcatcc
agctggtgca gacctacaac 600cagctgttcg aggaaaaccc catcaacgcc
agcggcgtgg acgccaaggc tatcctgtct 660gccagactga gcaagagcag
aaggctggaa aatctgatcg cccagctgcc cggcgagaag 720aagaacggcc
tgttcggcaa cctgattgcc ctgagcctgg gcctgacccc caacttcaag
780agcaacttcg acctggccga ggatgccaaa ctgcagctga gcaaggacac
ctacgacgac 840gacctggaca acctgctggc ccagatcggc gaccagtacg
ccgacctgtt cctggccgcc 900aagaacctgt ctgacgccat cctgctgagc
gacatcctga gagtgaacac cgagatcacc 960aaggcccccc tgagcgcctc
tatgatcaag agatacgacg agcaccacca ggacctgacc 1020ctgctgaaag
ctctcgtgcg gcagcagctg cctgagaagt acaaagaaat cttcttcgac
1080cagagcaaga acggctacgc cggctacatc gatggcggcg ctagccagga
agagttctac 1140aagttcatca agcccatcct ggaaaagatg gacggcaccg
aggaactgct cgtgaagctg 1200aacagagagg acctgctgag aaagcagaga
accttcgaca acggcagcat cccccaccag 1260atccacctgg gagagctgca
cgctatcctg agaaggcagg aagattttta cccattcctg 1320aaggacaacc
gggaaaagat cgagaagatc ctgaccttca ggatccccta ctacgtgggc
1380cccctggcca gaggcaacag cagattcgcc tggatgacca gaaagagcga
ggaaaccatc 1440accccctgga acttcgagga agtggtggac aagggcgcca
gcgcccagag cttcatcgag 1500agaatgacaa acttcgataa gaacctgccc
aacgagaagg tgctgcccaa gcacagcctg 1560ctgtacgagt acttcaccgt
gtacaacgag ctgaccaaag tgaaatacgt gaccgaggga 1620atgagaaagc
ccgccttcct gagcggcgag cagaaaaagg ccatcgtgga cctgctgttc
1680aagaccaaca gaaaagtgac cgtgaagcag ctgaaagagg actacttcaa
gaaaatcgag 1740tgcttcgact ccgtggaaat ctccggcgtg gaagatagat
tcaacgcctc cctgggcaca 1800taccacgatc tgctgaaaat tatcaaggac
aaggacttcc tggataacga agagaacgag 1860gacattctgg aagatatcgt
gctgaccctg acactgtttg aggaccgcga gatgatcgag 1920gaaaggctga
aaacctacgc tcacctgttc gacgacaaag tgatgaagca gctgaagaga
1980aggcggtaca ccggctgggg caggctgagc agaaagctga tcaacggcat
cagagacaag 2040cagagcggca agacaatcct ggatttcctg aagtccgacg
gcttcgccaa ccggaacttc 2100atgcagctga tccacgacga cagcctgaca
ttcaaagagg acatccagaa agcccaggtg 2160tccggccagg gcgactctct
gcacgagcat atcgctaacc tggccggcag ccccgctatc 2220aagaagggca
tcctgcagac agtgaaggtg gtggacgagc tcgtgaaagt gatgggcaga
2280cacaagcccg agaacatcgt gatcgagatg gctagagaga accagaccac
ccagaaggga 2340cagaagaact cccgcgagag gatgaagaga atcgaagagg
gcatcaaaga gctgggcagc 2400cagatcctga aagaacaccc cgtggaaaac
acccagctgc agaacgagaa gctgtacctg 2460tactacctgc agaatggccg
ggatatgtac gtggaccagg aactggacat caacagactg 2520tccgactacg
atgtggacca tatcgtgcct cagagctttc tgaaggacga ctccatcgat
2580aacaaagtgc tgactcggag cgacaagaac agaggcaaga gcgacaacgt
gccctccgaa 2640gaggtcgtga agaagatgaa gaactactgg cgacagctgc
tgaacgccaa gctgattacc 2700cagaggaagt tcgataacct gaccaaggcc
gagagaggcg gcctgagcga gctggataag 2760gccggcttca tcaagaggca
gctggtggaa accagacaga tcacaaagca cgtggcacag 2820atcctggact
cccggatgaa cactaagtac gacgaaaacg ataagctgat ccgggaagtg
2880aaagtgatca ccctgaagtc caagctggtg tccgatttcc ggaaggattt
ccagttttac 2940aaagtgcgcg agatcaacaa ctaccaccac gcccacgacg
cctacctgaa cgccgtcgtg 3000ggaaccgccc tgatcaaaaa gtaccctaag
ctggaaagcg agttcgtgta cggcgactac 3060aaggtgtacg acgtgcggaa
gatgatcgcc aagagcgagc aggaaatcgg caaggctacc 3120gccaagtact
tcttctacag caacatcatg aactttttca agaccgaaat caccctggcc
3180aacggcgaga tcagaaagcg ccctctgatc gagacaaacg gcgaaaccgg
ggagatcgtg 3240tgggataagg gcagagactt cgccacagtg cgaaaggtgc
tgagcatgcc ccaagtgaat 3300atcgtgaaaa agaccgaggt gcagacaggc
ggcttcagca aagagtctat cctgcccaag 3360aggaacagcg acaagctgat
cgccagaaag aaggactggg accccaagaa gtacggcggc 3420ttcgacagcc
ctaccgtggc ctactctgtg ctggtggtgg ctaaggtgga aaagggcaag
3480tccaagaaac tgaagagtgt gaaagagctg ctggggatca ccatcatgga
aagaagcagc 3540tttgagaaga accctatcga ctttctggaa gccaagggct
acaaagaagt gaaaaaggac 3600ctgatcatca agctgcctaa gtactccctg
ttcgagctgg aaaacggcag aaagagaatg 3660ctggcctctg ccggcgaact
gcagaaggga aacgagctgg ccctgcctag caaatatgtg 3720aacttcctgt
acctggcctc ccactatgag aagctgaagg gcagccctga ggacaacgaa
3780cagaaacagc tgtttgtgga acagcataag cactacctgg acgagatcat
cgagcagatc 3840agcgagttct ccaagagagt gatcctggcc gacgccaatc
tggacaaggt gctgtctgcc 3900tacaacaagc acagggacaa gcctatcaga
gagcaggccg agaatatcat ccacctgttc 3960accctgacaa acctgggcgc
tcctgccgcc ttcaagtact ttgacaccac catcgaccgg 4020aagaggtaca
ccagcaccaa agaggtgctg gacgccaccc tgatccacca gagcatcacc
4080ggcctgtacg agacaagaat cgacctgtct cagctgggag gcgacaagag
acctgccgcc 4140actaagaagg ccggacaggc caaaaagaag aagtga
4176941391PRTArtificial SequenceSyntheticMISC_FEATURE(4)..(10)5'
NLSMISC_FEATURE(1376)..(1391)3' NLS 94Met Asp Lys Pro Lys Lys Lys
Arg Lys Val Lys Tyr Ser Ile Gly Leu1 5 10 15Asp Ile Gly Thr Asn Ser
Val Gly Trp Ala Val Ile Thr Asp Glu Tyr 20 25 30Lys Val Pro Ser Lys
Lys Phe Lys Val Leu Gly Asn Thr Asp Arg His 35 40 45Ser Ile Lys Lys
Asn Leu Ile Gly Ala Leu Leu Phe Asp Ser Gly Glu 50 55 60Thr Ala Glu
Ala Thr Arg Leu Lys Arg Thr Ala Arg Arg Arg Tyr Thr65 70 75 80Arg
Arg Lys Asn Arg Ile Cys Tyr Leu Gln Glu Ile Phe Ser Asn Glu 85 90
95Met Ala Lys Val Asp Asp Ser Phe Phe His Arg Leu Glu Glu Ser Phe
100 105 110Leu Val Glu Glu Asp Lys Lys His Glu Arg His Pro Ile Phe
Gly Asn 115 120 125Ile Val Asp Glu Val Ala Tyr His Glu Lys Tyr Pro
Thr Ile Tyr His 130 135 140Leu Arg Lys Lys Leu Val Asp Ser Thr Asp
Lys Ala Asp Leu Arg Leu145 150 155 160Ile Tyr Leu Ala Leu Ala His
Met Ile Lys Phe Arg Gly His Phe Leu 165 170 175Ile Glu Gly Asp Leu
Asn Pro Asp Asn Ser Asp Val Asp Lys Leu Phe 180 185 190Ile Gln Leu
Val Gln Thr Tyr Asn Gln Leu Phe Glu Glu Asn Pro Ile 195 200 205Asn
Ala Ser Gly Val Asp Ala Lys Ala Ile Leu Ser Ala Arg Leu Ser 210 215
220Lys Ser Arg Arg Leu Glu Asn Leu Ile Ala Gln Leu Pro Gly Glu
Lys225 230 235 240Lys Asn Gly Leu Phe Gly Asn Leu Ile Ala Leu Ser
Leu Gly Leu Thr 245 250 255Pro Asn Phe Lys Ser Asn Phe Asp Leu Ala
Glu Asp Ala Lys Leu Gln 260 265 270Leu Ser Lys Asp Thr Tyr Asp Asp
Asp Leu Asp Asn Leu Leu Ala Gln 275 280 285Ile Gly Asp Gln Tyr Ala
Asp Leu Phe Leu Ala Ala Lys Asn Leu Ser 290 295 300Asp Ala Ile Leu
Leu Ser Asp Ile Leu Arg Val Asn Thr Glu Ile Thr305 310 315 320Lys
Ala Pro Leu Ser Ala Ser Met Ile Lys Arg Tyr Asp Glu His His 325 330
335Gln Asp Leu Thr Leu Leu Lys Ala Leu Val Arg Gln Gln Leu Pro Glu
340 345 350Lys Tyr Lys Glu Ile Phe Phe Asp Gln Ser Lys Asn Gly Tyr
Ala Gly 355 360 365Tyr Ile Asp Gly Gly Ala Ser Gln Glu Glu Phe Tyr
Lys Phe Ile Lys 370 375 380Pro Ile Leu Glu Lys Met Asp Gly Thr Glu
Glu Leu Leu Val Lys Leu385 390 395 400Asn Arg Glu Asp Leu Leu Arg
Lys Gln Arg Thr Phe Asp Asn Gly Ser 405 410 415Ile Pro His Gln Ile
His Leu Gly Glu Leu His Ala Ile Leu Arg Arg 420 425 430Gln Glu Asp
Phe Tyr Pro Phe Leu Lys Asp Asn Arg Glu Lys Ile Glu 435 440 445Lys
Ile Leu Thr Phe Arg Ile Pro Tyr Tyr Val Gly Pro Leu Ala Arg 450 455
460Gly Asn Ser Arg Phe Ala Trp Met Thr Arg Lys Ser Glu Glu Thr
Ile465 470 475 480Thr Pro Trp Asn Phe Glu Glu Val Val Asp Lys Gly
Ala Ser Ala Gln 485 490 495Ser Phe Ile Glu Arg Met Thr Asn Phe Asp
Lys Asn Leu Pro Asn Glu 500 505 510Lys Val Leu Pro Lys His Ser Leu
Leu Tyr Glu Tyr Phe Thr Val Tyr 515 520 525Asn Glu Leu Thr Lys Val
Lys Tyr Val Thr Glu Gly Met Arg Lys Pro 530 535 540Ala Phe Leu Ser
Gly Glu Gln Lys Lys Ala Ile Val Asp Leu Leu Phe545 550 555 560Lys
Thr Asn Arg Lys Val Thr Val Lys Gln Leu Lys Glu Asp Tyr Phe 565 570
575Lys Lys Ile Glu Cys Phe Asp Ser Val Glu Ile Ser Gly Val Glu Asp
580 585 590Arg Phe Asn Ala Ser Leu Gly Thr Tyr His Asp Leu Leu Lys
Ile Ile 595 600 605Lys Asp Lys Asp Phe Leu Asp Asn Glu Glu Asn Glu
Asp Ile Leu Glu 610 615 620Asp Ile Val Leu Thr Leu Thr Leu Phe Glu
Asp Arg Glu Met Ile Glu625 630 635 640Glu Arg Leu Lys Thr Tyr Ala
His Leu Phe Asp Asp Lys Val Met Lys 645 650 655Gln Leu Lys Arg Arg
Arg Tyr Thr Gly Trp Gly Arg Leu Ser Arg Lys 660 665 670Leu Ile Asn
Gly Ile Arg Asp Lys Gln Ser Gly Lys Thr Ile Leu Asp 675 680 685Phe
Leu Lys Ser Asp Gly Phe Ala Asn Arg Asn Phe Met Gln Leu Ile 690 695
700His Asp Asp Ser Leu Thr Phe Lys Glu Asp Ile Gln Lys Ala Gln
Val705 710 715 720Ser Gly Gln Gly Asp Ser Leu His Glu His Ile Ala
Asn Leu Ala Gly 725 730 735Ser Pro Ala Ile Lys Lys Gly Ile Leu Gln
Thr Val Lys Val Val Asp 740 745 750Glu Leu Val Lys Val Met Gly Arg
His Lys Pro Glu Asn Ile Val Ile 755 760 765Glu Met Ala Arg Glu Asn
Gln Thr Thr Gln Lys Gly Gln Lys Asn Ser 770 775 780Arg Glu Arg Met
Lys Arg Ile Glu Glu Gly Ile Lys Glu Leu Gly Ser785 790 795 800Gln
Ile Leu Lys Glu His Pro Val Glu Asn Thr Gln Leu Gln Asn Glu 805 810
815Lys Leu Tyr Leu Tyr Tyr Leu Gln Asn Gly Arg Asp Met Tyr Val Asp
820 825 830Gln Glu Leu Asp Ile Asn Arg Leu Ser Asp Tyr Asp Val Asp
His Ile 835 840 845Val Pro Gln Ser Phe Leu Lys Asp Asp Ser Ile Asp
Asn Lys Val Leu 850 855 860Thr Arg Ser Asp Lys Asn Arg Gly Lys Ser
Asp Asn Val Pro Ser Glu865 870 875 880Glu Val Val Lys Lys Met Lys
Asn Tyr Trp Arg Gln Leu Leu Asn Ala 885 890 895Lys Leu Ile Thr Gln
Arg Lys Phe Asp Asn Leu Thr Lys Ala Glu Arg 900 905 910Gly Gly Leu
Ser Glu Leu Asp Lys Ala Gly Phe Ile Lys Arg Gln Leu 915 920 925Val
Glu Thr Arg Gln Ile Thr Lys His Val Ala Gln Ile Leu Asp Ser 930 935
940Arg Met Asn Thr Lys Tyr Asp Glu Asn Asp Lys Leu Ile Arg Glu
Val945 950 955 960Lys Val Ile Thr Leu Lys Ser Lys Leu Val Ser Asp
Phe Arg Lys Asp 965 970 975Phe Gln Phe Tyr Lys Val Arg Glu Ile Asn
Asn Tyr His His Ala His 980 985 990Asp Ala Tyr Leu Asn Ala Val Val
Gly Thr Ala Leu Ile Lys Lys Tyr 995 1000 1005Pro Lys Leu Glu Ser
Glu Phe Val Tyr Gly Asp Tyr Lys Val Tyr 1010 1015 1020Asp Val Arg
Lys Met Ile Ala Lys Ser Glu Gln Glu Ile Gly Lys 1025 1030 1035Ala
Thr Ala Lys Tyr Phe Phe Tyr Ser Asn Ile Met Asn Phe Phe 1040 1045
1050Lys Thr Glu Ile Thr Leu Ala Asn Gly Glu Ile Arg Lys Arg Pro
1055 1060 1065Leu Ile Glu Thr Asn Gly Glu Thr Gly Glu Ile Val Trp
Asp Lys 1070 1075 1080Gly Arg Asp Phe Ala Thr Val Arg Lys Val Leu
Ser Met Pro Gln 1085 1090 1095Val Asn Ile Val Lys Lys Thr Glu Val
Gln Thr Gly Gly Phe Ser 1100 1105 1110Lys Glu Ser Ile Leu Pro Lys
Arg Asn Ser Asp Lys Leu Ile Ala 1115 1120 1125Arg Lys Lys Asp Trp
Asp Pro Lys Lys Tyr Gly Gly Phe Asp Ser 1130 1135 1140Pro Thr Val
Ala Tyr Ser Val Leu Val Val Ala Lys Val Glu Lys 1145 1150 1155Gly
Lys Ser Lys Lys Leu Lys Ser Val Lys Glu Leu Leu Gly Ile 1160 1165
1170Thr Ile Met Glu Arg Ser Ser Phe Glu Lys Asn Pro Ile Asp Phe
1175 1180 1185Leu Glu Ala Lys Gly Tyr Lys Glu Val Lys Lys Asp Leu
Ile Ile 1190 1195 1200Lys Leu Pro Lys Tyr Ser Leu Phe Glu Leu Glu
Asn Gly Arg Lys 1205 1210 1215Arg Met Leu Ala Ser Ala Gly Glu Leu
Gln Lys Gly Asn Glu Leu 1220 1225 1230Ala Leu Pro Ser Lys Tyr Val
Asn Phe Leu Tyr Leu Ala Ser His 1235 1240 1245Tyr Glu Lys Leu Lys
Gly Ser Pro Glu Asp Asn Glu Gln Lys Gln 1250 1255 1260Leu Phe Val
Glu Gln His Lys His Tyr Leu Asp Glu Ile Ile Glu 1265 1270 1275Gln
Ile Ser Glu Phe Ser Lys Arg Val Ile Leu Ala Asp Ala Asn 1280 1285
1290Leu Asp Lys Val Leu Ser Ala Tyr Asn Lys His Arg Asp Lys Pro
1295 1300 1305Ile Arg Glu Gln Ala Glu Asn Ile Ile His Leu Phe Thr
Leu Thr 1310 1315 1320Asn Leu Gly Ala Pro Ala Ala Phe Lys Tyr Phe
Asp Thr Thr Ile 1325 1330 1335Asp Arg Lys Arg Tyr Thr Ser Thr Lys
Glu Val Leu Asp Ala Thr 1340 1345 1350Leu Ile His Gln Ser Ile Thr
Gly Leu Tyr Glu Thr Arg Ile Asp 1355 1360 1365Leu Ser Gln Leu Gly
Gly Asp Lys Arg Pro Ala Ala Thr Lys Lys 1370 1375 1380Ala Gly Gln
Ala Lys Lys Lys Lys 1385 1390
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