U.S. patent application number 16/033067 was filed with the patent office on 2019-02-07 for modulation of enhancer rna mediated gene expression.
This patent application is currently assigned to Ionis Pharmaceuticals, Inc.. The applicant listed for this patent is Ionis Pharmaceuticals, Inc., The Regents of the University of California. Invention is credited to Susan M. Freier, Christopher K. Glass, Michael Tun Yin Lam, Wenbo Li, Michael G. Rosenfeld.
Application Number | 20190040386 16/033067 |
Document ID | / |
Family ID | 49624504 |
Filed Date | 2019-02-07 |
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United States Patent
Application |
20190040386 |
Kind Code |
A1 |
Freier; Susan M. ; et
al. |
February 7, 2019 |
MODULATION OF ENHANCER RNA MEDIATED GENE EXPRESSION
Abstract
Disclosed herein are methods and compounds for inhibiting gene
expression by inhibiting enhancer RNAs (eRNAs). Such methods and
compounds are useful for reducing expression of certain genes, many
of which are associated with a variety of diseases and
disorders.
Inventors: |
Freier; Susan M.; (San
Diego, CA) ; Glass; Christopher K.; (San Diego,
CA) ; Rosenfeld; Michael G.; (San Diego, CA) ;
Li; Wenbo; (San Diego, CA) ; Lam; Michael Tun
Yin; (La Jolla, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Ionis Pharmaceuticals, Inc.
The Regents of the University of California |
Carlsbad
Oakland |
CA
CA |
US
US |
|
|
Assignee: |
Ionis Pharmaceuticals, Inc.
Carlsbad
CA
The Regents of the University of California
Oakland
CA
|
Family ID: |
49624504 |
Appl. No.: |
16/033067 |
Filed: |
July 11, 2018 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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15283712 |
Oct 3, 2016 |
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16033067 |
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14403103 |
Nov 21, 2014 |
9518261 |
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PCT/US2013/042163 |
May 22, 2013 |
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15283712 |
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61650426 |
May 22, 2012 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12N 2310/11 20130101;
C12N 2310/321 20130101; C12N 2310/341 20130101; C12N 2310/315
20130101; C12N 15/113 20130101; C12N 15/85 20130101; C12N 2310/33
20130101; C12N 2310/113 20130101; C12N 2310/3231 20130101; C12N
2310/3341 20130101; C12N 2310/321 20130101; C12N 2310/3525
20130101 |
International
Class: |
C12N 15/113 20060101
C12N015/113 |
Goverment Interests
STATEMENT OF GOVERNMENT SUPPORT
[0001] This invention was made with Government support under Grant
No. CA52599, DK091183, DK062434, and DK039949, awarded by the
National Institutes of Health, and Grant No. W81XWH-08-01-0665 and
W81XWH-12-1-0015, awarded by the ARMY/MRMC. The Government has
certain rights in the invention.
Claims
1. A method of inhibiting gene expression in a cell comprising
contacting the cell with an antisense oligonucleotide inhibitor of
an enhancer RNA (eRNA) that enhances transcription of matrix
metalloproteinase 9 (MMP9), thereby inhibiting expression of one or
more genes in the cell, wherein the antisense compound comprises: a
gap segment consisting of linked deoxynucleosides; a 5' wing
segment consisting of linked nucleosides; and a 3' wing segment
consisting of linked nucleosides; wherein the gap segment is
positioned between the 5' wing segment and the 3' wing segment and
wherein each nucleoside of each wing segment comprises a modified
sugar.
2. The method of claim 1, wherein the eRNA is transcribed from a
genomic enhancer sequence or region.
3. The method of claim 2, wherein the cell is mammalian.
4. The method of claim 1, wherein the eRNA transcription is
initiated from a RNA polymerase II (PolII) binding site and is
capable of elongating bidirectionally.
5. The method of claim 1, wherein the eRNA is capable of enhancing
transcription of the one or more genes MMP9 gene.
6. The method of claim 2, wherein the genomic enhancer sequence or
region has a higher level of monomethylated lysine 4 of histone 3
(H3K4me1) than trimethylated lysine 4 of histone 3 (H3K4me3).
7. The method of claim 2, wherein the genomic enhancer sequence or
region is enriched for bound RNA polymerase II (PolII).
8. The method of claim 2, wherein the genomic enhancer sequence or
region is enriched for bound transcriptional co-activator
p300/CBP.
9. The method of claim 2, wherein the genomic enhancer sequence or
region is enriched for bound Rev-Erb.alpha. or Rev-Erb.beta..
10. The method of claim 2, wherein the genomic enhancer sequence or
region is enriched for bound estrogen receptor.
11. The method of claim 10, wherein the estrogen receptor is bound
to estradiol.
12. The method of claim 1, wherein the eRNA has a relatively short
half-life compared to mRNA.
13. The method of claim 12, wherein the eRNA has a half-life of
less than about 10-30 minutes.
14. (canceled)
15. (canceled)
16. The method of claim 2, wherein the transcriptional start site
of the one or more genes is located on a chromosome at least about
1 kilobase (kb) from the genomic enhancer sequence or region.
17. The method of claim 1, wherein the eRNA is not
polyadenylated.
18. The method of claim 1, wherein the cell is a hematopoietic
cell.
19. The method of claim 18, wherein the hematopoietic cell is a
monocyte.
20. The method of claim 18, wherein the hematopoietic cell is a
macrophage.
21. The method of claim 1, wherein the cell is a neuron.
22. The method of claim 1, wherein the cell is a breast cell.
23. The method of claim 1, wherein the cell is a cancer cell.
24. The method of claim 1, wherein the cell contacted with a
antisense oligonucleotide of an enhancer RNA (eRNA) is in a
subject.
25. (canceled)
26. The method of claim 1, wherein the antisense compound is
single-stranded.
27. The method of claim 26, wherein the antisense compound is
double-stranded.
28. The method of claim 1, wherein the antisense compound is
modified.
29.-40. (canceled)
41. The method of claim 1, wherein the antisense compound
comprises: a gap segment consisting of ten linked deoxynucleosides;
a 5' wing segment consisting of 3 linked nucleosides; and a 3' wing
segment consisting of 3 linked nucleosides; wherein the gap segment
is positioned between the 5' wing segment and the 3' wing segment,
wherein each nucleoside of each wing segment comprises a
2'-O-methoxyethyl sugar or a constrained ethyl sugar; and wherein
each internucleoside linkage is a phosphorothioate linkage.
42. The method of claim 41, wherein the 3 linked nucleosides of the
5' wing segment comprise a 2'-O-methoxyethyl sugar, a constrained
ethyl sugar, and a constrained ethyl sugar in the 5' to 3'
direction, and the 3 linked nucleosides of the 3' wing segment
comprise a constrained ethyl sugar, a constrained ethyl sugar, and
a 2'-O-methoxyethyl sugar in the 5' to 3' direction.
43. The method of claim 1, wherein the antisense oligonucleotide
comprises a gap segment of ten 2'-deoxynucleotides positioned
between wing segments of five 2'-MOE nucleotides.
44.-54. (canceled)
55. A compound comprising an antisense oligonucleotide inhibitor of
a MMP9 enhancer RNA (eRNA), wherein said MMP9 eRNA comprises the
nucleic acid sequence of SEQ ID NO:1, wherein the antisense
compound comprises: a gap segment consisting of linked
deoxynucleosides; a 5' wing segment consisting of linked
nucleosides; and a 3' wing segment consisting of linked
nucleosides; wherein the gap segment is positioned between the 5'
wing segment and the 3' wing segment and wherein each nucleoside of
each wing segment comprises a modified sugar.
56.-87. (canceled)
Description
SEQUENCE LISTING
[0002] The present application is being filed along with a Sequence
Listing in electronic format. The Sequence Listing is provided as a
file entitled BIOL0202USC2SEQ_ST25.txt created Jul. 11, 2018, which
is approximately 80 KB in size. The information in the electronic
format of the sequence listing is incorporated herein by reference
in its entirety.
FIELD
[0003] Certain embodiments are directed to methods and compounds
for inhibiting gene expression by inhibiting enhancer RNAs (eRNAs).
Such methods and compounds are useful for reducing expression of
certain genes, many of which are associated with a variety of
diseases and disorders.
BACKGROUND
[0004] Recent high-throughput transcriptomic analyses have revealed
that eukaryotic genomes transcribe up to 90% of the genomic DNA.
(The ENCODE Project Consortium. The ENCODE (ENCyclopedia of DNA
Elements) Project. Science 2004; 306:636-640). Only 1-2% of these
transcripts encode for proteins, whereas the vast majority are
transcribed as non-coding RNAs (ncRNAs).
[0005] The majority of the non-protein-coding transcripts belong to
the group of lncRNAs, which are considered as >200 nucleotides
in length. Most IncRNAs are characterized by nuclear localization,
low expression, low level of sequence conservation and are composed
of both poly A+ and poly A- transcripts. (Kapranov P, et al., "RNA
maps reveal new RNA classes and a possible function for pervasive
transcription." Science 2007; 316:1484-1488) (Wu Q, et al., "Poly
A- transcripts expressed in HeLa cells." PLoS One 2008;
3:e2803).
[0006] One subgroup of IncRNAs, termed large intergenic non-coding
RNAs (lincRNAs), was described based on distinctive chromatin
signature that marks actively transcribed genes. (Khalil A M et
al., "Many human large intergenic noncoding RNAs associate with
chromatin-modifying complexes and affect gene expression." Proc
Natl Acad Sci USA 2009; 106:11667-11672) (Guttman M et al.,
"Chromatin signature reveals over a thousand highly conserved large
non-coding RNAs in mammals." Nature 2009; 458:223-227). LincRNAs
are marked by trimethylation of lysine 4 of histone H3 (H3K4me3) at
their promoter and trimethylation of lysine 36 of histone H3
(H3K36me3) along the transcribed region.
[0007] Another subgroup of IncRNAs, termed enhancer RNAs (eRNAs),
was recently reported to be transcribed from genomic enhancer
regions. (Kim T K et al., "Widespread transcription at neuronal
activity-regulated enhancers." Nature 2010; 465:182-187) (De Santa
F et al., "A large fraction of extragenic RNA pol II transcription
sites overlap enhancers." PLoS Biol 2010; 8:e1000384). Distinct
from eRNAs, another subgroup of IncRNAs, termed ncRNA-activators
(ncRNA-a) was classified as mono-directional, polyadenylated, and
having a 1-1H3K4 trimethylation chromatin signature. (Orom U A,
Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G et al.
Long noncoding RNAs with enhancer-like function in human cells.
Cell 2010; 143:46-58.)
SUMMARY
[0008] Several embodiments provided herein relate to the discovery
that eRNAs are functional molecules that stimulate gene expression
and can be targeted for inhibition to modulate gene expression.
Prior to the present discovery manifest in several embodiments
described herein, it was unknown and uncertain in the field whether
eRNAs are functional molecules or merely products of
"transcriptional noise" arising from PolII mediated transcription
of genomic sequences adjacent to coding genes. (Struhl K,
"Transcriptional noise and the fidelity of initiation by RNA
polymerase II." Nat Struct Mol Biol 2007 14: 103-105) (Ponting C P
et al., "Evolution and functions of long noncoding RNAs." Cell 2009
136: 629-641). eRNAs are widely considered just a byproduct of a
transcriptional "ripple effect," a type of transcriptional noise in
which PolII causes a wave of transcription from genes into adjacent
sequences including intergenic regions. Ebisuya M et al., "Ripples
from neighbouring transcription." Nat Cell Biol 2008 10:
1106-1113.
[0009] The present embodiments demonstrate eRNAs are functional
molecules and targeting them for inhibition modulates gene
expression. Certain embodiments are directed to methods and
compounds for inhibiting gene expression by inhibiting enhancer
RNAs (eRNA). In certain several embodiments, a method of inhibiting
gene expression in a cell includes contacting the cell with a
specific inhibitor of an enhancer RNA (eRNA), thereby inhibiting
expression of one or more genes in the cell. In certain aspects,
the eRNA is transcribed from a genomic enhancer sequence or region;
the genomic enhancer sequence or region comprises any one of the
genomic coordinates identified in Mega-Tables 1-9 filed in U.S.
Provisional Application No. 61/650,426 in electronic format on May
22, 2012; the eRNA transcription is initiated from a RNA polymerase
II (PolII) binding site and is capable of elongating
bidirectionally; the eRNA is capable of enhancing transcription of
the one or more genes; the genomic enhancer sequence or region has
a higher level of monomethylated lysine 4 of histone 3 (H3K4me1)
than trimethylated lysine 4 of histone 3 (H3K4me3); the genomic
enhancer sequence or region is enriched for bound RNA polymerase II
(PolII); the genomic enhancer sequence or region is enriched for
bound transcriptional co-activator p300/CBP; the genomic enhancer
sequence or region is enriched for bound Rev-Erb.alpha. or
Rev-Erb.beta.; the genomic enhancer sequence or region is enriched
for bound estrogen receptor, such as estradiol-bound estrogen
receptor; eRNA has a relatively short half-life compared to mRNA,
such as less than about 10-30 minutes; the transcriptional start
site of the one or more genes is located on a chromosome at least
about 1 kilobase (kb) from the genomic enhancer sequence or region;
the eRNA is not polyadenylated or has a shorter polyA tail than
mRNA or ncRNA-a; the cell is a hematopoietic cell, such as a
monocyte or macrophage; the cell is a neuron; the cell is a breast
cell; the cell is a cancer cell; and/or the cell contacted with a
specific inhibitor of an enhancer RNA (eRNA) is in a subject. In
several embodiments, the eRNA enhances transcription of matrix
metalloproteinase 9 (MMP9), chemokine receptor CX3CR1, CA12, FOXC1,
GREB1, P2RY2, SMAD7, PGR, SIAH2, NRIP1, TFF1, or KCNK5.
[0010] In several embodiments, compounds, which can be used in the
aforementioned methods of inhibiting gene expression in a cell,
comprise a specific inhibitor of an enhancer RNA (eRNA). In certain
aspects, the specific inhibitor of an enhancer RNA (eRNA) is an
antisense compound. In several aspects, the antisense compound is
single-stranded; double-stranded; modified; 8 to 80 nucleosides in
length; 12 to 30 nucleosides in length; 16 nucleosides in length;
includes at least one modified sugar, such as a bicyclic sugar, a
2'-O-methoxyethyl group, and/or a 4'-CH(CH.sub.3)--O-2' group;
includes at least one modified internucleoside linkage, such as a
phosphorothioate internucleoside linkage; and/or includes at least
one modified nucleobase, such as a 5-methylcytosine.
[0011] In further aspects, the antisense compound includes a gap
segment consisting of linked deoxynucleosides; a 5' wing segment
consisting of linked nucleosides; and a 3' wing segment consisting
of linked nucleosides, wherein the gap segment is positioned
between the 5' wing segment and the 3' wing segment and wherein
each nucleoside of each wing segment comprises a modified
sugar.
[0012] In another aspect, the antisense compound includes a gap
segment consisting of ten linked deoxynucleosides; a 5' wing
segment consisting of 3 linked nucleosides; and a 3' wing segment
consisting of 3 linked nucleosides; wherein the gap segment is
positioned between the 5' wing segment and the 3' wing segment,
wherein each nucleoside of each wing segment comprises a
2'-O-methoxyethyl sugar or a constrained ethyl sugar; and wherein
each internucleoside linkage is a phosphorothioate linkage.
[0013] In certain aspects, the 3 linked nucleosides of the 5' wing
segment comprise a 2'-O-methoxyethyl sugar, a constrained ethyl
sugar, and a constrained ethyl sugar in the 5' to 3' direction, and
the 3 linked nucleosides of the 3' wing segment comprise a
constrained ethyl sugar, a constrained ethyl sugar, and a
2'-O-methoxyethyl sugar in the 5' to 3' direction.
[0014] In further aspects, the antisense oligonucleotide comprises
a gap segment of ten 2'-deoxynucleotides positioned between wing
segments of five 2'-MOE nucleotides.
[0015] In additional aspects, the antisense compound comprises the
sequence of any one of SEQ ID NOs: 2, 3, or 124-201 targeted to an
eRNA that enhances transcription of MMP9.
[0016] In certain aspects, the antisense compound is targeted to an
eRNA that enhances transcription of CX3CR1, CA12, FOXC1, GREB1,
P2RY2, SMAD7, PGR, SIAH2, NRIP1, TFF1, or KCNK5.
[0017] In several embodiments, antisense compounds comprise any one
of the following pairs of sequences: SEQ ID NOs: 11-12; SEQ ID NOs:
13-14; or SEQ ID NOs: 15-16, or any one of SEQ ID NOs: 60-63
targeted to an eRNA that enhances transcription of TFF1.
[0018] In several embodiments, antisense compounds comprise any one
of the following pairs of sequences: SEQ ID NOs: 17-18; SEQ ID NOs:
19-20; or SEQ ID NOs: 21-22 targeted to an eRNA that enhances
transcription of GREB1.
[0019] In several embodiments, antisense compounds comprise any one
of the following pairs of sequences: SEQ ID NOs: 23-24 or SEQ ID
NOs: 25-26 targeted to an eRNA that enhances transcription of
PGR.
[0020] In several embodiments, antisense compounds comprise any one
of the following pairs of sequences: SEQ ID NOs: 27-28 or SEQ ID
NOs: 29-30 targeted to an eRNA that enhances transcription of
SIAH2.
[0021] In several embodiments, antisense compounds comprise any one
of the following pairs of sequences: SEQ ID NOs: 31-32 or SEQ ID
NOs: 33-34, or any one of SEQ ID NOs: 68 and 69 targeted to an eRNA
that enhances transcription of NRIP1.
[0022] In several embodiments, antisense compounds comprise any one
of the following pairs of sequences: SEQ ID NOs: 35-36 or SEQ ID
NOs: 37-38, or any one of SEQ ID NOs: 66 and 77 targeted to an eRNA
that enhances transcription of FOXC1.
[0023] In several embodiments, antisense compounds comprise any one
of the following pairs of sequences: SEQ ID NOs: 39-40 or SEQ ID
NOs: 41-42 targeted to an eRNA that enhances transcription of
P2RY2.
[0024] In several embodiments, antisense compounds comprise any one
of the following pairs of sequences: SEQ ID NOs: 43-44 or SEQ ID
NOs: 45-46, or any one of SEQ ID NOs: 64 and 65 targeted to an eRNA
that enhances transcription of CA12.
[0025] In several embodiments, antisense compounds comprise any one
of the following pairs of sequences: SEQ ID NOs 47-48, SEQ ID NOs:
49-50, or SEQ ID NOs: 51-52 targeted to an eRNA that enhances
transcription of SMAD7.
[0026] In several embodiments, antisense compounds comprise any one
of the following pairs of sequences: SEQ ID NOs: 53-54, SEQ ID NOs:
55-56, or SEQ ID NOs: 57-5 targeted to an eRNA that enhances
transcription of KCNK5.
DETAILED DESCRIPTION
[0027] It is to be understood that both the foregoing general
description and the following detailed description are exemplary
and explanatory only and are not restrictive of the invention, as
claimed. Herein, the use of the singular includes the plural unless
specifically stated otherwise. As used herein, the use of"or" means
"and/or" unless stated otherwise. Furthermore, the use of the term
"including" as well as other forms, such as "includes" and
"included", is not limiting. Also, terms such as "element" or
"component" encompass both elements and components comprising one
unit and elements and components that comprise more than one
subunit, unless specifically stated otherwise.
[0028] The section headings used herein are for organizational
purposes only and are not to be construed as limiting the subject
matter described. All documents, or portions of documents, cited in
this application, including, but not limited to, patents, patent
applications, articles, books, and treatises, are hereby expressly
incorporated by reference for the portions of the document
discussed herein, as well as in their entirety.
Definitions
[0029] Unless specific definitions are provided, the nomenclature
utilized in connection with, and the procedures and techniques of,
analytical chemistry, synthetic organic chemistry, and medicinal
and pharmaceutical chemistry described herein are those well known
and commonly used in the art. Standard techniques may be used for
chemical synthesis, and chemical analysis. Where permitted, all
patents, applications, published applications and other
publications, GENBANK Accession Numbers and associated sequence
information obtainable through databases such as National Center
for Biotechnology Information (NCBI) and other data referred to
throughout in the disclosure herein are incorporated by reference
for the portions of the document discussed herein, as well as in
their entirety.
[0030] Unless otherwise indicated, the following terms have the
following meanings:
[0031] "2'-O-methoxyethyl" (also 2'-MOE and
2'-O(CH.sub.2).sub.2--OCH.sub.3) refers to an O-methoxy-ethyl
modification at the 2' position of a furanose ring. A
2'-O-methoxyethyl modified sugar is a modified sugar.
[0032] "2'-MOE nucleoside" (also 2'-O-methoxyethyl nucleoside)
means a nucleoside comprising a 2'-MOE modified sugar moiety.
[0033] "2'-substituted nucleoside" means a nucleoside comprising a
substituent at the 2'-position of the furanosyl ring other than H
or OH. In certain embodiments, 2' substituted nucleosides include
nucleosides with bicyclic sugar modifications.
[0034] "3' target site" refers to the nucleotide of a target
nucleic acid which is complementary to the 3'-most nucleotide of a
particular antisense compound.
[0035] "5' target site" refers to the nucleotide of a target
nucleic acid which is complementary to the 5'-most nucleotide of a
particular antisense compound.
[0036] "5-methylcytosine" means a cytosine modified with a methyl
group attached to the 5 position. A 5-methylcytosine is a modified
nucleobase.
[0037] "About" means within +7% of a value. For example, if it is
stated, "the compounds affected at least about 70% inhibition of
eRNA", it is implied that the eRNA levels are inhibited within a
range of 63% and 77%.
[0038] "Animal" refers to a human or non-human animal, including,
but not limited to, mice, rats, rabbits, dogs, cats, pigs, and
non-human primates, including, but not limited to, monkeys and
chimpanzees.
[0039] "Antibody" refers to a molecule characterized by reacting
specifically with an antigen in some way, where the antibody and
the antigen are each defined in terms of the other. Antibody may
refer to a complete antibody molecule or any fragment or region
thereof, such as the heavy chain, the light chain, F.sub.a region,
and F.sub.c region.
[0040] "Antisense activity" means any detectable or measurable
activity attributable to the hybridization of an antisense compound
to its target nucleic acid. In certain embodiments, antisense
activity is a decrease in the amount or expression of a target
nucleic acid or protein encoded by such target nucleic acid.
[0041] "Antisense compound" means an oligomeric compound that is is
capable of undergoing hybridization to a target nucleic acid
through hydrogen bonding. Examples of antisense compounds include
single-stranded and double-stranded compounds, such as, antisense
oligonucleotides, siRNAs, shRNAs, snoRNAs, miRNAs, and satellite
repeats.
[0042] "Antisense inhibition" means reduction of target nucleic
acid levels in the presence of an antisense compound complementary
to a target nucleic acid compared to target nucleic acid levels in
the absence of the antisense compound.
[0043] "Antisense mechanisms" are all those mechanisms involving
hybridization of a compound with target nucleic acid, wherein the
outcome or effect of the hybridization is either target degradation
or target occupancy with concomitant stalling of the cellular
machinery involving, for example, transcription or splicing.
[0044] "Antisense oligonucleotide" means a single-stranded
oligonucleotide having a nucleobase sequence that permits
hybridization to a corresponding region or segment of a target
nucleic acid.
[0045] "Base complementarity" refers to the capacity for the
precise base pairing of nucleobases of an antisense oligonucleotide
with corresponding nucleobases in a target nucleic acid (i.e.,
hybridization), and is mediated by Watson-Crick, Hoogsteen or
reversed Hoogsteen hydrogen binding between corresponding
nucleobases.
[0046] "Bicyclic sugar" means a furanose ring modified by the
bridging of two non-geminal carbon atoms. A bicyclic sugar is a
modified sugar.
[0047] "Bicyclic nucleic acid" or "BNA" or "BNA nucleosides" means
nucleic acid monomers having a bridge connecting two carbon atoms
between the 4' and 2' position of the nucleoside sugar unit,
thereby forming a bicyclic sugar. Examples of such bicyclic sugar
include, but are not limited to A) .alpha.-L-Methyleneoxy
(4'-CH.sub.2--O-2') LNA, (B) .beta.-D-Methyleneoxy
(4'-CH.sub.2--O-2') LNA, (C) Ethyleneoxy
(4'-(CH.sub.2).sub.2--O-2') LNA, (D) Aminooxy
(4'-CH.sub.2--O--N(R)-2') LNA and (E) Oxyamino
(4'-CH.sub.2--N(R)--O-2') LNA, as depicted below.
##STR00001##
[0048] As used herein, LNA compounds include, but are not limited
to, compounds having at least one bridge between the 4' and the 2'
position of the sugar wherein each of the bridges independently
comprises 1 or from 2 to 4 linked groups independently selected
from --[C(R.sub.1)(R.sub.2)].sub.n--,
--C(R.sub.1).dbd.C(R.sub.2)--, --C(R.sub.1).dbd.N--,
--C(.dbd.NR.sub.1)--, --C(.dbd.O)--, --C(.dbd.S)--, --O--,
--Si(R.sub.1).sub.2--, --S(.dbd.O).sub.x-- and --N(R.sub.1)--;
wherein: x is 0, 1, or 2; n is 1, 2, 3, or 4; each R.sub.1 and
R.sub.2 is, independently, H, a protecting group, hydroxyl,
C.sub.1-C.sub.12 alkyl, substituted C.sub.1-C.sub.12 alkyl,
C.sub.2-C.sub.12 alkenyl, substituted C.sub.2-C.sub.12 alkenyl,
C.sub.2-C.sub.12 alkynyl, substituted C.sub.2-C.sub.12 alkynyl,
C.sub.5-C.sub.20 aryl, substituted C.sub.5-C.sub.20 aryl, a
heterocycle radical, a substituted heterocycle radical, heteroaryl,
substituted heteroaryl, C.sub.5-C.sub.7 alicyclic radical,
substituted C.sub.5-C.sub.7 alicyclic radical, halogen, OJ.sub.1,
NJ.sub.1J.sub.2, SJ.sub.1, N.sub.3, COOJ.sub.1, acyl
(C(.dbd.O)--H), substituted acyl, CN, sulfonyl
(S(.dbd.O).sub.2-J.sub.1), or sulfoxyl (S(.dbd.O)-J.sub.1); and
each J.sub.1 and J.sub.2 is, independently, H, C.sub.1-C.sub.12
alkyl, substituted C.sub.1-C.sub.12 alkyl, C.sub.2-C.sub.12
alkenyl, substituted C.sub.2-C.sub.12 alkenyl, C.sub.2-C.sub.12
alkynyl, substituted C.sub.2-C.sub.12 alkynyl, C.sub.5-C.sub.20
aryl, substituted C.sub.5-C.sub.20 aryl, acyl (C(.dbd.O)--H),
substituted acyl, a heterocycle radical, a substituted heterocycle
radical, C.sub.1-C.sub.12 aminoalkyl, substituted C.sub.1-C.sub.12
aminoalkyl or a protecting group.
[0049] Examples of 4'-2' bridging groups encompassed within the
definition of LNA include, but are not limited to one of formulae:
--[C(R.sub.1)(R.sub.2)].sub.n--, --[C(R.sub.1)(R.sub.2)]n-O--,
--C(R.sub.1R.sub.2)--N(R.sub.1)--O-- or
--C(R.sub.1R.sub.2)--O--N(R.sub.1)--. Furthermore, other bridging
groups encompassed with the definition of LNA are 4'-CH.sub.2-2',
4'-(CH.sub.2).sub.2-2', 4'-(CH.sub.2).sub.3-2', 4'-CH.sub.2--O-2',
4'-(CH.sub.2).sub.2--O-2', 4'-CH.sub.2--O--N(R.sub.1)-2' and
4'-CH.sub.2--N(R.sub.1)--O-2'- bridges, wherein each R.sub.1 and
R.sub.2 is, independently, H, a protecting group or
C.sub.1-C.sub.12 alkyl.
[0050] Also included within the definition of LNA according to the
invention are LNAs in which the 2'-hydroxyl group of the ribosyl
sugar ring is connected to the 4' carbon atom of the sugar ring,
thereby forming a methyleneoxy (4'-CH.sub.2--O-2') bridge to form
the bicyclic sugar moiety. The bridge can also be a methylene
(--CH.sub.2--) group connecting the 2' oxygen atom and the 4'
carbon atom, for which the term methyleneoxy (4'-CH.sub.2--O-2')
LNA is used. Furthermore; in the case of the bicyclic sugar moiety
having an ethylene bridging group in this position, the term
ethyleneoxy (4'-CH.sub.2CH.sub.2--O-2') LNA is used.
.alpha.-L-methyleneoxy (4'-CH.sub.2--O-2'), an isomer of
methyleneoxy (4'-CH.sub.2--O-2') LNA is also encompassed within the
definition of LNA, as used herein.
[0051] "Cap structure" or "terminal cap moiety" means chemical
modifications, which have been incorporated at either terminus of
an antisense compound.
[0052] "cEt" or "constrained ethyl" means a bicyclic sugar moiety
comprising a bridge connecting the 4'-carbon and the 2'-carbon,
wherein the bridge has the formula: 4'-CH(CH.sub.3)--O-2'.
[0053] "Constrained ethyl nucleoside" (also cEt nucleoside) means a
nucleoside comprising a bicyclic sugar moiety comprising a
4'-CH(CH.sub.3)--O-2' bridge.
[0054] "Chemically distinct region" refers to a region of an
antisense compound that is in some way chemically different than
another region of the same antisense compound. For example, a
region having 2'-O-methoxyethyl nucleotides is chemically distinct
from a region having nucleotides without 2'-O-methoxyethyl
modifications.
[0055] "Chimeric antisense compounds" means antisense compounds
that have at least 2 chemically distinct regions, each position
having a plurality of subunits.
[0056] "Complementarity" means the capacity for pairing between
nucleobases of a first nucleic acid and a second nucleic acid.
[0057] "Comply" means the adherence with a recommended therapy by
an individual.
[0058] "Comprise," "comprises" and "comprising" will be understood
to imply the inclusion of a stated step or element or group of
steps or elements but not the exclusion of any other step or
element or group of steps or elements.
[0059] "Contiguous nucleobases" means nucleobases immediately
adjacent to each other.
[0060] "Deoxyribonucleotide" means a nucleotide having a hydrogen
at the 2' position of the sugar portion of the nucleotide.
Deoxyribonucleotides may be modified with any of a variety of
substituents.
[0061] "Designing" or "Designed to" refer to the process of
designing an oligomeric compound that specifically hybridizes with
a selected nucleic acid molecule.
[0062] "Efficacy" means the ability to produce a desired
effect.
[0063] "Enhancer" refers to a DNA sequence or region located at
some distance away from a gene and capable of stimulating
transcription of the gene. In certain embodiments, an enhancer is
capable of binding to transcription factors and stimulating
promoters
[0064] "Enhancer RNA (eRNA)" refers to a ribonucleotide transcribed
from a genomic enhancer nucleic acid sequence or region or
region.
[0065] "Expression" includes all the functions by which a gene's
coded information is converted into structures present and
operating in a cell. Such structures include, but are not limited
to the products of transcription and translation.
[0066] "Fully complementary" or "100% complementary" means each
nucleobase of a first nucleic acid has a complementary nucleobase
in a second nucleic acid. In certain embodiments, a first nucleic
acid is an antisense compound and a target nucleic acid is a second
nucleic acid.
[0067] "Fully modified motif" refers to an antisense compound
comprising a contiguous sequence of nucleosides wherein essentially
each nucleoside is a sugar modified nucleoside having uniform
modification.
[0068] "Gapmer" means a chimeric antisense compound in which an
internal region having a plurality of nucleosides that support
RNase H cleavage is positioned between external regions having one
or more nucleosides, wherein the nucleosides comprising the
internal region are chemically distinct from the nucleoside or
nucleosides comprising the external regions. The internal region
may be referred to as the "gap" and the external regions may be
referred to as the "wings."
[0069] "Gap-widened" means an antisense compound having a gap
segment of 12 or more contiguous 2'-deoxyribonucleotides positioned
between 5' and 3' wing segments having from one to six nucleotides
having modified sugar moieties.
[0070] "Hybridization" means the annealing of complementary nucleic
acid molecules. In certain embodiments, complementary nucleic acid
molecules include, but are not limited to, an antisense compound
and a nucleic acid target. In certain embodiments, complementary
nucleic acid molecules include, but are not limited to, an
antisense oligonucleotide and a nucleic acid target.
[0071] "Immediately adjacent" means there are no intervening
elements between the immediately adjacent elements.
[0072] "Individual" means a human or non-human animal selected for
treatment or therapy.
[0073] "Induce", "inhibit", "potentiate", "elevate", "increase",
"decrease" or the like, generally denote quantitative differences
between two states.
[0074] "Inhibiting the expression or activity" refers to a
reduction, blockade of the expression or activity and does not
necessarily indicate a total elimination of expression or
activity.
[0075] "Internucleoside linkage" refers to the chemical bond
between nucleosides.
[0076] "Lengthened" antisense oligonucleotides are those that have
one or more additional nucleosides relative to an antisense
oligonucleotide disclosed herein.
[0077] "Linked deoxynucleoside" means a nucleic acid base (A, G, C,
T, U) substituted by deoxyribose linked by a phosphate ester to
form a nucleotide.
[0078] "Linked nucleosides" means adjacent nucleosides linked
together by an internucleoside linkage.
[0079] "Mismatch" or "non-complementary nucleobase" refers to the
case when a nucleobase of a first nucleic acid is not capable of
pairing with the corresponding nucleobase of a second or target
nucleic acid.
[0080] "Modified internucleoside linkage" refers to a substitution
or any change from a naturally occurring internucleoside bond (i.e.
a phosphodiester internucleoside bond).
[0081] "Modified nucleobase" means any nucleobase other than
adenine, cytosine, guanine, thymidine, or uracil. An "unmodified
nucleobase" means the purine bases adenine (A) and guanine (G), and
the pyrimidine bases thymine (T), cytosine (C) and uracil (U).
[0082] "Modified nucleoside" means a nucleoside having,
independently, a modified sugar moiety and/or modified
nucleobase.
[0083] "Modified nucleotide" means a nucleotide having,
independently, a modified sugar moiety, modified internucleoside
linkage, or modified nucleobase.
[0084] "Modified oligonucleotide" means an oligonucleotide
comprising at least one modified internucleoside linkage, a
modified sugar, and/or a modified nucleobase.
[0085] "Modified sugar" means substitution and/or any change from a
natural sugar moiety.
[0086] "Monomer" refers to a single unit of an oligomer. Monomers
include, but are not limited to, nucleosides and nucleotides,
whether naturally occurring or modified.
[0087] "Motif" means the pattern of unmodified and modified
nucleosides in an antisense compound.
[0088] "Natural sugar moiety" means a sugar moiety found in DNA
(2'-H) or RNA (2'-OH).
[0089] "Naturally occurring internucleoside linkage" means a 3' to
5' phosphodiester linkage.
[0090] "Non-complementary nucleobase" refers to a pair of
nucleobases that do not form hydrogen bonds with one another or
otherwise support hybridization.
[0091] "Nucleic acid" refers to molecules composed of monomeric
nucleotides. A nucleic acid includes, but is not limited to,
ribonucleic acids (RNA), deoxyribonucleic acids (DNA),
single-stranded nucleic acids, double-stranded nucleic acids, small
interfering ribonucleic acids (siRNA), and microRNAs (miRNA).
[0092] "Nucleobase" means a heterocyclic moiety capable of pairing
with a base of another nucleic acid.
[0093] "Nucleobase complementarity" refers to a nucleobase that is
capable of base pairing with another nucleobase. For example, in
DNA, adenine (A) is complementary to thymine (T). For example, in
RNA, adenine (A) is complementary to uracil (U). In certain
embodiments, complementary nucleobase refers to a nucleobase of an
antisense compound that is capable of base pairing with a
nucleobase of its target nucleic acid. For example, if a nucleobase
at a certain position of an antisense compound is capable of
hydrogen bonding with a nucleobase at a certain position of a
target nucleic acid, then the position of hydrogen bonding between
the oligonucleotide and the target nucleic acid is considered to be
complementary at that nucleobase pair.
[0094] "Nucleobase sequence" means the order of contiguous
nucleobases independent of any sugar, linkage, and/or nucleobase
modification.
[0095] "Nucleoside" means a nucleobase linked to a sugar.
[0096] "Nucleoside mimetic" includes those structures used to
replace the sugar or the sugar and the base and not necessarily the
linkage at one or more positions of an oligomeric compound such as
for example nucleoside mimetics having morpholino, cyclohexenyl,
cyclohexyl, tetrahydropyranyl, bicyclo or tricyclo sugar mimetics,
e.g., non furanose sugar units. Nucleotide mimetic includes those
structures used to replace the nucleoside and the linkage at one or
more positions of an oligomeric compound such as for example
peptide nucleic acids or morpholinos (morpholinos linked by
--N(H)--C(.dbd.O)--O-- or other non-phosphodiester linkage). Sugar
surrogate overlaps with the slightly broader term nucleoside
mimetic but is intended to indicate replacement of the sugar unit
(furanose ring) only. The tetrahydropyranyl rings provided herein
are illustrative of an example of a sugar surrogate wherein the
furanose sugar group has been replaced with a tetrahydropyranyl
ring system. "Mimetic" refers to groups that are substituted for a
sugar, a nucleobase, and/or internucleoside linkage. Generally, a
mimetic is used in place of the sugar or sugar-internucleoside
linkage combination, and the nucleobase is maintained for
hybridization to a selected target.
[0097] "Nucleotide" means a nucleoside having a phosphate group
covalently linked to the sugar portion of the nucleoside.
[0098] "Off-target effect" refers to an unwanted or deleterious
biological effect associated with modulation of RNA or protein
expression of a gene other than the intended target nucleic
acid.
[0099] "Oligomeric compound" means a polymer of linked monomeric
subunits which is capable of hybridizing to at least a region of a
nucleic acid molecule.
[0100] "Oligonucleoside" means an oligonucleotide in which the
internucleoside linkages do not contain a phosphorus atom.
[0101] "Oligonucleotide" means a polymer of linked nucleosides each
of which can be modified or unmodified, independent one from
another.
[0102] "Peptide" means a molecule formed by linking at least two
amino acids by amide bonds. Without limitation, as used herein,
"peptide" refers to polypeptides and proteins.
[0103] "Phosphorothioate linkage" means a linkage between
nucleosides where the phosphodiester bond is modified by replacing
one of the non-bridging oxygen atoms with a sulfur atom. A
phosphorothioate linkage is a modified internucleoside linkage.
[0104] "Portion" means a defined number of contiguous (i.e.,
linked) nucleobases of a nucleic acid. In certain embodiments, a
portion is a defined number of contiguous nucleobases of a target
nucleic acid. In certain embodiments, a portion is a defined number
of contiguous nucleobases of an antisense compound
[0105] "Region" is defined as a portion of the target nucleic acid
having at least one identifiable structure, function, or
characteristic.
[0106] "Ribonucleotide" means a nucleotide having a hydroxy at the
2' position of the sugar portion of the nucleotide. Ribonucleotides
may be modified with any of a variety of substituents.
[0107] "Segments" are defined as smaller or sub-portions of regions
within a target nucleic acid.
[0108] "Sites," as used herein, are defined as unique nucleobase
positions within a target nucleic acid.
[0109] "Specifically hybridizable" refers to an antisense compound
having a sufficient degree of complementarity between an antisense
oligonucleotide and a target nucleic acid to induce a desired
effect, while exhibiting minimal or no effects on non-target
nucleic acids under conditions in which specific binding is
desired, i.e., under physiological conditions in the case of in
vivo assays and therapeutic treatments.
[0110] "Stringent hybridization conditions" or "stringent
conditions" refer to conditions under which an oligomeric compound
will hybridize to its target sequence, but to a minimal number of
other sequences.
[0111] "Subject" means a human or non-human animal selected for
treatment or therapy.
[0112] "Target" refers to a protein, the modulation of which is
desired.
[0113] "Target gene" refers to a gene encoding a target.
[0114] "Targeting" means the process of design and selection of an
antisense compound that will specifically hybridize to a target
nucleic acid and induce a desired effect.
[0115] "Target nucleic acid," "target RNA," "target RNA transcript"
and "nucleic acid target" all mean a nucleic acid capable of being
targeted by antisense compounds.
[0116] "Target region" means a portion of a target nucleic acid to
which one or more antisense compounds is targeted.
[0117] "Target segment" means the sequence of nucleotides of a
target nucleic acid to which an antisense compound is targeted. "5'
target site" refers to the 5'-most nucleotide of a target segment.
"3' target site" refers to the 3'-most nucleotide of a target
segment.
[0118] "Unmodified" nucleobases mean the purine bases adenine (A)
and guanine (G), and the pyrimidine bases thymine (T), cytosine (C)
and uracil (U).
[0119] "Unmodified nucleotide" means a nucleotide composed of
naturally occurring nucleobases, sugar moieties, and
internucleoside linkages. In certain embodiments, an unmodified
nucleotide is an RNA nucleotide (i.e. .beta.-D-ribonucleosides) or
a DNA nucleotide (i.e. .beta.-D-deoxyribonucleoside).
[0120] "Validated target segment" is defined as at least an
8-nucleobase portion (i.e. 8 consecutive nucleobases) of a target
region to which an antisense compound is targeted.
[0121] "Wing segment" means a plurality of nucleosides modified to
impart to an oligonucleotide properties such as enhanced inhibitory
activity, increased binding affinity for a target nucleic acid, or
resistance to degradation by in vivo nucleases.
Antisense Compounds
[0122] Oligomeric compounds include, but are not limited to,
oligonucleotides, oligonucleosides, oligonucleotide analogs,
oligonucleotide mimetics, antisense compounds, antisense
oligonucleotides, and siRNAs. An oligomeric compound may be
"antisense" to a target nucleic acid, meaning that is is capable of
undergoing hybridization to a target nucleic acid through hydrogen
bonding.
[0123] In certain embodiments, an antisense compound has a
nucleobase sequence that, when written in the 5' to 3' direction,
comprises the reverse complement of the target segment of a target
nucleic acid to which it is targeted. In certain such embodiments,
an antisense oligonucleotide has a nucleobase sequence that, when
written in the 5' to 3' direction, comprises the reverse complement
of the target segment of a target nucleic acid to which it is
targeted.
[0124] In certain embodiments, an antisense compound is 10-30
subunits in length. In certain embodiments, an antisense compound
is 12 to 30 subunits in length. In certain embodiments, an
antisense compound is 12 to 22 subunits in length. In certain
embodiments, an antisense compound is 14 to 30 subunits in length.
In certain embodiments, an antisense compound is 14 to 20 subunits
in length. In certain embodiments, an antisense compound is 15 to
30 subunits in length. In certain embodiments, an antisense
compound is 15 to 20 subunits in length. In certain embodiments, an
antisense compound is 16 to 30 subunits in length. In certain
embodiments, an antisense compound is 16 to 20 subunits in length.
In certain embodiments, an antisense compound is 17 to 30 subunits
in length. In certain embodiments, an antisense compound is 17 to
20 subunits in length. In certain embodiments, an antisense
compound is 18 to 30 subunits in length. In certain embodiments, an
antisense compound is 18 to 21 subunits in length. In certain
embodiments, an antisense compound is 18 to 20 subunits in length.
In certain embodiments, an antisense compound is 20 to 30 subunits
in length. In other words, such antisense compounds are from 12 to
30 linked subunits, 14 to 30 linked subunits, 14 to 20 subunits, 15
to 30 subunits, 15 to 20 subunits, 16 to 30 subunits, 16 to 20
subunits, 17 to 30 subunits, 17 to 20 subunits, 18 to 30 subunits,
18 to 20 subunits, 18 to 21 subunits, 20 to 30 subunits, or 12 to
22 linked subunits, respectively. In certain embodiments, an
antisense compound is 14 subunits in length. In certain
embodiments, an antisense compound is 16 subunits in length. In
certain embodiments, an antisense compound is 17 subunits in
length. In certain embodiments, an antisense compound is 18
subunits in length. In certain embodiments, an antisense compound
is 20 subunits in length. In other embodiments, the antisense
compound is 8 to 80, 12 to 50, 13 to 30, 13 to 50, 14 to 30, 14 to
50, 15 to 30, 15 to 50, 16 to 30, 16 to 50, 17 to 30, 17 to 50, 18
to 22, 18 to 24, 18 to 30, 18 to 50, 19 to 22, 19 to 30, 19 to 50,
or 20 to 30 linked subunits. In certain such embodiments, the
antisense compounds are 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52,
53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
70, 71, 72, 73, 74, 75, 76, 77, 78, 79, or 80 linked subunits in
length, or a range defined by any two of the above values. In some
embodiments the antisense compound is an antisense oligonucleotide,
and the linked subunits are nucleotides.
[0125] In certain embodiments antisense oligonucleotides may be
shortened or truncated. For example, a single subunit may be
deleted from the 5' end (5' truncation), or alternatively from the
3' end (3' truncation).
[0126] A shortened or truncated antisense compound targeted to an
eRNA nucleic acid may have two subunits deleted from the 5' end, or
alternatively may have two subunits deleted from the 3' end, of the
antisense compound.
[0127] Alternatively, the deleted nucleosides may be dispersed
throughout the antisense compound, for example, in an antisense
compound having one nucleoside deleted from the 5' end and one
nucleoside deleted from the 3' end.
[0128] When a single additional subunit is present in a lengthened
antisense compound, the additional subunit may be located at the 5'
or 3' end of the antisense compound. When two or more additional
subunits are present, the added subunits may be adjacent to each
other, for example, in an antisense compound having two subunits
added to the 5' end (5' addition), or alternatively to the 3' end
(3' addition), of the antisense compound. Alternatively, the added
subunits may be dispersed throughout the antisense compound, for
example, in an antisense compound having one subunit added to the
5' end and one subunit added to the 3' end.
[0129] It is possible to increase or decrease the length of an
antisense compound, such as an antisense oligonucleotide, and/or
introduce mismatch bases without eliminating activity. For example,
in Woolf et al. (Proc. Natl. Acad. Sci. USA 89:7305-7309, 1992), a
series of antisense oligonucleotides 13-25 nucleobases in length
were tested for their ability to induce cleavage of a target RNA in
an oocyte injection model. Antisense oligonucleotides 25
nucleobases in length with 8 or 11 mismatch bases near the ends of
the antisense oligonucleotides were able to direct specific
cleavage of the target mRNA, albeit to a lesser extent than the
antisense oligonucleotides that contained no mismatches. Similarly,
target specific cleavage was achieved using 13 nucleobase antisense
oligonucleotides, including those with 1 or 3 mismatches.
[0130] Gautschi et al. (J. Natl. Cancer Inst. 93:463-471, March
2001) demonstrated the ability of an oligonucleotide having 100%
complementarity to the bcl-2 mRNA and having 3 mismatches to the
bcl-xL mRNA to reduce the expression of both bcl-2 and bcl-xL in
vitro and in vivo. Furthermore, this oligonucleotide demonstrated
potent anti-tumor activity in vivo.
[0131] Maher and Dolnick (Nuc. Acid. Res. 16:3341-3358, 1988)
tested a series of tandem 14 nucleobase antisense oligonucleotides,
and a 28 and 42 nucleobase antisense oligonucleotides comprised of
the sequence of two or three of the tandem antisense
oligonucleotides, respectively, for their ability to arrest
translation of human DHFR in a rabbit reticulocyte assay. Each of
the three 14 nucleobase antisense oligonucleotides alone was able
to inhibit translation, albeit at a more modest level than the 28
or 42 nucleobase antisense oligonucleotides.
Certain Antisense Compound Motifs and Mechanisms
[0132] In certain embodiments, antisense compounds have chemically
modified subunits arranged in patterns, or motifs, to confer to the
antisense compounds properties such as enhanced inhibitory
activity, increased binding affinity for a target nucleic acid, or
resistance to degradation by in vivo nucleases.
[0133] Chimeric antisense compounds typically contain at least one
region modified so as to confer increased resistance to nuclease
degradation, increased cellular uptake, increased binding affinity
for the target nucleic acid, and/or increased inhibitory activity.
A second region of a chimeric antisense compound may confer another
desired property e.g., serve as a substrate for the cellular
endonuclease RNase H, which cleaves the RNA strand of an RNA:DNA
duplex.
[0134] Antisense activity may result from any mechanism involving
the hybridization of the antisense compound (e.g., oligonucleotide)
with a target nucleic acid, wherein the hybridization ultimately
results in a biological effect. In certain embodiments, the amount
and/or activity of the target nucleic acid is modulated. In certain
embodiments, the amount and/or activity of the target nucleic acid
is reduced. In certain embodiments, hybridization of the antisense
compound to the target nucleic acid ultimately results in target
nucleic acid degradation. In certain embodiments, hybridization of
the antisense compound to the target nucleic acid does not result
in target nucleic acid degradation. In certain such embodiments,
the presence of the antisense compound hybridized with the target
nucleic acid (occupancy) results in a modulation of antisense
activity. In certain embodiments, antisense compounds having a
particular chemical motif or pattern of chemical modifications are
particularly suited to exploit one or more mechanisms. In certain
embodiments, antisense compounds function through more than one
mechanism and/or through mechanisms that have not been elucidated.
Accordingly, the antisense compounds described herein are not
limited by particular mechanism.
[0135] Antisense mechanisms include, without limitation, RNase H
mediated antisense; RNAi mechanisms, which utilize the RISC pathway
and include, without limitation, siRNA, ssRNA and microRNA
mechanisms; and occupancy based mechanisms. Certain antisense
compounds may act through more than one such mechanism and/or
through additional mechanisms.
RNase H-Mediated Antisense
[0136] In certain embodiments, antisense activity results at least
in part from degradation of target RNA by RNase H. RNase H is a
cellular endonuclease that cleaves the RNA strand of an RNA:DNA
duplex. It is known in the art that single-stranded antisense
compounds which are "DNA-like" elicit RNase H activity in mammalian
cells. Accordingly, antisense compounds comprising at least a
portion of DNA or DNA-like nucleosides may activate RNase H,
resulting in cleavage of the target nucleic acid. In certain
embodiments, antisense compounds that utilize RNase H comprise one
or more modified nucleosides. In certain embodiments, such
antisense compounds comprise at least one block of 1-8 modified
nucleosides. In certain such embodiments, the modified nucleosides
do not support RNase H activity. In certain embodiments, such
antisense compounds are gapmers, as described herein. In certain
such embodiments, the gap of the gapmer comprises DNA nucleosides.
In certain such embodiments, the gap of the gapmer comprises
DNA-like nucleosides. In certain such embodiments, the gap of the
gapmer comprises DNA nucleosides and DNA-like nucleosides.
[0137] Certain antisense compounds having a gapmer motif are
considered chimeric antisense compounds. In a gapmer an internal
region having a plurality of nucleotides that supports RNaseH
cleavage is positioned between external regions having a plurality
of nucleotides that are chemically distinct from the nucleosides of
the internal region. In the case of an antisense oligonucleotide
having a gapmer motif, the gap segment generally serves as the
substrate for endonuclease cleavage, while the wing segments
comprise modified nucleosides. In certain embodiments, the regions
of a gapmer are differentiated by the types of sugar moieties
comprising each distinct region. The types of sugar moieties that
are used to differentiate the regions of a gapmer may in some
embodiments include .beta.-D-ribonucleosides,
.beta.-D-deoxyribonucleosides, 2'-modified nucleosides (such
2'-modified nucleosides may include 2'-MOE and 2'-O--CH.sub.3,
among others), and bicyclic sugar modified nucleosides (such
bicyclic sugar modified nucleosides may include those having a
constrained ethyl). In certain embodiments, nucleosides in the
wings may include several modified sugar moieties, including, for
example 2'-MOE and bicyclic sugar moieties such as constrained
ethyl or LNA. In certain embodiments, wings may include several
modified and unmodified sugar moieties. In certain embodiments,
wings may include various combinations of 2'-MOE nucleosides,
bicyclic sugar moieties such as constrained ethyl nucleosides or
LNA nucleosides, and 2'-deoxynucleosides.
[0138] Each distinct region may comprise uniform sugar moieties,
variant, or alternating sugar moieties. The wing-gap-wing motif is
frequently described as "X--Y--Z", where "X" represents the length
of the 5'-wing, "Y" represents the length of the gap, and "Z"
represents the length of the 3'-wing. "X" and "Z" may comprise
uniform, variant, or alternating sugar moieties. In certain
embodiments, "X" and "Y" may include one or more
2'-deoxynucleosides. "Y" may comprise 2'-deoxynucleosides. As used
herein, a gapmer described as "X--Y--Z" has a configuration such
that the gap is positioned immediately adjacent to each of the
5'-wing and the 3' wing. Thus, no intervening nucleotides exist
between the 5'-wing and gap, or the gap and the 3'-wing. Any of the
antisense compounds described herein can have a gapmer motif. In
certain embodiments, "X" and "Z" are the same; in other embodiments
they are different. In certain embodiments, "Y" is between 8 and 15
nucleosides. X, Y, or Z can be any of 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30 or more
nucleosides.
[0139] In certain embodiments, gapmers provided herein include, for
example, 11-mers having a motif of 1-9-1.
[0140] In certain embodiments, gapmers provided herein include, for
example, 12-mers having a motif of 1-9-2, 2-9-1, or 1-10-1.
[0141] In certain embodiments, gapmers provided herein include, for
example, 13-mers having a motif of 1-9-3, 2-9-2, 3-9-1, 1-10-2, or
2-10-1.
[0142] In certain embodiments, gapmers provided herein include, for
example, 14-mers having a motif of 1-9-4, 2-9-3, 3-9-2, 4-9-1,
1-10-3, 2-10-2, or 3-10-1.
[0143] In certain embodiments, gapmers provided herein include, for
example, 15-mers having a motif of 1-9-5, 2-9-4, 3-9-3, 4-9-2,
5-9-1, 1-10-4, 2-10-3, 3-10-2, or 4-10-1.
[0144] In certain embodiments, gapmers provided herein include, for
example, 16-mers having a motif of 4-8-4, 2-9-5, 3-9-4, 4-9-3,
5-9-2, 1-10-5, 2-10-4, 3-10-3, 4-10-2, 3-8-5, or 5-10-1.
[0145] In certain embodiments, gapmers provided herein include, for
example, 17-mers having a motif of 3-9-5, 3-10-4, 4-9-4, 5-9-3,
2-10-5, 3-10-4, 4-10-3, 5-10-2, 2-9-6, 5-8-4, 5-7-5, 6-7-4, or
6-9-2.
[0146] In certain embodiments, gapmers provided herein include, for
example, 18-mers having a motif of 4-9-5, 5-9-4, 3-10-5, 4-10-4, or
5-10-3.
[0147] In certain embodiments, gapmers provided herein include, for
example, 19-mers having a motif of 5-9-5, 4-10-5, or 5-10-4.
[0148] In certain embodiments, gapmers provided herein include, for
example, 20-mers having a motif of 5-10-5, 2-10-8, 8-10-2, 3-10-7,
7-10-3, 4-10-6, or 6-10-4.
[0149] In certain embodiments, the antisense compound has a
"wingmer" motif, having a wing-gap or gap-wing configuration, i.e.
an X--Y or Y--Z configuration as described above for the gapmer
configuration. Thus, wingmer configurations provided herein
include, but are not limited to, for example 5-10, 8-4, 4-12, 12-4,
3-14, 16-2, 18-1, 10-3, 2-10, 1-10, 8-2, 2-13, 5-13, 5-8, or
6-8.
[0150] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a 2-10-2 gapmer motif.
[0151] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a 3-10-3 gapmer motif.
[0152] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a 4-10-4 gapmer motif.
[0153] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a 5-10-5 gapmer motif.
[0154] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a 3-10-4 gapmer motif.
[0155] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a 2-10-4 gapmer motif.
[0156] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a 2-10-8 gapmer motif.
[0157] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a 8-10-2 gapmer motif.
[0158] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a 3-10-7 gapmer motif.
[0159] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a 7-10-3 gapmer motif.
[0160] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a 4-10-6 gapmer motif.
[0161] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a 6-10-4 gapmer motif.
[0162] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a 2-9-6 gapmer motif.
[0163] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a 6-9-2 gapmer motif.
[0164] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a 4-9-4 gapmer motif.
[0165] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a 5-9-3 gapmer motif.
[0166] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a 3-9-5 gapmer motif.
[0167] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a 5-9-2 gapmer motif.
[0168] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a 2-9-5 gapmer motif.
[0169] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a 4-9-3 gapmer motif.
[0170] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a 3-9-4 gapmer motif.
[0171] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a gap-widened motif.
[0172] In certain embodiments, the antisense compound targeted to
an eRNA nucleic acid has a gapmer motif in which the gap consists
of 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 16 linked
nucleosides.
[0173] In certain embodiments, the antisense compounds targeted to
an eRNA nucleic acid has any of the following sugar motifs:
k-d(10)-k
e-d(10)-k
k-d(10)-e
k-k-d(10)-k-k
k-k-d(10)-e-e
e-e-d(10)-k-k
k-k-k-d(10)-k-k-k
e-e-e-d(10)-k-k-k
k-k-k-d(10)-e-e-e
k-k-k-d(10)-k-k-k
e-k-k-d(10)-k-k-e
e-e-k-d(10)-k-k-e
e-d-k-d(10)-k-k-e
e-k-d(10)-k-e-k-e
k-d(10)-k-e-k-e-e
e-e-k-d(10)-k-e-k-e
e-d-d-k-d(9)-k-k-e
e-e-e-e-d(9)-k-k-e
e-e-e-e-e-d(10)-e-e-e-e-e
k-d-k-d-k-d(9)-e-e
e-e-k-k-d(9)-e-k-e-e
k-d-k-d-k-d(10)-e-e-e-e-e
k-e-k-d(10)-k-e-k
e-e-e-k-k-d(8)-e-e-e-e
e-e-e-k-k-d(7)-k-k-e-e-e
e-e-e-k-d(9)-k-e-e-e
e-e-e-k-k-d(7)-k-k-e-e-e
e-e-e-e-k-k-d(7)-e-e-e-e
e-k-e-k-d(9)-e-e-e-e
e-k-e-k-d-k-d(7)-e-e-e-e
e-e-e-k-k-d(7)-k-k-e-e-e
k-d-k-d-k-d(8)-e-e-e-e-e
wherein, k is a constrained ethyl nucleoside, e is a 2'-MOE
substituted nucleoside, and d is a 2'-deoxynucleoside.
[0174] In certain embodiments, the antisense oligonucleotide has a
sugar motif described by Formula A as follows:
(J).sub.m-(B).sub.n-(J).sub.p-(B).sub.r-(A).sub.t-(D).sub.g-(A).sub.v-(B)-
.sub.w-(J).sub.x-(B).sub.y-(J).sub.z wherein:
[0175] each A is independently a 2'-substituted nucleoside;
[0176] each B is independently a bicyclic nucleoside;
[0177] each J is independently either a 2'-substituted nucleoside
or a 2'-deoxynucleoside;
[0178] each D is a 2'-deoxynucleoside;
[0179] m is 0-4; n is 0-2; p is 0-2; r is 0-2; t is 0-2; v is 0-2;
w is 0-4; x is 0-2; y is 0-2; z is 0-4; g is 6-14; provided
that:
[0180] at least one of m, n, and r is other than 0;
[0181] at least one of w and y is other than 0;
[0182] the sum of m, n, p, r, and t is from 2 to 5; and the sum of
v, w, x, y, and z is from 2 to 5.
[0183] RNAi Compounds
[0184] In certain embodiments, antisense compounds are interfering
RNA compounds (RNAi), which include double-stranded RNA compounds
(also referred to as short-interfering RNA or siRNA) and
single-stranded RNAi compounds (or ssRNA). Such compounds work at
least in part through the RISC pathway to degrade and/or sequester
a target nucleic acid (thus, include microRNA/microRNA-mimic
compounds). In certain embodiments, antisense compounds comprise
modifications that make them particularly suited for such
mechanisms.
[0185] i. ssRNA compounds
[0186] In certain embodiments, antisense compounds including those
particularly suited for use as single-stranded RNAi compounds
(ssRNA) comprise a modified 5'-terminal end. In certain such
embodiments, the 5'-terminal end comprises a modified phosphate
moiety. In certain embodiments, such modified phosphate is
stabilized (e.g., resistant to degradation/cleavage compared to
unmodified 5'-phosphate). In certain embodiments, such 5'-terminal
nucleosides stabilize the 5'-phosphorous moiety. Certain modified
5'-terminal nucleosides may be found in the art, for example in
WO/2011/139702.
[0187] In certain embodiments, the 5'-nucleoside of an ssRNA
compound has Formula IIc:
##STR00002##
wherein:
[0188] T.sub.1 is an optionally protected phosphorus moiety;
[0189] T.sub.2 is an internucleoside linking group linking the
compound of Formula IIc to the oligomeric compound;
[0190] A has one of the formulas:
##STR00003##
[0191] Q.sub.1 and Q.sub.2 are each, independently, H, halogen,
C.sub.1-C.sub.6 alkyl, substituted C.sub.1-C.sub.6 alkyl,
C.sub.1-C.sub.6 alkoxy, substituted C.sub.1-C.sub.6 alkoxy,
C.sub.2-C.sub.6 alkenyl, substituted C.sub.2-C.sub.6 alkenyl,
C.sub.2-C.sub.6 alkynyl, substituted C.sub.2-C.sub.6 alkynyl or
N(R.sub.3)(R.sub.4);
[0192] Q.sub.3 is O, S, N(R.sub.5) or C(R.sub.6)(R.sub.7);
[0193] each R.sub.3, R.sub.4 R.sub.5, R.sub.6 and R.sub.7 is,
independently, H, C.sub.1-C.sub.6 alkyl, substituted
C.sub.1-C.sub.6 alkyl or C.sub.1-C.sub.6 alkoxy;
[0194] M.sub.3 is O, S, NR.sub.14, C(R.sub.15)(R.sub.16),
C(R.sub.15)(R.sub.16)C(R.sub.17)(R.sub.18),
C(R.sub.15).dbd.C(R.sub.17), OC(R.sub.15)(R.sub.16) or
OC(R.sub.15)(Bx.sub.2);
[0195] R.sub.14 is H, C.sub.1-C.sub.6 alkyl, substituted
C.sub.1-C.sub.6 alkyl, C.sub.1-C.sub.6 alkoxy, substituted
C.sub.1-C.sub.6 alkoxy, C.sub.2-C.sub.6 alkenyl, substituted
C.sub.2-C.sub.6 alkenyl, C.sub.2-C.sub.6 alkynyl or substituted
C.sub.2-C.sub.6 alkynyl; R.sub.15, R.sub.16, R.sub.17 and R.sub.18
are each, independently, H, halogen, C.sub.1-C.sub.6 alkyl,
substituted C.sub.1-C.sub.6 alkyl, C.sub.1-C.sub.6 alkoxy,
substituted C.sub.1-C.sub.6 alkoxy, C.sub.2-C.sub.6 alkenyl,
substituted C.sub.2-C.sub.6 alkenyl, C.sub.2-C.sub.6 alkynyl or
substituted C.sub.2-C.sub.6 alkynyl;
[0196] Bx.sub.1 is a heterocyclic base moiety;
[0197] or if Bx.sub.2 is present then Bx.sub.2 is a heterocyclic
base moiety and Bx.sub.1 is H, halogen, C.sub.1-C.sub.6 alkyl,
substituted C.sub.1-C.sub.6 alkyl, C.sub.1-C.sub.6 alkoxy,
substituted C.sub.1-C.sub.6 alkoxy, C.sub.2-C.sub.6 alkenyl,
substituted C.sub.2-C.sub.6 alkenyl, C.sub.2-C.sub.6 alkynyl or
substituted C.sub.2-C.sub.6 alkynyl;
[0198] J.sub.4, J.sub.5, J.sub.6 and J.sub.7 are each,
independently, H, halogen, C.sub.1-C.sub.6 alkyl, substituted
C.sub.1-C.sub.6 alkyl, C.sub.1-C.sub.6 alkoxy, substituted
C.sub.1-C.sub.6 alkoxy, C.sub.2-C.sub.6 alkenyl, substituted
C.sub.2-C.sub.6 alkenyl, C.sub.2-C.sub.6 alkynyl or substituted
C.sub.2-C.sub.6 alkynyl;
[0199] or J.sub.4 forms a bridge with one of J.sub.5 or J.sub.7
wherein said bridge comprises from 1 to 3 linked biradical groups
selected from O, S, NR.sub.19, C(R.sub.20)(R.sub.21),
C(R.sub.20).dbd.C(R.sub.21), C[.dbd.C(R.sub.20)(R.sub.21)] and
C(.dbd.O) and the other two of J.sub.5, J.sub.6 and J.sub.7 are
each, independently, H, halogen, C.sub.1-C.sub.6 alkyl, substituted
C.sub.1-C.sub.6 alkyl, C.sub.1-C.sub.6 alkoxy, substituted
C.sub.1-C.sub.6 alkoxy, C.sub.2-C.sub.6 alkenyl, substituted
C.sub.2-C.sub.6 alkenyl, C.sub.2-C.sub.6 alkynyl or substituted
C.sub.2-C.sub.6 alkynyl;
[0200] each R.sub.19, R.sub.20 and R.sub.21 is, independently, H,
C.sub.1-C.sub.6 alkyl, substituted C.sub.1-C.sub.6 alkyl,
C.sub.1-C.sub.6 alkoxy, substituted C.sub.1-C.sub.6 alkoxy,
C.sub.2-C.sub.6 alkenyl, substituted C.sub.2-C.sub.6 alkenyl,
C.sub.2-C.sub.6 alkynyl or substituted C.sub.2-C.sub.6 alkynyl;
[0201] G is H, OH, halogen or
O--[C(R.sub.8)(R.sub.9)]n-[(C.dbd.O).sub.m--X.sub.1].sub.j--Z;
[0202] each R.sub.8 and R.sub.9 is, independently, H, halogen,
C.sub.1-C.sub.6 alkyl or substituted C.sub.1-C.sub.6 alkyl;
[0203] X.sub.1 is O, S or N(E.sub.1);
[0204] Z is H, halogen, C.sub.1-C.sub.6 alkyl, substituted
C.sub.1-C.sub.6 alkyl, C.sub.2-C.sub.6 alkenyl, substituted
C.sub.2-C.sub.6 alkenyl, C.sub.2-C.sub.6 alkynyl, substituted
C.sub.2-C.sub.6 alkynyl or N(E.sub.2)(E.sub.3);
[0205] E.sub.1, E.sub.2 and E.sub.3 are each, independently, H,
C.sub.1-C.sub.6 alkyl or substituted C.sub.1-C.sub.6 alkyl;
[0206] n is from 1 to about 6;
[0207] m is 0 or 1;
[0208] j is 0 or 1;
[0209] each substituted group comprises one or more optionally
protected substituent groups independently selected from halogen,
OJ.sub.1, N(J.sub.1)(J.sub.2), =NJ.sub.1, SJ.sub.1, N.sub.3, CN,
OC(.dbd.X.sub.2)J.sub.1, OC(.dbd.X.sub.2)N(J.sub.1)(J.sub.2) and
C(.dbd.X.sub.2)N(J.sub.1)(J.sub.2); X.sub.2 is O, S or
NJ.sub.3;
[0210] each J.sub.1, J.sub.2 and J.sub.3 is, independently, H or
C.sub.1-C.sub.6 alkyl;
[0211] when j is 1 then Z is other than halogen or
N(E.sub.2)(E.sub.3); and
[0212] wherein said oligomeric compound comprises from 8 to 40
monomeric subunits and is hybridizable to at least a portion of a
target nucleic acid.
[0213] In certain embodiments, M.sub.3 is O, CH.dbd.CH, OCH.sub.2
or OC(H)(Bx.sub.2). In certain embodiments, M.sub.3 is O.
[0214] In certain embodiments, J.sub.4, J.sub.5, J.sub.6 and
J.sub.7 are each H. In certain embodiments, J.sub.4 forms a bridge
with one of J.sub.5 or J.sub.7.
[0215] In certain embodiments, A has one of the formulas:
##STR00004##
wherein:
[0216] Q.sub.1 and Q.sub.2 are each, independently, H, halogen,
C.sub.1-C.sub.6 alkyl, substituted C.sub.1-C.sub.6 alkyl,
C.sub.1-C.sub.6 alkoxy or substituted C.sub.1-C.sub.6 alkoxy. In
certain embodiments, Q.sub.1 and Q.sub.2 are each H. In certain
embodiments, Q.sub.1 and Q.sub.2 are each, independently, H or
halogen. In certain embodiments, Q.sub.1 and Q.sub.2 is H and the
other of Q.sub.1 and Q.sub.2 is F, CH.sub.3 or OCH.sub.3.
[0217] In certain embodiments, T.sub.1 has the formula:
##STR00005##
wherein:
[0218] R.sub.a and R.sub.c are each, independently, protected
hydroxyl, protected thiol, C.sub.1-C.sub.6 alkyl, substituted
C.sub.1-C.sub.6 alkyl, C.sub.1-C.sub.6 alkoxy, substituted
C.sub.1-C.sub.6 alkoxy, protected amino or substituted amino;
and
[0219] R.sub.b is O or S. In certain embodiments, R.sub.b is O and
R.sub.a and R.sub.c are each, independently, OCH.sub.3,
OCH.sub.2CH.sub.3 or CH(CH.sub.3).sub.2.
[0220] In certain embodiments, G is halogen, OCH.sub.3, OCH.sub.2F,
OCHF.sub.2, OCF.sub.3, OCH.sub.2CH.sub.3, O(CH.sub.2).sub.2F,
OCH.sub.2CHF.sub.2, OCH.sub.2CF.sub.3, OCH.sub.2--CH.dbd.CH.sub.2,
O(CH.sub.2).sub.2--OCH.sub.3, O(CH.sub.2).sub.2--SCH.sub.3,
O(CH.sub.2).sub.2--OCF.sub.3,
O(CH.sub.2).sub.3--N(R.sub.10)(R.sub.11),
O(CH.sub.2).sub.2--ON(R.sub.10)(R.sub.11),
O(CH.sub.2).sub.2--O(CH.sub.2).sub.2--N(R.sub.10)(R.sub.1),
OCH.sub.2C(.dbd.O)--N(R.sub.10)(R.sub.11),
OCH.sub.2C(.dbd.O)--N(R.sub.12)--(CH.sub.2).sub.2--N(R.sub.10)(R.sub.1)
or
O(CH.sub.2).sub.2--N(R.sub.12)--C(.dbd.NR.sub.13)[N(R.sub.10)(R.sub.11-
)] wherein R.sub.10, R.sub.11, R.sub.12 and R.sub.13 are each,
independently, H or C.sub.1-C.sub.6 alkyl. In certain embodiments,
G is halogen, OCH.sub.3, OCF.sub.3, OCH.sub.2CH.sub.3,
OCH.sub.2CF.sub.3, OCH.sub.2--CH.dbd.CH.sub.2,
O(CH.sub.2).sub.2--OCH.sub.3,
O(CH.sub.2).sub.2--O(CH.sub.2).sub.2--N(CH.sub.3).sub.2,
OCH.sub.2C(.dbd.O)--N(H)CH.sub.3,
OCH.sub.2C(.dbd.O)--N(H)--(CH.sub.2).sub.2--N(CH.sub.3).sub.2 or
OCH.sub.2--N(H)--C(.dbd.NH)NH.sub.2. In certain embodiments, G is
F, OCH.sub.3 or O(CH.sub.2).sub.2--OCH.sub.3. In certain
embodiments, G is O(CH.sub.2).sub.2--OCH.sub.3.
[0221] In certain embodiments, the 5'-terminal nucleoside has
Formula IIe:
##STR00006##
[0222] In certain embodiments, antisense compounds, including those
particularly suitable for ssRNA comprise one or more type of
modified sugar moieties and/or naturally occurring sugar moieties
arranged along an oligonucleotide or region thereof in a defined
pattern or sugar modification motif. Such motifs may include any of
the sugar modifications discussed herein and/or other known sugar
modifications.
[0223] In certain embodiments, the oligonucleotides comprise or
consist of a region having uniform sugar modifications. In certain
such embodiments, each nucleoside of the region comprises the same
RNA-like sugar modification. In certain embodiments, each
nucleoside of the region is a 2'-F nucleoside. In certain
embodiments, each nucleoside of the region is a 2'-OMe nucleoside.
In certain embodiments, each nucleoside of the region is a 2'-MOE
nucleoside. In certain embodiments, each nucleoside of the region
is a cEt nucleoside. In certain embodiments, each nucleoside of the
region is an LNA nucleoside. In certain embodiments, the uniform
region constitutes all or essentially all of the oligonucleotide.
In certain embodiments, the region constitutes the entire
oligonucleotide except for 1-4 terminal nucleosides.
[0224] In certain embodiments, oligonucleotides comprise one or
more regions of alternating sugar modifications, wherein the
nucleosides alternate between nucleotides having a sugar
modification of a first type and nucleotides having a sugar
modification of a second type. In certain embodiments, nucleosides
of both types are RNA-like nucleosides. In certain embodiments the
alternating nucleosides are selected from: 2'-OMe, 2'-F, 2'-MOE,
LNA, and cEt. In certain embodiments, the alternating modifications
are 2'-F and 2'-OMe. Such regions may be contiguous or may be
interrupted by differently modified nucleosides or conjugated
nucleosides.
[0225] In certain embodiments, the alternating region of
alternating modifications each consist of a single nucleoside
(i.e., the pattern is (AB).sub.xA.sub.y wherein A is a nucleoside
having a sugar modification of a first type and B is a nucleoside
having a sugar modification of a second type; x is 1-20 and y is 0
or 1). In certain embodiments, one or more alternating regions in
an alternating motif includes more than a single nucleoside of a
type. For example, oligonucleotides may include one or more regions
of any of the following nucleoside motifs:
AABBAA;
ABBABB;
AABAAB;
ABBABAABB;
ABABAA;
AABABAB;
ABABAA;
ABBAABBABABAA;
BABBAABBABABAA; or
ABABBAABBABABAA;
[0226] wherein A is a nucleoside of a first type and B is a
nucleoside of a second type. In certain embodiments, A and B are
each selected from 2'-F, 2'-OMe, BNA, and MOE.
[0227] In certain embodiments, oligonucleotides having such an
alternating motif also comprise a modified 5' terminal nucleoside,
such as those of formula IIc or IIe.
[0228] In certain embodiments, oligonucleotides comprise a region
having a 2-2-3 motif. Such regions comprises the following
motif:
-(A)-(B).sub.x-(A).sub.2-(C)-(A).sub.3-
[0229] wherein: A is a first type of modified nucleoside;
[0230] B and C, are nucleosides that are differently modified than
A, however, B and C may have the same or different modifications as
one another;
[0231] x and y are from 1 to 15.
[0232] In certain embodiments, A is a 2'-OMe modified nucleoside.
In certain embodiments, B and C are both 2'-F modified nucleosides.
In certain embodiments, A is a 2'-OMe modified nucleoside and B and
C are both 2'-F modified nucleosides.
[0233] In certain embodiments, oligonucleosides have the following
sugar motif:
5'-(Q)-(AB).sub.xA.sub.y-(D).sub.z
wherein:
[0234] Q is a nucleoside comprising a stabilized phosphate moiety.
In certain embodiments, Q is a nucleoside having Formula IIc or
IIe;
[0235] A is a first type of modified nucleoside;
[0236] B is a second type of modified nucleoside;
[0237] D is a modified nucleoside comprising a modification
different from the nucleoside adjacent to it. Thus, if y is 0, then
D must be differently modified than B and if y is 1, then D must be
differently modified than A. In certain embodiments, D differs from
both A and B.
[0238] X is 5-15;
[0239] Y is 0 or 1;
[0240] Z is 0-4.
[0241] In certain embodiments, oligonucleosides have the following
sugar motif:
5'-(Q)-(A).sub.x-(D).sub.z
wherein:
[0242] Q is a nucleoside comprising a stabilized phosphate moiety.
In certain embodiments, Q is a nucleoside having Formula IIc or
IIe;
[0243] A is a first type of modified nucleoside;
[0244] D is a modified nucleoside comprising a modification
different from A.
[0245] X is 11-30;
[0246] Z is 0-4.
[0247] In certain embodiments A, B, C, and D in the above motifs
are selected from: 2'-OMe, 2'-F, 2'-MOE, LNA, and cEt. In certain
embodiments, D represents terminal nucleosides. In certain
embodiments, such terminal nucleosides are not designed to
hybridize to the target nucleic acid (though one or more might
hybridize by chance). In certain embodiments, the nucleobase of
each D nucleoside is adenine, regardless of the identity of the
nucleobase at the corresponding position of the target nucleic
acid. In certain embodiments the nucleobase of each D nucleoside is
thymine.
[0248] In certain embodiments, antisense compounds, including those
particularly suited for use as ssRNA comprise modified
internucleoside linkages arranged along the oligonucleotide or
region thereof in a defined pattern or modified internucleoside
linkage motif. In certain embodiments, oligonucleotides comprise a
region having an alternating internucleoside linkage motif. In
certain embodiments, oligonucleotides comprise a region of
uniformly modified internucleoside linkages. In certain such
embodiments, the oligonucleotide comprises a region that is
uniformly linked by phosphorothioate internucleoside linkages. In
certain embodiments, the oligonucleotide is uniformly linked by
phosphorothioate internucleoside linkages. In certain embodiments,
each internucleoside linkage of the oligonucleotide is selected
from phosphodiester and phosphorothioate. In certain embodiments,
each internucleoside linkage of the oligonucleotide is selected
from phosphodiester and phosphorothioate and at least one
internucleoside linkage is phosphorothioate.
[0249] In certain embodiments, the oligonucleotide comprises at
least 6 phosphorothioate internucleoside linkages. In certain
embodiments, the oligonucleotide comprises at least 8
phosphorothioate internucleoside linkages. In certain embodiments,
the oligonucleotide comprises at least 10 phosphorothioate
internucleoside linkages. In certain embodiments, the
oligonucleotide comprises at least one block of at least 6
consecutive phosphorothioate internucleoside linkages. In certain
embodiments, the oligonucleotide comprises at least one block of at
least 8 consecutive phosphorothioate internucleoside linkages. In
certain embodiments, the oligonucleotide comprises at least one
block of at least 10 consecutive phosphorothioate internucleoside
linkages. In certain embodiments, the oligonucleotide comprises at
least one block of at least one 12 consecutive phosphorothioate
internucleoside linkages. In certain such embodiments, at least one
such block is located at the 3' end of the oligonucleotide. In
certain such embodiments, at least one such block is located within
3 nucleosides of the 3' end of the oligonucleotide.
[0250] Oligonucleotides having any of the various sugar motifs
described herein, may have any linkage motif. For example, the
oligonucleotides, including but not limited to those described
above, may have a linkage motif selected from non-limiting the
table below:
TABLE-US-00001 5' most linkage Central region 3'-region PS
Alternating PO/PS 6 PS PS Alternating PO/PS 7 PS PS Alternating
PO/PS 8 PS
[0251] ii. siRNA Compounds
[0252] In certain embodiments, antisense compounds are
double-stranded RNAi compounds (siRNA). In such embodiments, one or
both strands may comprise any modification motif described above
for ssRNA. In certain embodiments, ssRNA compounds may be
unmodified RNA. In certain embodiments, siRNA compounds may
comprise unmodified RNA nucleosides, but modified internucleoside
linkages.
[0253] Several embodiments relate to double-stranded compositions
wherein each strand comprises a motif defined by the location of
one or more modified or unmodified nucleosides. In certain
embodiments, compositions are provided comprising a first and a
second oligomeric compound that are fully or at least partially
hybridized to form a duplex region and further comprising a region
that is complementary to and hybridizes to a nucleic acid target.
It is suitable that such a composition comprise a first oligomeric
compound that is an antisense strand having full or partial
complementarity to a nucleic acid target and a second oligomeric
compound that is a sense strand having one or more regions of
complementarity to and forming at least one duplex region with the
first oligomeric compound.
[0254] The compositions of several embodiments modulate gene
expression by hybridizing to a nucleic acid target resulting in
loss of its normal function. In some embodiments, the target
nucleic acid is an eRNA. In certain embodiment, the degradation of
the targeted eRNA is facilitated by an activated RISC complex that
is formed with compositions of the invention.
[0255] Several embodiments are directed to double-stranded
compositions wherein one of the strands is useful in, for example,
influencing the preferential loading of the opposite strand into
the RISC (or cleavage) complex. The compositions are useful for
targeting selected nucleic acid molecules and modulating the
expression of one or more genes. In some embodiments, the
compositions of the present invention hybridize to a portion of a
target RNA resulting in loss of normal function of the target
RNA.
[0256] Certain embodiments are drawn to double-stranded
compositions wherein both the strands comprises a hemimer motif, a
fully modified motif, a positionally modified motif or an
alternating motif. Each strand of the compositions of the present
invention can be modified to fulfil a particular role in for
example the siRNA pathway. Using a different motif in each strand
or the same motif with different chemical modifications in each
strand permits targeting the antisense strand for the RISC complex
while inhibiting the incorporation of the sense strand. Within this
model, each strand can be independently modified such that it is
enhanced for its particular role. The antisense strand can be
modified at the 5'-end to enhance its role in one region of the
RISC while the 3'-end can be modified differentially to enhance its
role in a different region of the RISC.
[0257] The double-stranded oligonucleotide molecules can be a
double-stranded polynucleotide molecule comprising
self-complementary sense and antisense regions, wherein the
antisense region comprises nucleotide sequence that is
complementary to nucleotide sequence in a target nucleic acid
molecule or a portion thereof and the sense region having
nucleotide sequence corresponding to the target nucleic acid
sequence or a portion thereof. The double-stranded oligonucleotide
molecules can be assembled from two separate oligonucleotides,
where one strand is the sense strand and the other is the antisense
strand, wherein the antisense and sense strands are
self-complementary (i.e. each strand comprises nucleotide sequence
that is complementary to nucleotide sequence in the other strand;
such as where the antisense strand and sense strand form a duplex
or double-stranded structure, for example wherein the
double-stranded region is about 15 to about 30, e.g., about 15, 16,
17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 base
pairs; the antisense strand comprises nucleotide sequence that is
complementary to nucleotide sequence in a target nucleic acid
molecule or a portion thereof and the sense strand comprises
nucleotide sequence corresponding to the target nucleic acid
sequence or a portion thereof (e.g., about 15 to about 25 or more
nucleotides of the double-stranded oligonucleotide molecule are
complementary to the target nucleic acid or a portion thereof).
Alternatively, the double-stranded oligonucleotide is assembled
from a single oligonucleotide, where the self-complementary sense
and antisense regions of the siRNA are linked by means of a nucleic
acid based or non-nucleic acid-based linker(s).
[0258] The double-stranded oligonucleotide can be a polynucleotide
with a duplex, asymmetric duplex, hairpin or asymmetric hairpin
secondary structure, having self-complementary sense and antisense
regions, wherein the antisense region comprises nucleotide sequence
that is complementary to nucleotide sequence in a separate target
nucleic acid molecule or a portion thereof and the sense region
having nucleotide sequence corresponding to the target nucleic acid
sequence or a portion thereof. The double-stranded oligonucleotide
can be a circular single-stranded polynucleotide having two or more
loop structures and a stem comprising self-complementary sense and
antisense regions, wherein the antisense region comprises
nucleotide sequence that is complementary to nucleotide sequence in
a target nucleic acid molecule or a portion thereof and the sense
region having nucleotide sequence corresponding to the target
nucleic acid sequence or a portion thereof, and wherein the
circular polynucleotide can be processed either in vivo or in vitro
to generate an active siRNA molecule capable of mediating RNAi.
[0259] In certain embodiments, the double-stranded oligonucleotide
comprises separate sense and antisense sequences or regions,
wherein the sense and antisense regions are covalently linked by
nucleotide or non-nucleotide linkers molecules as is known in the
art, or are alternately non-covalently linked by ionic
interactions, hydrogen bonding, van der waals interactions,
hydrophobic interactions, and/or stacking interactions. In certain
embodiments, the double-stranded oligonucleotide comprises
nucleotide sequence that is complementary to nucleotide sequence of
a target gene. In another embodiment, the double-stranded
oligonucleotide interacts with nucleotide sequence of a target gene
in a manner that causes inhibition of expression of the target
gene.
[0260] As used herein, double-stranded oligonucleotides need not be
limited to those molecules containing only RNA, but further
encompasses chemically modified nucleotides and non-nucleotides. In
certain embodiments, the short interfering nucleic acid molecules
lack 2'-hydroxy (2'-OH) containing nucleotides. In certain
embodiments short interfering nucleic acids optionally do not
include any ribonucleotides (e.g., nucleotides having a 2'-OH
group). Such double-stranded oligonucleotides that do not require
the presence of ribonucleotides within the molecule to support RNAi
can however have an attached linker or linkers or other attached or
associated groups, moieties, or chains containing one or more
nucleotides with 2'-OH groups. Optionally, double-stranded
oligonucleotides can comprise ribonucleotides at about 5, 10, 20,
30, 40, or 50% of the nucleotide positions. As used herein, the
term siRNA is meant to be equivalent to other terms used to
describe nucleic acid molecules that are capable of mediating
sequence specific RNAi, for example short interfering RNA (siRNA),
double-stranded RNA (dsRNA), micro-RNA (miRNA), short hairpin RNA
(shRNA), short interfering oligonucleotide, short interfering
nucleic acid, short interfering modified oligonucleotide,
chemically modified siRNA, post-transcriptional gene silencing RNA
(ptgsRNA), and others. In addition, as used herein, the term RNAi
is meant to be equivalent to other terms used to describe sequence
specific RNA interference, such as post transcriptional gene
silencing, translational inhibition, or epigenetics. For example,
double-stranded oligonucleotides can be used to epigenetically
silence genes at both the post-transcriptional level and the
pre-transcriptional level. In a non-limiting example, epigenetic
regulation of gene expression by siRNA molecules of the invention
can result from siRNA mediated modification of chromatin structure
or methylation pattern to alter gene expression (see, for example,
Verdel et al., 2004, Science, 303, 672-676; Pal-Bhadra et al.,
2004, Science, 303, 669-672; Allshire, 2002, Science, 297,
1818-1819; Volpe et al., 2002, Science, 297, 1833-1837; Jenuwein,
2002, Science, 297, 2215-2218; and Hall et al., 2002, Science, 297,
2232-2237).
[0261] It is contemplated that compounds and compositions of
several embodiments provided herein can target eRNAs by a
dsRNA-mediated gene silencing or RNAi mechanism, including, e.g.,
"hairpin" or stem-loop double-stranded RNA effector molecules in
which a single RNA strand with self-complementary sequences is
capable of assuming a double-stranded conformation, or duplex dsRNA
effector molecules comprising two separate strands of RNA. In
various embodiments, the dsRNA consists entirely of ribonucleotides
or consists of a mixture of ribonucleotides and deoxynucleotides,
such as the RNA/DNA hybrids disclosed, for example, by WO 00/63364,
filed Apr. 19, 2000, or U.S. Ser. No. 60/130,377, filed Apr. 21,
1999. The dsRNA or dsRNA effector molecule may be a single molecule
with a region of self-complementarity such that nucleotides in one
segment of the molecule base pair with nucleotides in another
segment of the molecule. In various embodiments, a dsRNA that
consists of a single molecule consists entirely of ribonucleotides
or includes a region of ribonucleotides that is complementary to a
region of deoxyribonucleotides. Alternatively, the dsRNA may
include two different strands that have a region of complementarity
to each other.
[0262] In various embodiments, both strands consist entirely of
ribonucleotides, one strand consists entirely of ribonucleotides
and one strand consists entirely of deoxyribonucleotides, or one or
both strands contain a mixture of ribonucleotides and
deoxyribonucleotides. In certain embodiments, the regions of
complementarity are at least 70, 80, 90, 95, 98, or 100%
complementary to each other and to a target nucleic acid sequence.
In certain embodiments, the region of the dsRNA that is present in
a double-stranded conformation includes at least 19, 20, 21, 22,
23, 24, 25, 26, 27, 28, 29, 30, 50, 75, 100, 200, 500, 1000, 2000
or 5000 nucleotides or includes all of the nucleotides in a cDNA or
other target nucleic acid sequence being represented in the
dsRNA.
[0263] In some embodiments, the dsRNA does not contain any single
stranded regions, such as single stranded ends, or the dsRNA is a
hairpin. In other embodiments, the dsRNA has one or more single
stranded regions or overhangs. In certain embodiments, RNA/DNA
hybrids include a DNA strand or region that is an antisense strand
or region (e.g, has at least 70, 80, 90, 95, 98, or 100%
complementarity to a target nucleic acid) and an RNA strand or
region that is a sense strand or region (e.g, has at least 70, 80,
90, 95, 98, or 100% identity to a target nucleic acid), and vice
versa.
[0264] In various embodiments, the RNA/DNA hybrid is made in vitro
using enzymatic or chemical synthetic methods such as those
described herein or those described in WO 00/63364, filed Apr. 19,
2000, or U.S. Ser. No. 60/130,377, filed Apr. 21, 1999. In other
embodiments, a DNA strand synthesized in vitro is complexed with an
RNA strand made in vivo or in vitro before, after, or concurrent
with the transformation of the DNA strand into the cell. In yet
other embodiments, the dsRNA is a single circular nucleic acid
containing a sense and an antisense region, or the dsRNA includes a
circular nucleic acid and either a second circular nucleic acid or
a linear nucleic acid (see, for example, WO 00/63364, filed Apr.
19, 2000, or U.S. Ser. No. 60/130,377, filed Apr. 21, 1999.)
Exemplary circular nucleic acids include lariat structures in which
the free 5' phosphoryl group of a nucleotide becomes linked to the
2' hydroxyl group of another nucleotide in a loop back fashion.
[0265] In other embodiments, the dsRNA includes one or more
modified nucleotides in which the 2' position in the sugar contains
a halogen (such as fluorine group) or contains an alkoxy group
(such as a methoxy group) which increases the half-life of the
dsRNA in vitro or in vivo compared to the corresponding dsRNA in
which the corresponding 2' position contains a hydrogen or an
hydroxyl group. In yet other embodiments, the dsRNA includes one or
more linkages between adjacent nucleotides other than a
naturally-occurring phosphodiester linkage. Examples of such
linkages include phosphoramide, phosphorothioate, and
phosphorodithioate linkages. The dsRNAs may also be chemically
modified nucleic acid molecules as taught in U.S. Pat. No.
6,673,661. In other embodiments, the dsRNA contains one or two
capped strands, as disclosed, for example, by WO 00/63364, filed
Apr. 19, 2000, or U.S. Ser. No. 60/130,377, filed Apr. 21,
1999.
[0266] In other embodiments, the dsRNA can be any of the at least
partially dsRNA molecules disclosed in WO 00/63364, as well as any
of the dsRNA molecules described in U.S. Provisional Application
60/399,998; and U.S. Provisional Application 60/419,532, and
PCT/US2003/033466, the teaching of which is hereby incorporated by
reference. Any of the dsRNAs may be expressed in vitro or in vivo
using the methods described herein or standard methods, such as
those described in WO 00/63364.
Occupancy
[0267] In certain embodiments, antisense compounds are not expected
to result in cleavage or the target nucleic acid via RNase H or to
result in cleavage or sequestration through the RISC pathway. In
certain such embodiments, antisense activity may result from
occupancy, wherein the presence of the hybridized antisense
compound disrupts the activity of the target nucleic acid. In
certain such embodiments, the antisense compound may be uniformly
modified or may comprise a mix of modifications and/or modified and
unmodified nucleosides.
Target eRNAs and associated gene expression
[0268] Several embodiments are directed to methods of modulating
gene expression by inhibiting eRNAs. In certain embodiments,
transcriptional start site of such a gene is located on a
chromosome at least about 1 kilobase (kb) from the genomic enhancer
nucleic acid sequence. In certain embodiments, eRNAs suitable for
inhibition include RNA transcripts characterized by any one or more
of the following: (1) transcribed from genomic regions
characterized by high levels of monomethylation on lysine 4 of
histone 3 (H3K4me1) and low levels of trimethylation on lysine 4 of
histone 3 (H3K4me3) (2) transcribed from genomic regions that are
enriched for RNA polymerase II (Polll); (3) transcribed from
genomic regions that are enriched for transcriptional
co-regulators, such as the p300 co-activator; (4) their
transcription is initiated from Poll-binding sites and elongated
bidirectionally; (5) evolutionarily conserved DNA sequences
encoding eRNAs; (6) short half-life; (7) dynamically regulated upon
signaling, and/or (7) positively correlated to levels of nearby
mRNA expression. In certain aspects, the half-life of the eRNA is
less than about 10-30 minutes.
[0269] In certain embodiments, eRNAs suitable for inhibition with
compounds described herein include eRNAs from hematopoietic cells,
such as monocytes or macrophages. Examples of such eRNAs include,
but are not limited to, those transcribed from enhancers identified
by genomic coordinates in Mega-Tables 1 and 2 filed in U.S.
Provisional Application No. 61/650,426 in electronic format on May
22, 2012. Additional information on the eRNAs transcribed from
enhancers listed in Mega-Table 2 is reported in De Santa F, et al.,
"A large fraction of extragenic RNA pol II transcription sites
overlap enhancers." PLoS Biol 2010; 8:e1000384, which is herein
incorporated by reference in its entirety.
[0270] In certain embodiments, eRNAs suitable for inhibition with
compounds described herein include eRNAs from neurons. Examples of
such eRNAs include, but are not limited to, those transcribed from
enhancers identified by genomic coordinates in Mega-Table 3 filed
in U.S. Provisional Application No. 61/650,426 in electronic format
on May 22, 2012. Additional information on the eRNAs transcribed
from enhancers listed in Mega-Table 3 is reported in Kim T K, et
al., "Widespread transcription at neuronal activity-regulated
enhancers." Nature 2010; 465:182-187, which is herein incorporated
by reference in its entirety.
[0271] In certain embodiments, eRNAs suitable for inhibition with
compounds described herein include eRNAs transcribed from enhancers
identified as highly conserved among human, mouse, and rat species.
Examples of such eRNAs include, but are not limited to, those
transcribed from enhancers identified by genomic coordinates in
Mega-Table 4 and Mega-Table 5 filed in U.S. Provisional Application
No. 61/650,426 in electronic format on May 22, 2012. Mega-Tables 4
and 5 are in 4-column format: chr start end log 10(1/pvalue).
[0272] Additional information on the enhancers listed in Mega-Table
4 is reported in Pennacchio et al, Nature 2006; 444:499-502,
Prabhakar S, et al. Genome Res. 2006; 16:855-863, and
(pga.jgi-psf.org/gumby/), each of which is incorporated herein by
reference in its entirety. Chromosome coordinates provided in
Mega-Table 4 correspond to the hg17 human genome assembly.
Additional information on the enhancers listed in Mega-Table 5 is
reported in Visel et al., "VISTA Enhancer Browser--a database of
tissue-specific human enhancers," Nucleic Acids Research 2007
(35):D88-92 and (pga.jgi-psf.org/gumby/), each of which is
incorporated herein by reference in its entirety. Chromosome
coordinates provided in Mega-Table 5 correspond to the hg18 human
genome assembly.
[0273] In certain embodiments, eRNAs suitable for inhibition with
compounds described herein include eRNAs transcribed from human
enhancers identified by genomic coordinates in Mega-Table 6 filed
in U.S. Provisional Application No. 61/650,426 in electronic format
on May 22, 2012. Chromosome coordinates provided in Mega-Table 6
correspond to the hg19 human genome assembly. Additional
information on the enhancers listed in Mega-Table 6 is reported in
Visel et al., "VISTA Enhancer Browser--a database of
tissue-specific human enhancers," Nucleic Acids Research 2007
(35):D88-92 and the VISTA database website (enhancer.lbl.gov/),
each of which is incorporated herein by reference in its
entirety.
[0274] In certain embodiments, eRNAs suitable for inhibition with
compounds described herein include eRNAs transcribed from mouse
enhancers identified by genomic coordinates in Mega-Table 7 filed
in U.S. Provisional Application No. 61/650,426 in electronic format
on May 22, 2012. Chromosome coordinates provided in Mega-Table 7
correspond to the mouse mm9 genome assembly. Additional information
on the enhancers listed in Mega-Table 7 is reported in Visel et
al., "VISTA Enhancer Browser--a database of tissue-specific human
enhancers," Nucleic Acids Research 2007 (35):D88-92 and the VISTA
database website (enhancer.lbl.gov/), each of which is incorporated
herein by reference in its entirety.
[0275] In certain embodiments, eRNAs suitable for inhibition with
compounds described herein include eRIAs transcribed from enhancers
in human prostate cells. Examples of such eRNAs include, but are
not limited to, those identified in LNCaP cells as reported in Wang
D et al., "Reprogramming transcription by distinct classes of
enhancers functionally defined by eRNA," Nature. 2011
474(7351):390-4 and further described at
nature.com/nature/journal/v474/n7351/full/nature10006.html, each of
which is incorporated herein by reference in its entirety. Further
description of the eRNAs identified in Wang et al. are available as
high-throughput data deposited at Gene Expression Omnibus
(ncbi.nlm.nih.gov/geo/) under accession number OSE27823, which is
incorporated herein by reference in its entirety.
[0276] In certain embodiments, eRNAs suitable for inhibition with
compounds described herein include eRNAs transcribed from enhancers
in human breast cells, such as breast cancer cells. Examples of
such eRNAs include, but are not limited to, those transcribed from
enhancers identified in MCF-7 human breast cancer cells and listed
in Mega-Table 8 and Mega-Table 9 filed in U.S. Provisional
Application No. 61/650,426 in electronic format on May 22, 2012.
Chromosome coordinates provided in Mega-Table 8 and Mega-Table 9
correspond to the hg18 human genome assembly. Additional examples
of such eRNAs include, but are not limited to, those transcribed
from enhancers identified in MCF-7 human breast cancer cells as
reported in the UCSC Genome Browser located at
(genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgSotherUserName-
=Bogdantanasa&hgS_otherUserSessionName=EReRNAs), which is
incorporated herein by reference in its entirety.
[0277] In certain embodiments, eRNAs suitable for inhibition with
compounds described herein exclude ncRNA-activators (ncRNA-a), such
as those described in Orom U A et al., "Long noncoding RNAs with
enhancer-like function in human cells." Cell 2010; 143:46-58. In
certain embodiments, eRNAs suitable for inhibition with compounds
described herein exclude transcripts that are characterized by one
or more of the following features: (1) produced via unidirectional
transcription; (2) polyadenylated; and/or (3), transcribed from a
genomic sequence or region having a H3K4 trimethylation chromatin
signature.
[0278] In certain embodiments, a method of inhibiting gene
expression in a macrophage cell comprises administering to the
macrophage cell an antisense compound targeted to an eRNA
transcribed from a genomic enhancer nucleic acid sequence or region
that is enriched for binding to Rev-Erb.alpha. or
Rev-Erb.beta..
[0279] In certain embodiments, a method of inhibiting MMP9 gene
expression in a cell comprises administering to the cell an
antisense compound targeted to an eRNA transcript of a MMP9
enhancer. In several embodiments, the MMP9 eRNA sequence is the
product of transcription of SEQ ID NO: 1 (GENBANK Accession No.
NT_039207.7 truncated from 105809972 to 105810309).
[0280] In certain aspects, the antisense compound is an antisense
oligonucleotide that targets the MMP9 eRNA at nucleotides 247 to
262 of the transcribed product of SEQ ID NO:1 In certain aspects,
the antisense compound is an antisense oligonucleotide having the
nucleic acid sequence of SEQ ID NO:2 In some aspects, the antisense
compound is ISIS 566237.
[0281] In certain aspects, the antisense compound is an antisense
oligonucleotide that targets the MMP9 eRNA at nucleotides 260 to
275 of the transcribed product of SEQ ID NO:1 In certain aspects,
the antisense compound is an antisense oligonucleotide having the
nucleic acid sequence of SEQ ID NO:3. In some aspects, the
antisense compound is ISIS 566241.
[0282] In certain aspects, the antisense compound is an antisense
oligonucleotide that targets the MMP9 eRNA transcribed from SEQ ID
NO: 202 (GENBANK Accession number NT_039207.7 truncated from
105809967 to 105810417). In certain aspects, the antisense compound
is an antisense oligonucleotide having the nucleic acid sequence of
any one of SEQ ID NOs: 2, 3, or 124-201. MMP9 is known to be
associated with atherosclerosis, inflammation, apoptosis, and
cancer metastasis; methods and compounds provided herein are useful
for inhibiting MMP9 gene expression.
[0283] In certain embodiments, a method of inhibiting CX3CR1 gene
expression in a cell comprises administering to the cell an
antisense compound targeted to an eRNA transcript of a CX3CR1
enhancer. In several embodiments, the CX3CR1 eRNA sequence is the
product of transcription of nucleotides 11132282 to 11132781 of SEQ
ID NO: 4 (Genbank Accession No. NT_039482.7), which is incorporated
herein by reference. In several embodiments, the CX3CR1 eRNA
sequence is the product of transcription of nucleotides 11132134 to
11131599 of SEQ ID NO: 4 (Genbank Accession No. NT_039482.7), which
is incorporated herein by reference. CX3CR1 is known to be
associated with atherosclerosis; methods and compounds provided
herein are useful for inhibiting CX3CR1 gene expression.
[0284] In certain embodiments, a method of inhibiting TFF1 gene
expression in a cell comprises administering to the cell an
antisense compound targeted to an eRNA transcript of a TFF1
enhancer. In several embodiments, the antisense compound is a
double-stranded siRNA having any one of the following pairs of
sequences: SEQ ID NOs: 11-12; SEQ ID NOs: 13-14; or SEQ ID NOs:
15-16. In several embodiments, the antisense compound is a
single-stranded oligonucleotide having a nucleotide sequence of any
one of SEQ ID NOs: 60-63.
[0285] In certain embodiments, a method of inhibiting GREB1 gene
expression in a cell comprises administering to the cell an
antisense compound targeted to an eRNA transcript of a GREB1
enhancer. In several embodiments, the antisense compound is a
double-stranded siRNA having any one of the following pairs of
sequences: SEQ ID NOs: 17-18; SEQ ID NOs: 19-20; or SEQ ID NOs:
21-22.
[0286] In certain embodiments, a method of inhibiting PGR gene
expression in a cell comprises administering to the cell an
antisense compound targeted to an eRNA transcript of a PGR
enhancer. In several embodiments, the antisense compound is a
double-stranded siRNA having any one of the following pairs of
sequences: SEQ ID NOs: 23-24 or SEQ ID NOs: 25-26.
[0287] In certain embodiments, a method of inhibiting SIAH2 gene
expression in a cell comprises administering to the cell an
antisense compound targeted to an eRNA transcript of a SIAH2
enhancer. In several embodiments, the antisense compound is a
double-stranded siRNA having any one of the following pairs of
sequences: SEQ ID NOs: 27-28 or SEQ ID NOs: 29-30.
[0288] In certain embodiments, a method of inhibiting NRIP1 gene
expression in a cell comprises administering to the cell an
antisense compound targeted to an eRNA transcript of a NRIP1
enhancer. In several embodiments, the antisense compound is a
double-stranded siRNA having any one of the following pairs of
sequences: SEQ ID NOs: 31-32 or SEQ ID NOs: 33-34. In several
embodiments, the antisense compound is a single-stranded
oligonucleotide having a nucleotide sequence of any one of SEQ ID
NOs: 68 or 69.
[0289] In certain embodiments, a method of inhibiting FOXC1 gene
expression in a cell comprises administering to the cell an
antisense compound targeted to an eRNA transcript of a FOXC1
enhancer. In several embodiments, the antisense compound is a
double-stranded siRNA having any one of the following pairs of
sequences: SEQ ID NOs: 35-36 or SEQ ID NOs: 37-38. In several
embodiments, the antisense compound is a single-stranded
oligonucleotide having a nucleotide sequence of any one of SEQ ID
NOs: 66 or 67.
[0290] In certain embodiments, a method of inhibiting P2RY2 gene
expression in a cell comprises administering to the cell an
antisense compound targeted to an eRNA transcript of a P2RY2
enhancer. In several embodiments, the antisense compound is a
double-stranded siRNA having any one of the following pairs of
sequences: SEQ ID NOs: 39-40 or SEQ ID NOs: 41-42.
[0291] In certain embodiments, a method of inhibiting CA12 gene
expression in a cell comprises administering to the cell an
antisense compound targeted to an eRNA transcript of a CA12
enhancer. In several embodiments, the antisense compound is a
double-stranded siRNA having any one of the following pairs of
sequences: SEQ ID NOs: 43-44 or SEQ ID NOs: 45-46. In several
embodiments, the antisense compound is a single-stranded
oligonucleotide having a nucleotide sequence of any one of SEQ ID
NOs: 64 or 65.
[0292] In certain embodiments, a method of inhibiting SMAD7 gene
expression in a cell comprises administering to the cell an
antisense compound targeted to an eRNA transcript of a SMAD7
enhancer. In several embodiments, the antisense compound is a
double-stranded siRNA having any one of the following pairs of
sequences: SEQ ID NOs: 47-48, SEQ ID NOs: 49-50, or SEQ ID NOs:
51-52.
[0293] In certain embodiments, a method of inhibiting KCNK5 gene
expression in a cell comprises administering to the cell an
antisense compound targeted to an eRNA transcript of a KCNK5
enhancer. In several embodiments, the antisense compound is a
double-stranded siRNA having any one of the following pairs of
sequences: SEQ ID NOs: 53-54, SEQ ID NOs: 55-56, or SEQ ID NOs:
57-58.
Hybridization
[0294] In some embodiments, hybridization occurs between an
antisense compound disclosed herein and an eRNA. The most common
mechanism of hybridization involves hydrogen bonding (e.g.,
Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding)
between complementary nucleobases of the nucleic acid
molecules.
[0295] Hybridization can occur under varying conditions. Stringent
conditions are sequence-dependent and are determined by the nature
and composition of the nucleic acid molecules to be hybridized.
[0296] Methods of determining whether a sequence is specifically
hybridizable to a target nucleic acid are well known in the art. In
certain embodiments, the antisense compounds provided herein are
specifically hybridizable with an eRNA.
Complementarity
[0297] An antisense compound and a target nucleic acid are
complementary to each other when a sufficient number of nucleobases
of the antisense compound can hydrogen bond with the corresponding
nucleobases of the target nucleic acid, such that a desired effect
will occur (e.g., antisense inhibition of a target nucleic acid,
such as an eRNA nucleic acid).
[0298] Non-complementary nucleobases between an antisense compound
and an eRNA nucleic acid may be tolerated provided that the
antisense compound remains able to specifically hybridize to a
target nucleic acid. Moreover, an antisense compound may hybridize
over one or more segments of an eRNA nucleic acid such that
intervening or adjacent segments are not involved in the
hybridization event (e.g., a loop structure, mismatch or hairpin
structure).
[0299] In certain embodiments, the antisense compounds provided
herein, or a specified portion thereof, are, or are at least, 70%,
80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%, 98%, 99%, or 100% complementary to an eRNA nucleic acid, a
target region, target segment, or specified portion thereof.
Percent complementarity of an antisense compound with a target
nucleic acid can be determined using routine methods.
[0300] For example, an antisense compound in which 18 of 20
nucleobases of the antisense compound are complementary to a target
region, and would therefore specifically hybridize, would represent
90 percent complementarity. In this example, the remaining
noncomplementary nucleobases may be clustered or interspersed with
complementary nucleobases and need not be contiguous to each other
or to complementary nucleobases. As such, an antisense compound
which is 18 nucleobases in length having four noncomplementary
nucleobases which are flanked by two regions of complete
complementarity with the target nucleic acid would have 77.8%
overall complementarity with the target nucleic acid and would thus
fall within the scope of the present invention. Percent
complementarity of an antisense compound with a region of a target
nucleic acid can be determined routinely using BLAST programs
(basic local alignment search tools) and PowerBLAST programs known
in the art (Altschul et al., J Mol. Biol., 1990, 215, 403 410;
Zhang and Madden, Genome Res., 1997, 7, 649 656). Percent homology,
sequence identity or complementarity, can be determined by, for
example, 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 (Adv. Appl. Math., 1981, 2, 482
489).
[0301] In certain embodiments, the antisense compounds provided
herein, or specified portions thereof, are fully complementary
(i.e. 100% complementary) to a target nucleic acid, or specified
portion thereof. For example, an antisense compound may be fully
complementary to an eRNA nucleic acid, or a target region, or a
target segment or target sequence thereof. As used herein, "fully
complementary" means each nucleobase of an antisense compound is
capable of precise base pairing with the corresponding nucleobases
of a target nucleic acid. For example, a 20 nucleobase antisense
compound is fully complementary to a target sequence that is 400
nucleobases long, so long as there is a corresponding 20 nucleobase
portion of the target nucleic acid that is fully complementary to
the antisense compound. Fully complementary can also be used in
reference to a specified portion of the first and/or the second
nucleic acid. For example, a 20 nucleobase portion of a 30
nucleobase antisense compound can be "fully complementary" to a
target sequence that is 400 nucleobases long. The 20 nucleobase
portion of the 30 nucleobase oligonucleotide is fully complementary
to the target sequence if the target sequence has a corresponding
20 nucleobase portion wherein each nucleobase is complementary to
the 20 nucleobase portion of the antisense compound. At the same
time, the entire 30 nucleobase antisense compound may or may not be
fully complementary to the target sequence, depending on whether
the remaining 10 nucleobases of the antisense compound are also
complementary to the target sequence.
[0302] The location of a non-complementary nucleobase may be at the
5' end or 3' end of the antisense compound. Alternatively, the
non-complementary nucleobase or nucleobases may be at an internal
position of the antisense compound. When two or more
non-complementary nucleobases are present, they may be contiguous
(i.e. linked) or non-contiguous. In one embodiment, a
non-complementary nucleobase is located in the wing segment of a
gapmer antisense oligonucleotide.
[0303] In certain embodiments, antisense compounds that are, or are
up to 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleobases in
length comprise no more than 4, no more than 3, no more than 2, or
no more than 1 non-complementary nucleobase(s) relative to a target
nucleic acid, such as an eRNA nucleic acid, or specified portion
thereof.
[0304] In certain embodiments, antisense compounds that are, or are
up to 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,
26, 27, 28, 29, or 30 nucleobases in length comprise no more than
6, no more than 5, no more than 4, no more than 3, no more than 2,
or no more than 1 non-complementary nucleobase(s) relative to a
target nucleic acid, such as an eRNA nucleic acid, or specified
portion thereof.
[0305] The antisense compounds provided also include those which
are complementary to a portion of a target nucleic acid. As used
herein, "portion" refers to a defined number of contiguous (i.e.
linked) nucleobases within a region or segment of a target nucleic
acid. A "portion" can also refer to a defined number of contiguous
nucleobases of an antisense compound. In certain embodiments, the
antisense compounds, are complementary to at least an 8 nucleobase
portion of a target segment. In certain embodiments, the antisense
compounds are complementary to at least a 9 nucleobase portion of a
target segment. In certain embodiments, the antisense compounds are
complementary to at least a 10 nucleobase portion of a target
segment. In certain embodiments, the antisense compounds are
complementary to at least an 11 nucleobase portion of a target
segment. In certain embodiments, the antisense compounds are
complementary to at least a 12 nucleobase portion of a target
segment. In certain embodiments, the antisense compounds are
complementary to at least a 13 nucleobase portion of a target
segment. In certain embodiments, the antisense compounds are
complementary to at least a 14 nucleobase portion of a target
segment. In certain embodiments, the antisense compounds are
complementary to at least a 15 nucleobase portion of a target
segment. Also contemplated are antisense compounds that are
complementary to at least a 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, or more nucleobase portion of a target segment, or a range
defined by any two of these values.
Identity
[0306] The antisense compounds provided herein may also have a
defined percent identity to a particular nucleotide sequence, SEQ
ID NO, or compound represented by a specific Isis number, or
portion thereof. As used herein, an antisense compound is identical
to the sequence disclosed herein if it has the same nucleobase
pairing ability. For example, a RNA which contains uracil in place
of thymidine in a disclosed DNA sequence would be considered
identical to the DNA sequence since both uracil and thymidine pair
with adenine. Shortened and lengthened versions of the antisense
compounds described herein as well as compounds having
non-identical bases relative to the antisense compounds provided
herein also are contemplated. The non-identical bases may be
adjacent to each other or dispersed throughout the antisense
compound. Percent identity of an antisense compound is calculated
according to the number of bases that have identical base pairing
relative to the sequence to which it is being compared.
[0307] In certain embodiments, the antisense compounds, or portions
thereof, are at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%,
99% or 100% identical to one or more of the antisense compounds or
SEQ ID NOs, or a portion thereof, disclosed herein.
[0308] In certain embodiments, a portion of the antisense compound
is compared to an equal length portion of the target nucleic acid.
In certain embodiments, an 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
18, 19, 20, 21, 22, 23, 24, or 25 nucleobase portion is compared to
an equal length portion of the target nucleic acid.
[0309] In certain embodiments, a portion of the antisense
oligonucleotide is compared to an equal length portion of the
target nucleic acid. In certain embodiments, an 8, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleobase
portion is compared to an equal length portion of the target
nucleic acid.
Modifications
[0310] A nucleoside is a base-sugar combination. The nucleobase
(also known as base) portion of the nucleoside is normally a
heterocyclic base moiety. Nucleotides are nucleosides that further
include a phosphate group covalently linked to the sugar portion of
the nucleoside. For those nucleosides that include a pentofuranosyl
sugar, the phosphate group can be linked to the 2', 3' or 5'
hydroxyl moiety of the sugar.
[0311] Oligonucleotides are formed through the covalent linkage of
adjacent nucleosides to one another, to form a linear polymeric
oligonucleotide. Within the oligonucleotide structure, the
phosphate groups are commonly referred to as forming the
internucleoside linkages of the oligonucleotide.
[0312] Modifications to antisense compounds encompass substitutions
or changes to internucleoside linkages, sugar moieties, or
nucleobases. Modified antisense compounds are often preferred over
native forms because of desirable properties such as, for example,
enhanced cellular uptake, enhanced affinity for nucleic acid
target, increased stability in the presence of nucleases, or
increased inhibitory activity.
[0313] Chemically modified nucleosides may also be employed to
increase the binding affinity of a shortened or truncated antisense
oligonucleotide for its target nucleic acid. Consequently,
comparable results can often be obtained with shorter antisense
compounds that have such chemically modified nucleosides.
Modified Internucleoside Linkages
[0314] The naturally occurring internucleoside linkage of RNA and
DNA is a 3' to 5' phosphodiester linkage. Antisense compounds
having one or more modified, i.e. non-naturally occurring,
internucleoside linkages are often selected over antisense
compounds having naturally occurring internucleoside linkages
because of desirable properties such as, for example, enhanced
cellular uptake, enhanced affinity for target nucleic acids, and
increased stability in the presence of nucleases.
[0315] Oligonucleotides having modified internucleoside linkages
include internucleoside linkages that retain a phosphorus atom as
well as internucleoside linkages that do not have a phosphorus
atom. Representative phosphorus containing internucleoside linkages
include, but are not limited to, phosphodiesters, phosphotriesters,
methylphosphonates, phosphoramidate, and phosphorothioates. Methods
of preparation of phosphorous-containing and
non-phosphorous-containing linkages are well known.
[0316] In certain embodiments, antisense compounds targeted to an
eRNA nucleic acid comprise one or more modified internucleoside
linkages. In certain embodiments, the modified internucleoside
linkages are phosphorothioate linkages. In certain embodiments,
each internucleoside linkage of an antisense compound is a
phosphorothioate internucleoside linkage.
Modified Sugar Moieties
[0317] Antisense compounds can optionally contain one or more
nucleosides wherein the sugar group has been modified. Such sugar
modified nucleosides may impart enhanced nuclease stability,
increased binding affinity, or some other beneficial biological
property to the antisense compounds. In certain embodiments,
nucleosides comprise chemically modified ribofuranose ring
moieties. Examples of chemically modified ribofuranose rings
include without limitation, addition of substitutent groups
(including 5' and 2' substituent groups, bridging of non-geminal
ring atoms to form bicyclic nucleic acids (BNA), replacement of the
ribosyl ring oxygen atom with S, N(R), or C(R.sub.1)(R.sub.2) (R,
R.sub.1 and R.sub.2 are each independently H, C.sub.1-C.sub.12
alkyl or a protecting group) and combinations thereof. Examples of
chemically modified sugars include 2'-F-5'-methyl substituted
nucleoside (see PCT International Application WO 2008/101157
Published on Aug. 21, 2008 for other disclosed 5',2'-bis
substituted nucleosides) or replacement of the ribosyl ring oxygen
atom with S with further substitution at the 2'-position (see
published U.S. Patent Application US2005-0130923, published on Jun.
16, 2005) or alternatively 5'-substitution of a BNA (see PCT
International Application WO 2007/134181 Published on Nov. 22, 2007
wherein LNA is substituted with for example a 5'-methyl or a
5'-vinyl group).
[0318] Examples of nucleosides having modified sugar moieties
include without limitation nucleosides comprising 5'-vinyl,
5'-methyl (R or S), 4'-S, 2'-F, 2'-OCH.sub.3, 2'-OCH.sub.2CH.sub.3,
2'-OCH.sub.2CH.sub.2F and 2'-O(CH.sub.2).sub.2OCH.sub.3 substituent
groups. The substituent at the 2' position can also be selected
from allyl, amino, azido, thio, 0-allyl, O--C.sub.1-C.sub.10 alkyl,
OCF.sub.3, OCH.sub.2F, O(CH.sub.2).sub.2SCH.sub.3,
O(CH.sub.2).sub.z--O--N(R.sub.m)(R.sub.n),
O--CH.sub.2--C(.dbd.O)--N(R.sub.m)(R.sub.n), and
O--CH.sub.2--C(.dbd.O)--N(R)--(CH.sub.2).sub.2--N(R.sub.m)(R.sub.n),
where each R.sub.l, R.sub.m and R.sub.n is, independently, H or
substituted or unsubstituted C.sub.1-C.sub.10 alkyl.
[0319] As used herein, "bicyclic nucleosides" refer to modified
nucleosides comprising a bicyclic sugar moiety. Examples of
bicyclic nucleosides include without limitation nucleosides
comprising a bridge between the 4' and the 2' ribosyl ring atoms.
In certain embodiments, antisense compounds provided herein include
one or more bicyclic nucleosides comprising a 4' to 2' bridge.
Examples of such 4' to 2' bridged bicyclic nucleosides, include but
are not limited to one of the formulae: 4'-(CH.sub.2)--O-2' (LNA);
4'-(CH.sub.2)--S-2'; 4'-(CH.sub.2).sub.2-0-2' (ENA);
4'-CH(CH.sub.3)--O-2' (also referred to as constrained ethyl or
cEt) and 4'-CH(CH.sub.2OCH.sub.3)--O-2' (and analogs thereof see
U.S. Pat. No. 7,399,845, issued on Jul. 15, 2008);
4'-C(CH.sub.3)(CH.sub.3)--O-2' (and analogs thereof see published
International Application WO/2009/006478, published Jan. 8, 2009);
4'-CH.sub.2--N(OCH.sub.3)-2' (and analogs thereof see published
International Application WO/2008/150729, published Dec. 11, 2008);
4'-CH.sub.2--O--N(CH.sub.3)-2' (see published U.S. Patent
Application US2004-0171570, published Sep. 2, 2004);
4'-CH.sub.2--N(R)--O-2', wherein R is H, C.sub.1-C.sub.12 alkyl, or
a protecting group (see U.S. Pat. No. 7,427,672, issued on Sep. 23,
2008); 4'-CH.sub.2--C(H)(CH.sub.3)-2' (see Chattopadhyaya et al., J
Org. Chem., 2009, 74, 118-134); and
4'-CH.sub.2--C(.dbd.CH.sub.2)-2' (and analogs thereof see published
International Application WO 2008/154401, published on Dec. 8,
2008).
[0320] Further reports related to bicyclic nucleosides can also be
found in published literature (see for example: Singh et al., Chem.
Commun., 1998, 4, 455-456; Koshkin et al., Tetrahedron, 1998, 54,
3607-3630; Wahlestedt et al., Proc. Natl. Acad. Sci. U.S.A, 2000,
97, 5633-5638; Kumar et al., Bioorg. Med. Chem. Lett., 1998, 8,
2219-2222; Singh et al., J Org. Chem., 1998, 63, 10035-10039;
Srivastava et al., J Am. Chem. Soc., 2007, 129(26) 8362-8379;
Elayadi et al., Curr. Opinion Invest. Drugs, 2001, 2, 558-561;
Braasch et al., Chem. Biol., 2001, 8, 1-7; and Orum et al., Curr.
Opinion Mol. Ther., 2001, 3, 239-243; U.S. Pat. Nos. 6,268,490;
6,525,191; 6,670,461; 6,770,748; 6,794,499; 7,034,133; 7,053,207;
7,399,845; 7,547,684; and 7,696,345; U.S. Patent Publication No.
US2008-0039618; US2009-0012281; U.S. Patent Serial Nos. 60/989,574;
61/026,995; 61/026,998; 61/056,564; 61/086,231; 61/097,787; and
61/099,844; Published PCT International applications WO
1994/014226; WO 2004/106356; WO 2005/021570; WO 2007/134181; WO
2008/150729; WO 2008/154401; and WO 2009/006478. Each of the
foregoing bicyclic nucleosides can be prepared having one or more
stereochemical sugar configurations including for example
.alpha.-L-ribofuranose and .beta.-D-ribofuranose (see PCT
international application PCT/DK98/00393, published on Mar. 25,
1999 as WO 99/14226).
[0321] In certain embodiments, bicyclic sugar moieties of BNA
nucleosides include, but are not limited to, compounds having at
least one bridge between the 4' and the 2' position of the
pentofuranosyl sugar moiety wherein such bridges independently
comprises 1 or from 2 to 4 linked groups independently selected
from --[C(R.sub.a)(R.sub.b)].sub.n--,
--C(R.sub.a).dbd.C(R.sub.b)--, --C(R.sub.a).dbd.N--, --C(.dbd.O)--,
--C(.dbd.NR.sub.a)--, --C(.dbd.S)--, --O--, --Si(R.sub.a).sub.2--,
--S(.dbd.O).sub.x- , and --N(R.sub.a)--;
[0322] wherein:
[0323] x is 0, 1, or 2;
[0324] n is 1, 2, 3, or 4;
[0325] each R.sub.a and R.sub.b is, independently, H, a protecting
group, hydroxyl, C.sub.1-C.sub.12 alkyl, substituted
C.sub.1-C.sub.12 alkyl, C.sub.2-C.sub.12 alkenyl, substituted
C.sub.2-C.sub.12 alkenyl, C.sub.2-C.sub.12 alkynyl, substituted
C.sub.2-C.sub.12 alkynyl, C.sub.5-C.sub.20 aryl, substituted
C.sub.5-C.sub.20 aryl, heterocycle radical, substituted heterocycle
radical, heteroaryl, substituted heteroaryl, C.sub.5-C.sub.7
alicyclic radical, substituted C.sub.5-C.sub.7 alicyclic radical,
halogen, OJ.sub.1, NJ.sub.1J.sub.2, SJ.sub.1, N.sub.3, COOJ.sub.1,
acyl (C(.dbd.O)--H), substituted acyl, CN, sulfonyl
(S(.dbd.O).sub.2-J.sub.1), or sulfoxyl (S(.dbd.O)-J.sub.1); and
each J.sub.1 and J.sub.2 is, independently, H, C.sub.1-C.sub.12
alkyl, substituted C.sub.1-C.sub.12 alkyl, C.sub.2-C.sub.12
alkenyl, substituted C.sub.2-C.sub.12 alkenyl, C.sub.2-C.sub.12
alkynyl, substituted C.sub.2-C.sub.12 alkynyl, C.sub.5-C.sub.20
aryl, substituted C.sub.5-C.sub.20 aryl, acyl (C(.dbd.O)--H),
substituted acyl, a heterocycle radical, a substituted heterocycle
radical, C.sub.1-C.sub.12 aminoalkyl, substituted C.sub.1-C.sub.12
aminoalkyl or a protecting group.
[0326] In certain embodiments, the bridge of a bicyclic sugar
moiety is --[C(R.sub.a)(R.sub.b)].sub.n--,
--[C(R.sub.a)(R.sub.b)].sub.n--O--, --C(R.sub.aR.sub.b)--N(R)--O--
or --C(R.sub.aR.sub.b)--O--N(R)--. In certain embodiments, the
bridge is 4'-CH.sub.2-2', 4'-(CH.sub.2).sub.2-2',
4'--(CH.sub.2).sub.3-2', 4'-CH.sub.2--O-2',
4'-(CH.sub.2).sub.2--O-2', 4'-CH.sub.2--O--N(R)-2' and
4'-CH.sub.2--N(R)--O-2'- wherein each R is, independently, H, a
protecting group or C.sub.1-C.sub.12 alkyl.
[0327] In certain embodiments, bicyclic nucleosides are further
defined by isomeric configuration. For example, a nucleoside
comprising a 4'-2' methylene-oxy bridge, may be in the .alpha.-L
configuration or in the .beta.-D configuration. Previously,
.alpha.-L-methyleneoxy (4'-CH.sub.2--O-2') BNA's have been
incorporated into antisense oligonucleotides that showed antisense
activity (Frieden et al., Nucleic Acids Research, 2003, 21,
6365-6372).
[0328] In certain embodiments, bicyclic nucleosides include, but
are not limited to, (A) .alpha.-L-methyleneoxy (4'-CH.sub.2--O-2')
BNA, (B) .beta.-D-methyleneoxy (4'-CH.sub.2--O-2') BNA, (C)
ethyleneoxy (4'-(CH.sub.2).sub.2--O-2') BNA, (D) aminooxy
(4'-CH.sub.2--O--N(R)-2') BNA, (E) oxyamino
(4'-CH.sub.2--N(R)--O-2') BNA, and (F) methyl(methyleneoxy)
(4'-CH(CH.sub.3)--O-2') BNA, (G) methylene-thio (4'-CH.sub.2--S-2')
BNA, (H) methylene-amino (4'-CH.sub.2--N(R)-2') BNA, (I) methyl
carbocyclic (4'-CH.sub.2--CH(CH.sub.3)-2') BNA, (J) propylene
carbocyclic (4'-(CH.sub.2).sub.3-2') BNA and (K) vinyl BNA as
depicted below:
##STR00007## ##STR00008##
[0329] wherein Bx is the base moiety and R is independently H, a
protecting group, C.sub.1-C.sub.12 alkyl or C.sub.1-C.sub.12
alkoxy.
[0330] In certain embodiments, bicyclic nucleosides are provided
having Formula I:
##STR00009##
wherein:
[0331] Bx is a heterocyclic base moiety;
[0332] -Q.sub.a-Q.sub.b-Q.sub.c- is
--CH.sub.2--N(R.sub.c)--CH.sub.2--,
--C(.dbd.O)--N(R.sub.c)--CH.sub.2--, --CH.sub.2--O--N(R.sub.c)--,
--CH.sub.2--N(R.sub.c)--O-- or --N(R.sub.c)--O--CH.sub.2;
[0333] R.sub.c is C.sub.1-C.sub.12 alkyl or an amino protecting
group; and
[0334] T.sub.a and T.sub.b are each, independently H, a hydroxyl
protecting group, a conjugate group, a reactive phosphorus group, a
phosphorus moiety or a covalent attachment to a support medium.
[0335] In certain embodiments, bicyclic nucleosides are provided
having Formula II:
##STR00010##
wherein:
[0336] Bx is a heterocyclic base moiety;
[0337] T.sub.a and T.sub.b are each, independently H, a hydroxyl
protecting group, a conjugate group, a reactive phosphorus group, a
phosphorus moiety or a covalent attachment to a support medium;
[0338] Z.sub.a is C.sub.1-C.sub.6 alkyl, C.sub.2-C.sub.6 alkenyl,
C.sub.2-C.sub.6 alkynyl, substituted C.sub.1-C.sub.6 alkyl,
substituted C.sub.2-C.sub.6 alkenyl, substituted C.sub.2-C.sub.6
alkynyl, acyl, substituted acyl, substituted amide, thiol or
substituted thio.
[0339] In one embodiment, each of the substituted groups is,
independently, mono or poly substituted with substituent groups
independently selected from halogen, oxo, hydroxyl, OJ.sub.c,
NJ.sub.cJ.sub.d, SJ.sub.c, N.sub.3, OC(.dbd.X)J.sub.c, and
NJ.sub.eC(.dbd.X)NJ.sub.cJ.sub.d, wherein each J.sub.c, J.sub.d and
J.sub.e is, independently, H, C.sub.1-C.sub.6 alkyl, or substituted
C.sub.1-C.sub.6 alkyl and X is O or NJ.sub.c.
[0340] In certain embodiments, bicyclic nucleosides are provided
having Formula III:
##STR00011##
wherein:
[0341] Bx is a heterocyclic base moiety;
[0342] T.sub.a and T.sub.b are each, independently H, a hydroxyl
protecting group, a conjugate group, a reactive phosphorus group, a
phosphorus moiety or a covalent attachment to a support medium;
[0343] Z.sub.b is C.sub.1-C.sub.6 alkyl, C.sub.2-C.sub.6 alkenyl,
C.sub.2-C.sub.6 alkynyl, substituted C.sub.1-C.sub.6 alkyl,
substituted C.sub.2-C.sub.6 alkenyl, substituted C.sub.2-C.sub.6
alkynyl or substituted acyl (C(.dbd.O)--).
[0344] In certain embodiments, bicyclic nucleosides are provided
having Formula IV:
##STR00012##
wherein:
[0345] Bx is a heterocyclic base moiety;
[0346] T.sub.a and T.sub.b are each, independently H, a hydroxyl
protecting group, a conjugate group, a reactive phosphorus group, a
phosphorus moiety or a covalent attachment to a support medium;
[0347] R.sub.d is C.sub.1-C.sub.6 alkyl, substituted
C.sub.1-C.sub.6 alkyl, C.sub.2-C.sub.6 alkenyl, substituted
C.sub.2-C.sub.6 alkenyl, C.sub.2-C.sub.6 alkynyl or substituted
C.sub.2-C.sub.6 alkynyl;
[0348] each q.sub.a, q.sub.b, q.sub.c and q.sub.d is,
independently, H, halogen, C.sub.1-C.sub.6 alkyl, substituted
C.sub.1-C.sub.6 alkyl, C.sub.2-C.sub.6 alkenyl, substituted
C.sub.2-C.sub.6 alkenyl, C.sub.2-C.sub.6 alkynyl or substituted
C.sub.2-C.sub.6 alkynyl, C.sub.1-C.sub.6 alkoxyl, substituted
C.sub.1-C.sub.6 alkoxyl, acyl, substituted acyl, C.sub.1-C.sub.6
aminoalkyl or substituted C.sub.1-C.sub.6 aminoalkyl;
[0349] In certain embodiments, bicyclic nucleosides are provided
having Formula V:
##STR00013##
wherein:
[0350] Bx is a heterocyclic base moiety;
[0351] T.sub.a and T.sub.b are each, independently H, a hydroxyl
protecting group, a conjugate group, a reactive phosphorus group, a
phosphorus moiety or a covalent attachment to a support medium;
[0352] q.sub.a, q.sub.b, q.sub.e and q.sub.f are each,
independently, hydrogen, halogen, C.sub.1-C.sub.12 alkyl,
substituted C.sub.1-C.sub.12 alkyl, C.sub.2-C.sub.12 alkenyl,
substituted C.sub.2-C.sub.12 alkenyl, C.sub.2-C.sub.12 alkynyl,
substituted C.sub.2-C.sub.12 alkynyl, C.sub.1-C.sub.12 alkoxy,
substituted C.sub.1-C.sub.12 alkoxy, OJ.sub.j, SJ.sub.j, SOJ.sub.j,
SO.sub.2J.sub.j, NJ.sub.iJ.sub.k, N.sub.3, CN, C(.dbd.O)OJ.sub.j,
C(.dbd.O)NJ.sub.jJ.sub.k, C(.dbd.O)J.sub.j,
O--C(.dbd.O)NJ.sub.jJ.sub.k, N(H)C(.dbd.NH)NJ.sub.jJ.sub.k,
N(H)C(.dbd.O)NJ.sub.jJ.sub.k or N(H)C(.dbd.S)NJ.sub.jJ.sub.k;
[0353] or q.sub.e and q.sub.f together are
.dbd.C(q.sub.g)(q.sub.h);
[0354] q.sub.g and q.sub.h are each, independently, H, halogen,
C.sub.1-C.sub.12 alkyl or substituted C.sub.1-C.sub.12 alkyl.
[0355] The synthesis and preparation of the methyleneoxy
(4'-CH.sub.2--O-2') BNA monomers adenine, cytosine, guanine,
5-methyl-cytosine, thymine and uracil, along with their
oligomerization, and nucleic acid recognition properties have been
described (Koshkin et al., Tetrahedron, 1998, 54, 3607-3630). BNAs
and preparation thereof are also described in WO 98/39352 and WO
99/14226.
[0356] Analogs of methyleneoxy (4'-CH.sub.2--O-2') BNA and
2'-thio-BNAs, have also been prepared (Kumar et al., Bioorg. Med.
Chem. Lett., 1998, 8, 2219-2222). Preparation of locked nucleoside
analogs comprising oligodeoxyribonucleotide duplexes as substrates
for nucleic acid polymerases has also been described (Wengel et
al., WO 99/14226). Furthermore, synthesis of 2'-amino-BNA, a novel
comformationally restricted high-affinity oligonucleotide analog
has been described in the art (Singh et al., J Org. Chem., 1998,
63, 10035-10039). In addition, 2'-amino- and 2'-methylamino-BNA's
have been prepared and the thermal stability of their duplexes with
complementary RNA and DNA strands has been previously reported.
[0357] In certain embodiments, bicyclic nucleosides are provided
having Formula VI:
##STR00014##
wherein:
[0358] Bx is a heterocyclic base moiety;
[0359] T.sub.a and T.sub.b are each, independently H, a hydroxyl
protecting group, a conjugate group, a reactive phosphorus group, a
phosphorus moiety or a covalent attachment to a support medium;
[0360] each q.sub.i, q.sub.j, q.sub.k and q.sub.l is,
independently, H, halogen, C.sub.1-C.sub.12 alkyl, substituted
C.sub.1-C.sub.12 alkyl, C.sub.2-C.sub.12 alkenyl, substituted
C.sub.2-C.sub.12 alkenyl, C.sub.2-C.sub.12 alkynyl, substituted
C.sub.2-C.sub.12 alkynyl, C.sub.1-C.sub.12 alkoxyl, substituted
C.sub.1-C.sub.12 alkoxyl, OJ.sub.j, SJ.sub.j, SOJ.sub.j,
SO.sub.2J.sub.j, NJ.sub.jJ.sub.k, N.sub.3, CN, C(.dbd.O)OJ.sub.j,
C(.dbd.O)NJ.sub.jJ.sub.k, C(.dbd.O)J.sub.j,
O--C(.dbd.O)NJ.sub.jJ.sub.k, N(H)C(.dbd.NH)NJ.sub.jJ.sub.k,
N(H)C(.dbd.O)NJ.sub.jJ.sub.k or N(H)C(.dbd.S)NJ.sub.jJ.sub.k; and
q.sub.i and q.sub.j or q.sub.i and q.sub.k together are
.dbd.C(q.sub.g)(q.sub.h), wherein q.sub.g and q.sub.h are each,
independently, H, halogen, C.sub.1-C.sub.12 alkyl or substituted
C.sub.1-C.sub.12 alkyl.
[0361] One carbocyclic bicyclic nucleoside having a
4'-(CH.sub.2).sub.3-2' bridge and the alkenyl analog bridge
4'-CH.dbd.CH--CH.sub.2-2' have been described (Freier et al.,
Nucleic Acids Research, 1997, 25(22), 4429-4443 and Albaek et al.,
J. Org. Chem., 2006, 71, 7731-7740). The synthesis and preparation
of carbocyclic bicyclic nucleosides along with their
oligomerization and biochemical studies have also been described
(Srivastava et al., J. Am. Chem. Soc., 2007, 129(26),
8362-8379).
[0362] As used herein, "4'-2' bicyclic nucleoside" or "4' to 2'
bicyclic nucleoside" refers to a bicyclic nucleoside comprising a
furanose ring comprising a bridge connecting two carbon atoms of
the furanose ring connects the 2' carbon atom and the 4' carbon
atom of the sugar ring.
[0363] As used herein, "monocyclic nucleosides" refer to
nucleosides comprising modified sugar moieties that are not
bicyclic sugar moieties. In certain embodiments, the sugar moiety,
or sugar moiety analogue, of a nucleoside may be modified or
substituted at any position.
[0364] As used herein, "2'-modified sugar" means a furanosyl sugar
modified at the 2' position. In certain embodiments, such
modifications include substituents selected from: a halide,
including, but not limited to substituted and unsubstituted alkoxy,
substituted and unsubstituted thioalkyl, substituted and
unsubstituted amino alkyl, substituted and unsubstituted alkyl,
substituted and unsubstituted allyl, and substituted and
unsubstituted alkynyl. In certain embodiments, 2' modifications are
selected from substituents including, but not limited to:
O[(CH.sub.2).sub.nO].sub.mCH.sub.3, O(CH.sub.2).sub.nNH.sub.2,
O(CH.sub.2).sub.nCH.sub.3, O(CH.sub.2).sub.nF,
O(CH.sub.2).sub.nONH.sub.2, OCH.sub.2C(.dbd.O)N(H)CH.sub.3, and
O(CH.sub.2).sub.nON[(CH.sub.2).sub.nCH.sub.3].sub.2, where n and m
are from 1 to about 10. Other 2'-substituent groups can also be
selected from: C.sub.1-C.sub.12 alkyl, substituted alkyl, alkenyl,
alkynyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH.sub.3,
OCN, Cl, Br, CN, F, CF.sub.3, OCF.sub.3, SOCH.sub.3,
SO.sub.2CH.sub.3, ONO.sub.2, NO.sub.2, N.sub.3, NH.sub.2,
heterocycloalkyl, heterocycloalkaryl, aminoalkylamino,
polyalkylamino, substituted silyl, an RNA cleaving group, a
reporter group, an intercalator, a group for improving
pharmacokinetic properties, or a group for improving the
pharmacodynamic properties of an antisense compound, and other
substituents having similar properties. In certain embodiments,
modified nucleosides comprise a 2'-MOE side chain (Baker et al., J
Biol. Chem., 1997, 272, 11944-12000). Such 2'-MOE substitution have
been described as having improved binding affinity compared to
unmodified nucleosides and to other modified nucleosides, such as
2'-O-methyl, O-propyl, and O-aminopropyl. Oligonucleotides having
the 2'-MOE substituent also have been shown to be antisense
inhibitors of gene expression with promising features for in vivo
use (Martin, Helv. Chim. Acta, 1995, 78, 486-504; Altmann et al.,
Chimia, 1996, 50, 168-176; Altmann et al., Biochem. Soc. Trans.,
1996, 24, 630-637; and Altmann et al., Nucleosides Nucleotides,
1997, 16, 917-926).
[0365] As used herein, a "modified tetrahydropyran nucleoside" or
"modified THP nucleoside" means a nucleoside having a six-membered
tetrahydropyran "sugar" substituted in for the pentofuranosyl
residue in normal nucleosides (a sugar surrogate). Modified THP
nucleosides include, but are not limited to, what is referred to in
the art as hexitol nucleic acid (HNA), anitol nucleic acid (ANA),
manitol nucleic acid (MNA) (see Leumann, Bioorg. Med. Chem., 2002,
10, 841-854) or fluoro HNA (F-HNA) having a tetrahydropyran ring
system as illustrated below:
##STR00015##
[0366] In certain embodiments, sugar surrogates are selected having
Formula VII:
##STR00016##
wherein independently for each of said at least one tetrahydropyran
nucleoside analog of Formula VII:
[0367] Bx is a heterocyclic base moiety;
[0368] T.sub.a and T.sub.b are each, independently, an
internucleoside linking group linking the tetrahydropyran
nucleoside analog to the antisense compound or one of T.sub.a and
T.sub.b is an internucleoside linking group linking the
tetrahydropyran nucleoside analog to the antisense compound and the
other of T.sub.a and T.sub.b is H, a hydroxyl protecting group, a
linked conjugate group or a 5' or 3'-terminal group;
[0369] q.sub.1, q.sub.2, q.sub.3, q.sub.4, q.sub.5, q.sub.6 and
q.sub.7 are each independently, H, C.sub.1-C.sub.6 alkyl,
substituted C.sub.1-C.sub.6 alkyl, C.sub.2-C.sub.6 alkenyl,
substituted C.sub.2-C.sub.6 alkenyl, C.sub.2-C.sub.6 alkynyl or
substituted C.sub.2-C.sub.6 alkynyl; and each of R.sub.1 and
R.sub.2 is selected from hydrogen, hydroxyl, halogen, substituted
or unsubstituted alkoxy, NJ.sub.1J.sub.2, SJ.sub.1, N.sub.3,
OC(.dbd.X)J.sub.1, OC(.dbd.X)NJ.sub.1J.sub.2,
NJ.sub.3C(.dbd.X)NJ.sub.1J.sub.2 and CN, wherein X is O, S or
NJ.sub.1 and each J.sub.1, J.sub.2 and J.sub.3 is, independently, H
or C.sub.1-C.sub.6 alkyl.
[0370] In certain embodiments, the modified THP nucleosides of
Formula VII are provided wherein q.sub.1, q.sub.2, q.sub.3,
q.sub.4, q.sub.5, q.sub.6 and q.sub.7 are each H. In certain
embodiments, at least one of q.sub.1, q.sub.2, q.sub.3, q.sub.4,
q.sub.5, q.sub.6 and q.sub.7 is other than H.
[0371] In certain embodiments, at least one of q.sub.1, q.sub.2,
q.sub.3, q.sub.4, q.sub.5, q.sub.6 and q.sub.7 is methyl. In
certain embodiments, THP nucleosides of Formula VII are provided
wherein one of R.sub.1 and R.sub.2 is fluoro. In certain
embodiments, R.sub.1 is fluoro and R.sub.2 is H; R.sub.1 is methoxy
and R.sub.2 is H, and R.sub.1 is methoxyethoxy and R.sub.2 is
H.
[0372] In certain embodiments, sugar surrogates comprise rings
having more than 5 atoms and more than one heteroatom. For example
nucleosides comprising morpholino sugar moieties and their use in
oligomeric compounds has been reported (see for example: Braasch et
al., Biochemistry, 2002, 41, 4503-4510; and U.S. Pat. Nos.
5,698,685; 5,166,315; 5,185,444; and 5,034,506). As used here, the
term "morpholino" means a sugar surrogate having the following
formula:
##STR00017##
In certain embodiments, morpholinos may be modified, for example by
adding or altering various substituent groups from the above
morpholino structure. Such sugar surrogates are referred to herein
as "modified morpholinos."
[0373] Combinations of modifications are also provided without
limitation, such as 2'-F-5'-methyl substituted nucleosides (see PCT
International Application WO 2008/101157 published on Aug. 21, 2008
for other disclosed 5', 2'-bis substituted nucleosides) and
replacement of the ribosyl ring oxygen atom with S and further
substitution at the 2'-position (see published U.S. Patent
Application US2005-0130923, published on Jun. 16, 2005) or
alternatively 5'-substitution of a bicyclic nucleic acid (see PCT
International Application WO 2007/134181, published on Nov. 22,
2007 wherein a 4'-CH.sub.2--O-2' bicyclic nucleoside is further
substituted at the 5' position with a 5'-methyl or a 5'-vinyl
group). The synthesis and preparation of carbocyclic bicyclic
nucleosides along with their oligomerization and biochemical
studies have also been described (see, e.g., Srivastava et al., J
Am. Chem. Soc. 2007, 129(26), 8362-8379).
[0374] In certain embodiments, antisense compounds comprise one or
more modified cyclohexenyl nucleosides, which is a nucleoside
having a six-membered cyclohexenyl in place of the pentofuranosyl
residue in naturally occurring nucleosides. Modified cyclohexenyl
nucleosides include, but are not limited to those described in the
art (see for example commonly owned, published PCT Application WO
2010/036696, published on Apr. 10, 2010, Robeyns et al., J Am.
Chem. Soc., 2008, 130(6), 1979-1984; Horvath et al., Tetrahedron
Letters, 2007, 48, 3621-3623; Nauwelaerts et al., J. Am. Chem.
Soc., 2007, 129(30), 9340-9348; Gu et al., Nucleosides, Nucleotides
& Nucleic Acids, 2005, 24(5-7), 993-998; Nauwelaerts et al.,
Nucleic Acids Research, 2005, 33(8), 2452-2463; Robeyns et al.,
Acta Crystallographica, Section F: Structural Biology and
Crystallization Communications, 2005, F61(6), 585-586; Gu et al.,
Tetrahedron, 2004, 60(9), 2111-2123; Gu et al., Oligonucleotides,
2003, 13(6), 479-489; Wang et al., J. Org. Chem., 2003, 68,
4499-4505; Verbeure et al., Nucleic Acids Research, 2001, 29(24),
4941-4947; Wang et al., J. Org. Chem., 2001, 66, 8478-82; Wang et
al., Nucleosides, Nucleotides & Nucleic Acids, 2001, 20(4-7),
785-788; Wang et al., J. Am. Chem., 2000, 122, 8595-8602; Published
PCT application, WO 06/047842; and Published PCT Application WO
01/049687; the text of each is incorporated by reference herein, in
their entirety). Certain modified cyclohexenyl nucleosides have
Formula X.
##STR00018##
[0375] wherein independently for each of said at least one
cyclohexenyl nucleoside analog of Formula X:
[0376] Bx is a heterocyclic base moiety;
[0377] T.sub.3 and T.sub.4 are each, independently, an
internucleoside linking group linking the cyclohexenyl nucleoside
analog to an antisense compound or one of T.sub.3 and T.sub.4 is an
internucleoside linking group linking the tetrahydropyran
nucleoside analog to an antisense compound and the other of T.sub.3
and T.sub.4 is H, a hydroxyl protecting group, a linked conjugate
group, or a 5'- or 3'-terminal group; and
[0378] q.sub.1, q.sub.2, q.sub.3, q.sub.4, q.sub.5, q.sub.6,
q.sub.7, q.sub.8 and q.sub.9 are each, independently, H,
C.sub.1-C.sub.6 alkyl, substituted C.sub.1-C.sub.6 alkyl,
C.sub.2-C.sub.6 alkenyl, substituted C.sub.2-C.sub.6 alkenyl,
C.sub.2-C.sub.6 alkynyl, substituted C.sub.2-C.sub.6 alkynyl or
other sugar substituent group.
[0379] As used herein, "2'-modified" or "2'-substituted" refers to
a nucleoside comprising a sugar comprising a substituent at the 2'
position other than H or OH. 2'-modified nucleosides, include, but
are not limited to, bicyclic nucleosides wherein the bridge
connecting two carbon atoms of the sugar ring connects the 2'
carbon and another carbon of the sugar ring; and nucleosides with
non-bridging 2' substituents, such as allyl, amino, azido, thio,
O-allyl, O--C.sub.1-C.sub.10 alkyl, --OCF.sub.3,
O--(CH.sub.2).sub.2--O--CH.sub.3, 2'-O(CH.sub.2).sub.2SCH.sub.3,
O--(CH.sub.2).sub.2--O--N(R.sub.m)(R.sub.n), or
O--CH.sub.2--C(.dbd.O)--N(R.sub.m)(R.sub.n), where each R.sub.m and
R.sub.n is, independently, H or substituted or unsubstituted
C.sub.1-C.sub.10 alkyl. 2'-modified nucleosides may further
comprise other modifications, for example at other positions of the
sugar and/or at the nucleobase.
[0380] As used herein, "2'-F" refers to a nucleoside comprising a
sugar comprising a fluoro group at the 2' position of the sugar
ring.
[0381] As used herein, "2'-OMe" or "2'-OCH.sub.3" or "2'-O-methyl"
each refers to a nucleoside comprising a sugar comprising an
--OCH.sub.3 group at the 2' position of the sugar ring.
[0382] As used herein, "MOE" or "2'-MOE" or
"2'-OCH.sub.2CH.sub.2OCH.sub.3" or "2'-O-methoxyethyl" each refers
to a nucleoside comprising a sugar comprising a
--OCH.sub.2CH.sub.2OCH.sub.3 group at the 2' position of the sugar
ring.
[0383] As used herein, "oligonucleotide" refers to a compound
comprising a plurality of linked nucleosides. In certain
embodiments, one or more of the plurality of nucleosides is
modified. In certain embodiments, an oligonucleotide comprises one
or more ribonucleosides (RNA) and/or deoxyribonucleosides
(DNA).
[0384] Many other bicyclo and tricyclo sugar surrogate ring systems
are also known in the art that can be used to modify nucleosides
for incorporation into antisense compounds (see for example review
article: Leumann, Bioorg. Med. Chem., 2002, 10, 841-854). Such ring
systems can undergo various additional substitutions to enhance
activity.
[0385] Methods for the preparations of modified sugars are well
known to those skilled in the art. Some representative U.S. patents
that teach the preparation of such modified sugars include without
limitation, U.S.: 4,981,957; 5,118,800; 5,319,080; 5,359,044;
5,393,878; 5,446,137; 5,466,786; 5,514,785; 5,519,134; 5,567,811;
5,576,427; 5,591,722; 5,597,909; 5,610,300; 5,627,053; 5,639,873;
5,646,265; 5,670,633; 5,700,920; 5,792,847 and 6,600,032 and
International Application PCT/US2005/019219, filed Jun. 2, 2005 and
published as WO 2005/121371 on Dec. 22, 2005, and each of which is
herein incorporated by reference in its entirety.
[0386] In nucleotides having modified sugar moieties, the
nucleobase moieties (natural, modified or a combination thereof)
are maintained for hybridization with an appropriate nucleic acid
target.
[0387] In certain embodiments, antisense compounds comprise one or
more nucleosides having modified sugar moieties. In certain
embodiments, the modified sugar moiety is 2'-MOE. In certain
embodiments, the 2'-MOE modified nucleosides are arranged in a
gapmer motif. In certain embodiments, the modified sugar moiety is
a bicyclic nucleoside having a (4'-CH(CH.sub.3)--O-2') bridging
group. In certain embodiments, the (4'-CH(CH.sub.3)--O-2') modified
nucleosides are arranged throughout the wings of a gapmer
motif.
Modified Nucleobases
[0388] Nucleobase (or base) modifications or substitutions are
structurally distinguishable from, yet functionally interchangeable
with, naturally occurring or synthetic unmodified nucleobases. Both
natural and modified nucleobases are capable of participating in
hydrogen bonding. Such nucleobase modifications can impart nuclease
stability, binding affinity or some other beneficial biological
property to antisense compounds. Modified nucleobases include
synthetic and natural nucleobases such as, for example,
5-methylcytosine (5-me-C). Certain nucleobase substitutions,
including 5-methylcytosine substitutions, are particularly useful
for increasing the binding affinity of an antisense compound for a
target nucleic acid. For example, 5-methylcytosine substitutions
have been shown to increase nucleic acid duplex stability by
0.6-1.2.degree. C. (Sanghvi, Y. S., Crooke, S. T. and Lebleu, B.,
eds., Antisense Research and Applications, CRC Press, Boca Raton,
1993, pp. 276-278).
[0389] Additional modified nucleobases include 5-hydroxymethyl
cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and
other alkyl derivatives of adenine and guanine, 2-propyl and other
alkyl derivatives of adenine and guanine, 2-thiouracil,
2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine,
5-propynyl (--C.ident.C--CH3) uracil and cytosine and other alkynyl
derivatives of pyrimidine bases, 6-azo uracil, cytosine and
thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino,
8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines
and guanines, 5-halo particularly 5-bromo, 5-trifluoromethyl and
other 5-substituted uracils and cytosines, 7-methylguanine and
7-methyladenine, 2-F-adenine, 2-amino-adenine, 8-azaguanine and
8-azaadenine, 7-deazaguanine and 7-deazaadenine and 3-deazaguanine
and 3-deazaadenine.
[0390] Heterocyclic base moieties can also include those in which
the purine or pyrimidine base is replaced with other heterocycles,
for example 7-deaza-adenine, 7-deazaguanosine, 2-aminopyridine and
2-pyridone.
[0391] Nucleobases that are particularly useful for increasing the
binding affinity of antisense compounds include 5-substituted
pyrimidines, 6-azapyrimidines and N-2, N-6 and 0-6 substituted
purines, including 2 aminopropyladenine, 5-propynyluracil and
5-propynylcytosine.
[0392] In certain embodiments, antisense compounds comprise one or
more modified nucleobases. In certain embodiments, shortened or
gap-widened antisense oligonucleotides comprise one or more
modified nucleobases. In certain embodiments, the modified
nucleobase is 5-methylcytosine. In certain embodiments, each
cytosine is a 5-methylcytosine.
Conjugated Antisense Compounds
[0393] Antisense compounds may be covalently linked to one or more
moieties or conjugates which enhance the activity, cellular
distribution or cellular uptake of the resulting antisense
oligonucleotides. Typical conjugate groups include cholesterol
moieties and lipid moieties. Additional conjugate groups include
carbohydrates, phospholipids, biotin, phenazine, folate,
phenanthridine, anthraquinone, acridine, fluoresceins, rhodamines,
coumarins, and dyes.
[0394] Antisense compounds can also be modified to have one or more
stabilizing groups that are generally attached to one or both
termini of antisense compounds to enhance properties such as, for
example, nuclease stability. Included in stabilizing groups are cap
structures. These terminal modifications protect the antisense
compound having terminal nucleic acid from exonuclease degradation,
and can help in delivery and/or localization within a cell. The cap
can be present at the 5'-terminus (5'-cap), or at the 3'-terminus
(3'-cap), or can be present on both termini. Cap structures are
well known in the art and include, for example, inverted deoxy
abasic caps. Further 3' and 5'-stabilizing groups that can be used
to cap one or both ends of an antisense compound to impart nuclease
stability include those disclosed in WO 03/004602 published on Jan.
16, 2003.
[0395] In certain embodiments, antisense compounds, including, but
not limited to those particularly suited for use as ssRNA, are
modified by attachment of one or more conjugate groups. In general,
conjugate groups modify one or more properties of the attached
oligonucleotide, including but not limited to pharmacodynamics,
pharmacokinetics, stability, binding, absorption, cellular
distribution, cellular uptake, charge and clearance.
[0396] Conjugate groups are routinely used in the chemical arts and
are linked directly or via an optional conjugate linking moiety or
conjugate linking group to a parent compound such as an
oligonucleotide. Conjugate groups includes without limitation,
intercalators, reporter molecules, polyamines, polyamides,
polyethylene glycols, thioethers, polyethers, cholesterols,
thiocholesterols, cholic acid moieties, folate, lipids,
phospholipids, biotin, phenazine, phenanthridine, anthraquinone,
adamantane, acridine, fluoresceins, rhodamines, coumarins and dyes.
Certain conjugate groups have been described previously, for
example: cholesterol moiety (Letsinger et al., Proc. Natl. Acad.
Sci. USA, 1989, 86, 6553-6556), cholic acid (Manoharan et al.,
Bioorg. Med. Chem. Let., 1994, 4, 1053-1060), a thioether, e.g.,
hexyl-S-tritylthiol (Manoharan et al., Ann. N.Y. Acad. Sci., 1992,
660, 306-309; Manoharan et al., Bioorg. Med. Chem. Let., 1993, 3,
2765-2770), a thiocholesterol (Oberhauser et al., Nucl. Acids Res.,
1992, 20, 533-538), an aliphatic chain, e.g., do-decan-diol or
undecyl residues (Saison-Behmoaras et al., EMBO J., 1991, 10,
1111-1118; Kabanov et al., FEBS Lett., 1990, 259, 327-330;
Svinarchuk et al., Biochimie, 1993, 75, 49-54), a phospholipid,
e.g., di-hexadecyl-rac-glycerol or triethyl-ammonium
1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate (Manoharan et al.,
Tetrahedron Lett., 1995, 36, 3651-3654; Shea et al., Nucl. Acids
Res., 1990, 18, 3777-3783), a polyamine or a polyethylene glycol
chain (Manoharan et al., Nucleosides & Nucleotides, 1995, 14,
969-973), or adamantane acetic acid (Manoharan et al., Tetrahedron
Lett., 1995, 36, 3651-3654), a palmityl moiety (Mishra et al.,
Biochim. Biophys. Acta, 1995, 1264, 229-237), or an octadecylamine
or hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J.
Pharmacol. Exp. Ther., 1996, 277, 923-937).
[0397] For additional conjugates including those useful for ssRNA
and their placement within antisense compounds, see e.g., U.S.
Application No. 61/583,963.
In Vitro Testing of Antisense Oligonucleotides
[0398] Described herein are methods for treatment of cells with
antisense oligonucleotides, which can be modified appropriately for
treatment with other antisense compounds.
[0399] Cells may be treated with antisense oligonucleotides when
the cells reach approximately 60-80% confluency in culture.
[0400] One reagent commonly used to introduce antisense
oligonucleotides into cultured cells includes the cationic lipid
transfection reagent LIPOFECTIN (Invitrogen, Carlsbad, Calif.).
Antisense oligonucleotides may be mixed with LIPOFECTIN in OPTI-MEM
1 (Invitrogen, Carlsbad, Calif.) to achieve the desired final
concentration of antisense oligonucleotide and a LIPOFECTIN
concentration that may range from 2 to 12 ug/mL per 100 nM
antisense oligonucleotide.
[0401] Another reagent used to introduce antisense oligonucleotides
into cultured cells includes LIPOFECTAMINE (Invitrogen, Carlsbad,
Calif.). Antisense oligonucleotide is mixed with LIPOFECTAMINE in
OPTI-MEM 1 reduced serum medium (Invitrogen, Carlsbad, Calif.) to
achieve the desired concentration of antisense oligonucleotide and
a LIPOFECTAMINE concentration that may range from 2 to 12 ug/mL per
100 nM antisense oligonucleotide.
[0402] Another technique used to introduce antisense
oligonucleotides into cultured cells includes electroporation.
[0403] Cells are treated with antisense oligonucleotides by routine
methods. Cells may be harvested 16-24 hours after antisense
oligonucleotide treatment, at which time RNA or protein levels of
target nucleic acids are measured by methods known in the art and
described herein. In general, when treatments are performed in
multiple replicates, the data are presented as the average of the
replicate treatments.
[0404] The concentration of antisense oligonucleotide used varies
from cell line to cell line. Methods to determine the optimal
antisense oligonucleotide concentration for a particular cell line
are well known in the art. Antisense oligonucleotides are typically
used at concentrations ranging from 1 nM to 300 nM when transfected
with LIPOFECTAMINE. Antisense oligonucleotides are used at higher
concentrations ranging from 625 to 20,000 nM when transfected using
electroporation.
RNA Isolation
[0405] RNA analysis can be performed on total cellular RNA or
poly(A)+mRNA. Methods of RNA isolation are well known in the art.
RNA is prepared using methods well known in the art, for example,
using the TRIZOL Reagent (Invitrogen, Carlsbad, Calif.) according
to the manufacturer's recommended protocols.
EXAMPLES
Non-Limiting Disclosure and Incorporation by Reference
[0406] While certain compounds, compositions and methods described
herein have been described with specificity in accordance with
certain embodiments, the following examples serve only to
illustrate the compounds described herein and are not intended to
limit the same. Each of the references recited in the present
application is incorporated herein by reference in its
entirety.
Example 1: Determination of Genome-Wide Binding Profiles in
Engineered RAW264.7 Macrophages
[0407] To understand the mechanisms underlying Rev-Erb regulation
of macrophage gene expression, genome-wide binding profiles in
RAW264.7 macrophages engineered to contain biotin-tagged
Rev-Erb.alpha. and Rev-Erb.beta. were determined. Rev-Erb.alpha.
and Rev-Erb.beta. were tagged with biotin-ligase recognition
peptide for in vivo biotinylation in RAW264.7 macrophages
expressing biotin ligase from E. coli (Heinz, S. et al., Mol. Cell.
2010. 38: 576-589). Biotin-based or antibody-based Chromatin
immunoprecipitation linked to deep sequencing (ChIP-Seq) was
performed. ChIP-Seq indicated enrichment for both Rev-Erb.alpha.
and Rev-Erb.beta. at the promoter of the circadian target gene
BmalI. Previous studies (Preitner, N. et al., Cell. 2002. 110:
251-260; Yin, L. and Lazar, M. A. Mol. Endocrinol. 2005. 19:
1452-1459) have also demonstrated a high degree of overlap in the
Rev-Erb.alpha. and Rev-Erb.beta. cistromes in several independent
cell lines.
[0408] To focus on transcriptional programs common to
Rev-Erb.alpha. and Rev-Erb.beta.3, a core set of 2,079 of the
highest confidence peaks occupied by both proteins was selected for
detailed analysis. As seen in Table 1, the majority (.about.88%) of
these peaks were in intra- and intergenic regions at least 1
kilobase away from annotated transcription start sites.
TABLE-US-00002 TABLE 1 Distribution of Rev-Erb localization
relative to the nearest protein-coding genes. % Promoter (1 kb-500
bp) 10 Intergenic 49 Exon 2 intron 39
[0409] This was exemplified by intergenic Rev-Erb binding sites
vicinal to the Mmp9 and Cxcr1 genes. In addition, 70% of Rev-Erb
bound sites were in regions demarcated by high enrichment for
H3K4me1 and low enrichment for H3K4me3, a histone signature for
enhancer elements (Feng, D. et al., Science. 2011. 331: 1315-1319).
De novo motif discovery of Rev-Erb-bound loci returned significant
enrichment for binding sites for Rev-Erb, PU.1, AP1 and C/EBP, as
presented in Table 2, with significant p-values and percentage of
expected vs. observed instances of motifs.
TABLE-US-00003 TABLE 2 Top-enriched transcription factor motifs
identified % % Transcription Factor p-value observed expected AP1
1e-449 31 4 PU.1 1e-354 40 9 Rev-Erb DR2 1e-174 7 1 C/EBP 1e-49 6
1
[0410] PU.1, AP-1 and C/EBP transcription factors are required for
macrophage differentiation (Solt, L. A. et al., Nature. 2012.
doi:10.1038/nature11030) and have recently been shown to establish
the majority of the enhancer-like elements in macrophages
(Fontaine, C. et al., Mol. Endocrinol. 2008. 22: 1797-1811).
Co-localization of Rev-Erbs with PU.1 and C/EBP in macrophages was
confirmed by comparison with direct binding data for these factors.
Consistent with these findings, the Rev-Erb bound sites defined
above localized to enhancer-like elements specific for macrophages,
as defined by H3K4me1. The data is presented in Table 3, which
shows the results of distribution of averaged ChIP-Seq signal of
H3K4me1 at Rev-Erb bound H3K4me1.sup.hi H3K4me3.sup.lo (n=1,388)
region in macrophages (Heinz, S. et al., Mol. Cell 2010. 38:
576-589), B-cell (Lin, Y. C. et al., Nat. Immunol. 2010. 11: 635),
liver (Creyghton, M. P. et al., Proc. Natl. Acad. Sci. USA 2010.
107: 21931-21936), mouse embryonic stell cells (mES), and neural
progenitor (NP)(Meissner, A. et al., Nature. 2008. 454:
766-770).
TABLE-US-00004 TABLE 3 Normalized Tag density in different cell
types vs. distance from center of Rev-Erb bound enhancers Distance
from Center (bp) Macrophages Liver mES NP B Cell -1800 0.17 0.06
0.07 0.05 0.10 -1600 0.19 0.06 0.07 0.06 0.11 -1400 0.21 0.06 0.07
0.06 0.12 -1200 0.24 0.06 0.07 0.07 0.14 -1000 0.28 0.07 0.07 0.07
0.15 -800 0.35 0.08 0.07 0.08 0.17 -600 0.41 0.09 0.08 0.09 0.20
-400 0.48 0.09 0.08 0.10 0.22 -200 0.40 0.11 0.08 0.11 0.22 0 0.18
0.11 0.08 0.10 0.18 200 0.40 0.10 0.08 0.10 0.22 400 0.48 0.10 0.08
0.10 0.23 600 0.42 0.08 0.08 0.08 0.20 800 0.34 0.08 0.07 0.08 0.18
1000 0.29 0.07 0.07 0.06 0.16 1200 0.24 0.07 0.07 0.06 0.14 1400
0.21 0.06 0.06 0.06 0.13 1600 0.19 0.06 0.06 0.06 0.12 1800 0.18
0.06 0.06 0.06 0.12
Example 2: Gene Expression Analysis in Wild-Type Macrophages and in
Macrophages Deficient for Both Rev-Erb.alpha. and Rev-Erb.beta.
[0411] Gene expression analysis was performed in wild-type (WT)
macrophages and macrophages deficient for both Rev-Erb.alpha. and
Rev-Erb.beta..
[0412] Bone marrow derived macrophages (BMDMs) and
thioglycollate-elicited (ThioMac) macrophages were generated from
4-6 week old Rev-Erb.alpha..sup.flox/flox;
Rev-Erb.beta..sup.flox/flox with or without Tie2-Cre as previously
described (Huang, W. et al., Nature. 2011. 470: 414-418). Rev-Erb
double knockout (DKO) macrophages were generated from bone marrow
differentiation of Tie2-Cre; Rev-Erbd.alpha..sup.flox/flox;
Rev-Erb.beta..sup.flox/flox animals (RevErb DKO) and were compared
to control macrophages derived from Cre-negative littermates (WT).
Tie2-Cre expression in hematopoietic stem cells (Schlaeger, T. M.
et al., Blood. 2005. 105: 3871-3874) resulted in excision
efficiencies in DKO macrophages of 85% of Rev-Erb.alpha. and 92%
for Rev-Erb.beta.3, as determined by Q-PCR. Knockout of
Rev-Erb.beta. dramatically increased Rev-Erb.alpha. expression.
Excision of Rev-Erb.alpha. was estimated by comparing the
derepression between the floxed region versus a non-excised
region.
[0413] Global Run-On sequencing (GRO-Seq) was performed to
investigate the relationship between Rev-Erb binding sites and
target genes. Preparation for GRO was performed as described
previously (Wang, D. et al., Nature. 2011.
doi:10.1038/nature10006). GRO-Seq analysis indicated that 142 genes
were significantly up-regulated in DKO macrophages (p-value
<0.005), while 71 genes were down-regulated (p-value <0.005).
The distance between transcription start sites of annotated genes
to the nearest Rev-Erb peaks in all, up-, or down-regulated genes
is presented in Table 4. The results indicate that genes that were
up-regulated in DKO macrophages were significantly closer to
Rev-Erb binding sites than down-regulated genes, consistent with
the primary roles of Rev-Erbs as dedicated transcriptional
repressors. However, only 3 of the 142 up-regulated genes had
Rev-Erb peaks within 2 kb of annotated transcription start sites,
suggesting that Rev-Erbs primarily act to repress gene expression
at enhancer-like elements.
TABLE-US-00005 TABLE 4 Distance of nearest Rev-Erb peaks to TSS (bp
in log2 scale) compared to gene expression in Rev-Erb DKO
macrophages Gene expression in Rev-Erb DKO Up-regulated
Down-regulated All genes genes average distance 3181221 755558
3457211 (bp) 1st quartile 112798 45767 122946 3rd quartile 998603
627405 1603662 gene # 24741 142 71
[0414] For expression analysis, RNA was harvested from macrophages
using RNEasy kit (Qiagen), treated with Turbo-DNases (Ambion) and
reverse-transcribed, using SuperScript III Reverse-Trasncriptase
(Invitrogen) with random hexamers. Values determined for mRNA,
using Quantitative reverse transcriptase-dependent PCR (Q-PCR),
were normalized to 36B4 mRNA content from at least three
independent experiments in triplicates. Quantitative reverse
transcriptase-dependent PCR was used to validate GRO-Seq data in WT
and DKO macrophages for the Mmp9 and Cx3cr1 genes at the level of
mature mRNA. The results are presented in Table 5 and present the
analysis in Rev-Erb DKO (WT=8 and DKO=7 in number) and
Rev-Erb.alpha. (control=17 and alpha phenotype=18 independent
lines), or Rev-Erb.beta. (control=13 and beta phenotype=18
independent lines) over-expressing macrophages. Statistical
significance was determined by two tail Student's t-test. P-value
is represented as ** for P<0.01 and by .sctn. for P<0.05
versus the control. Mature mRNA for both genes was significantly
increased in the Rev-Erb DKO macrophages. Conversely, constitutive
expression of either Rev-Erb.alpha. or Rev-Erb.beta. in RAW264.7
macrophages resulted in repression of Mmp9 and Cx3cr1
expression.
TABLE-US-00006 TABLE 5 Q-PCR analysis of relative normalized
expression of Mmp9 and Cx3cr1 mRNA in Rev-Erb DKO and
Rev-Erb.alpha. or Rev-Erb.beta. overexpressing macrophages Mmp9
Cx3cr1 WT 0.43 0.19 DKO 1.65.sctn. 1.93.sctn. Control 1.72 1.18
Rev-Erb.alpha. 0.32** 0.83.sctn. Control 1.69 1.26 Rev-Erb.beta.
0.50** 0.81**
[0415] By evaluating multiple independent clones, the extent of
Mmp9 and Cx3cr1 repression was observed to be inversely correlated
with Rev-Erb expression levels. The data was generated by Q-PCR
analysis of Mmp9 and Cx3cr1 mRNA expression in independent RAW264.7
macrophage cell lines expressing Rev-Erb.alpha. (n=17),
Rev-Erb.beta.(n=18), or empty expression vector. The data was found
to be statistically significant, as determined by Spearman rank
correlation test.
Example 3: Testing of Genomic Regions Containing Rev-Erb Binding
Sites for Enhancer Activity
[0416] A 983 bp region surrounding the Rev-Erb-bound site at
.about.5 kb from the Mmp9 transcription start site (TSS) was cloned
downstream of a luciferase reporter driven by a TATA-like promoter.
The region was cloned into a pGL4-based reporter and tested in
RAW264.7, as described previously (Heinz, S. et al., Mol. Cell.
2010. 38: 576-589). The presence of this Rev-Erb-containing region
increased reporter gene activity in RAW264.7 macrophages, while a
control genomic region devoid of Rev-Erb binding sites or other
enhancer-like features did not. This enhancer activity was also
sensitive to Rev-Erb repression, as determined by luciferase
reporter activity.
[0417] Sequencing libraries were prepared by ligating separate
modified single-stranded adapters to 3' and 5'-RNA ends using
mutant (K227Q) truncated RNA ligase 2 (NEB) and RNA ligase 1,
respectively, reverse-transcribed with SuperScript III reverse
transcriptase (Invitrogen), and PCR-amplified with primers bearing
primer landing sites compatible with Illumina sequencing.
RAR-related orphan nuclear receptors (RORs) also bind to Rev-Erb
response elements and constitutively activate gene expression
(Giguere, V et al., Genes Dev. 1994. 8: 538-553). Consistent with
this, constitutive expression of ROR.alpha. increased activity of
the Mmp9 enhancer element. Co-expression of wild type
Rev-Erb.beta., but not Rev-Erb.beta. with a mutation disrupting
sequence-specific DNA binding, antagonized ROR.alpha. activation.
For this assay, luciferase activity of reporters containing Rev-Erb
bound enhancer from the genomic regions was measured after
co-transfection of ROR.alpha. and Rev-Erb.alpha. or Rev-Erb.beta.
with mutation in the DNA binding domain. BmalI promoter was used as
the positive control. A 1 kb genomic region without enhancer-like
element was used as a negative control. Data generated was the mean
of at least 3 independent experiments and was found to be
statistically significant, as determined by one-way ANOVA followed
by Tukey HSD test.
[0418] Similar experiments were performed for six other
Rev-Erb-bound distal regions, all of which were sensitive to
ROR.alpha. activation. Four of the six could be antagonized by
Rev-Erb co-transfection. Collectively, these findings suggest that
Rev-Erbs confer a macrophage-specific program of repression by
regulating the activities of enhancers that are established by
collaborative interactions between macrophage lineage-determining
transcription factors, such as PU.1 and C/EBPs, and
signal-dependent factors, such as RORs.
[0419] Among the 2,079 common Rev-Erb binding sites, 1,388 loci
were located at least .+-.1 kb from annotated transcription start
sites and were associated with the enhancer histone signature
H3K4me1 h/H3K4me3.sup.lo. ChIP-sequencing experiments indicated
that many of these sites were co-enriched for the engaged, serine-5
phosphorylated RNA Polymerase II (RNAPII). The data was derived
from a cluster plot of ChIP-Seq signal for H3K4me1, H3K4me3, and
serine-5 phosphorylated RNA polymeriase II (RNAPII) at 1,388
Rev-Erb bound, H3K4me1.sup.hiH3K4me3l.sup.o regions.
[0420] In addition, examination of GRO-Seq data at these sites
indicated the presence of bi-directional RNA transcription,
consistent with recent studies indicating that RNAs are transcribed
from distal enhancer elements on a genome-wide scale (Kim, T.-K. et
al., Nature. 2010. 465: 182; Wang, D. et al., Nature. 2011.
doi:10.1038/nature10006; Hah, N. et al., Cell. 2011. 145: 622-634).
The data is presented in Table 6 as the distribution of averaged
macrophage GRO-Seq eRNA signal flanking Rev-Erb intergenic sites
defined in macrophages (n=722) and liver (n=521). No significant
RNA signal was detected from the locations of intergenic
Rev-Erb.alpha. peaks defined in liver (Feng, D. et al., Science.
2011. 331: 1315-1319), indicating that RNA expression at distal
regulatory elements is cell-type specific.
TABLE-US-00007 TABLE 6 Distribution of macrophage GRO-Seq eRNA
signal flanking Rev-Erb intergenic sites in macrophages and liver
distance from Rev- macrophages Liver Erb intergenic sites
Rev-Erb.alpha. Rev-Erb.alpha. Rev-Erb.alpha. Rev-Erb.alpha. (bp)
Plus Minus Plus Minus -1820 0.0028 0.0025 0.0010 0.0007 -1700
0.0031 0.0028 0.0011 0.0007 -1500 0.0032 0.0030 0.0010 0.0008 -1300
0.0032 0.0033 0.0009 0.0007 -1100 0.0031 0.0041 0.0010 0.0008 -900
0.0030 0.0052 0.0010 0.0009 -700 0.0030 0.0066 0.0009 0.0010 -500
0.0031 0.0076 0.0009 0.0013 -300 0.0036 0.0087 0.0009 0.0014 -100
0.0042 0.0071 0.0011 0.0014 -20 0.0054 0.0059 0.0012 0.0013 20
0.0060 0.0053 0.0012 0.0013 100 0.0070 0.0039 0.0013 0.0012 300
0.0087 0.0033 0.0012 0.0009 500 0.0079 0.0032 0.0010 0.0009 700
0.0071 0.0030 0.0011 0.0009 900 0.0055 0.0030 0.0010 0.0009 1100
0.0046 0.0030 0.0008 0.0009 1300 0.0039 0.0027 0.0010 0.0009 1500
0.0032 0.0026 0.0011 0.0009 1700 0.0028 0.0026 0.0009 0.0009 1820
0.0026 0.0026 0.0007 0.0008
Example 4: Determination of the Role of Rev-Erbs in Regulating
Enhancer-RNA (eRNA) Expression
[0421] To determine whether Rev-Erbs regulate eRNA expression,
transcription of nascent RNA at Rev-Erb bound enhancers was
examined in both loss of function and gain of function models.
[0422] Using GRO-Seq, analysis of averaged RNA signal distribution
from the 100 highest enriched Rev-Erb bound intergenic enhancers
indicated an overall increase of RNA signal in Rev-Erb DKO
macrophages compared to WT control. Conversely, overexpression of
Rev-Erb.alpha. resulted in decreased eRNA expression at the most
confident Rev-Erb binding sites. To precisely define the eRNA start
sites, the GRO-Seq protocol was modified to detect nascent RNA with
a 5' 7-methylguanylated cap (5'GROseq), thus focusing on detecting
transcriptional events at initiation sites. 5'GRO-Seq was perfomed
with the following modifications from the GRO-Seq protocol (Wang,
D. et al., Nature. 2011. doi:10.1038/nature10006). Briefly, GRO-RNA
was 3' and 5'-dephosphorylated with polynucleotide kinase
(Enzymatics) and calf intestinal phosphatase (NEB), respectively,
and then capped fragments were de-capped with tobacco acid
pyrophosphatase (Epicentre) to leave 5' phosphates. Analysis of
averaged RNA signal distribution at the top 100 Rev-Erb intergenic
enhancers showed a striking decrease of eRNA initiation in
macrophages overexpressing Rev-Erb.alpha. compared to control
macrophages. The data is presented in Tables 7 and 8. Table 7
presents the distribution of averaged GRO-Seq eRNA signal from
Rev-Erb DKO and control BMDM at the top 100 Rev-Erb bound
intergenic sites. Table 8 shows the distribution of average 5'
capped RNA (5' GRO-Seq) signal from Rev-Erb.alpha. overexpressing
and control RAW264.7 macrophages flanking the top 100 Rev-Erb-bound
intergenic sites.
TABLE-US-00008 TABLE 7 Distribution of averaged GRO-Seq eRNA signal
from Rev-Erb DKO and control BMDM distance from center of Wild type
DKO Rev-Erb sites (bp) plus minus plus minus -1820 0.002 0.003
0.003 0.003 -1700 0.003 0.003 0.003 0.003 -1500 0.003 0.003 0.003
0.003 -1300 0.003 0.004 0.003 0.004 -1100 0.002 0.005 0.003 0.006
-900 0.002 0.006 0.003 0.008 -700 0.003 0.008 0.004 0.009 -500
0.004 0.008 0.004 0.009 -300 0.004 0.009 0.004 0.011 -100 0.004
0.009 0.005 0.010 -20 0.005 0.008 0.007 0.008 20 0.006 0.007 0.007
0.008 100 0.007 0.005 0.008 0.006 300 0.009 0.004 0.010 0.005 500
0.008 0.004 0.009 0.005 700 0.008 0.004 0.009 0.004 900 0.006 0.003
0.008 0.003 1100 0.005 0.003 0.007 0.003 1300 0.004 0.002 0.005
0.003 1500 0.004 0.003 0.004 0.004 1700 0.003 0.004 0.004 0.004
1820 0.003 0.003 0.003 0.004
TABLE-US-00009 TABLE 8 Distribution of 5'GRO-Seq eRNA signal from
Rev-Erb.alpha. macrophages and control macrophages flanking
Rev-Erb-bound intergenic sites distance from center of Rev- Control
Rev-Erb Erb sites (bp) plus minus plus minus -480 0.034 0.027 0.013
0.016 -400 0.032 0.044 0.021 0.018 -300 0.032 0.050 0.026 0.031
-200 0.015 0.078 0.008 0.044 -100 0.020 0.309 0.012 0.172 -10 0.175
0.169 0.108 0.120 0 0.198 0.148 0.117 0.109 10 0.245 0.161 0.153
0.107 100 0.242 0.032 0.162 0.027 200 0.114 0.017 0.055 0.013 300
0.058 0.047 0.030 0.025 400 0.045 0.015 0.026 0.006 480 0.055 0.011
0.033 0.005
[0423] In either loss or gain of function experiment, the eRNA
signal at the global set of PU.1-bound enhancers showed no
significant changes, as presented in Table 9, indicating that the
changes in eRNA are specific to Rev-Erb-bound enhancer elements.
Table 9 presents the distribution of average 5' capped RNA
(5'GRO-Seq) signal from Rev-Erb.alpha. overexpressing and control
RAW264.7 macrophages flanking the top 100 PU.1-bound intergenic
sites.
TABLE-US-00010 TABLE 9 Distribution of 5'GRO-Seq eRNA signal from
Rev-Erb.alpha. macrophages and control macrophages flanking
PU.1-bound intergenic sites distance from center Control
RevErb.alpha. of PU.1 sites (bp) plus minus plus minus -480 0.027
0.023 0.020 0.018 -400 0.015 0.029 0.010 0.026 -300 0.034 0.035
0.036 0.033 -200 0.012 0.049 0.009 0.074 -100 0.013 0.199 0.014
0.188 -10 0.105 0.163 0.097 0.161 0 0.152 0.127 0.161 0.129 10
0.180 0.085 0.189 0.079 100 0.225 0.013 0.233 0.019 200 0.059 0.013
0.050 0.020 300 0.046 0.018 0.039 0.017 400 0.022 0.015 0.022 0.014
480 0.013 0.010 0.012 0.013
[0424] Moreover, the de-repression level of eRNA in Rev-Erb DKO is
inversely correlated to eRNA repression level upon constitutive
expression of Rev-Erb.alpha. (p=-0.39, p-value=0.008), indicating a
strong agreement between the experimental sets. For this assay, 53
Rev-Erb bound enhancers with de-repressed eRNA expression in
Rev-Erb DKO macrophages was plotted against changes of eRNA level
upon overexpression of Rev-Erb.alpha. in RAW264.7 macrophages.
Changes in eRNA was determined by the log.sub.2 difference of
expression between DKO and WT mancrophages, or between
Rev-Erb.alpha. over-expressing and control macrophages. The data
was considered statistically significant, as determined by Spearman
rank correlation test.
[0425] GRO-Seq results indicating Rev-Erb mediated negative
regulation of eRNA expression were confirmed using RT-PCR for eRNA
of Mmp9-5 kb and Cx3cr1 28 kb enhancers. Q-PCR analysis of the
.about.5 kb Mmp9 and 28 kb Cx3cr1 enhancer RNA in Rev-Erb DKO (wild
type=6) and DKO-5 in number) and Rev-Erb.alpha. overexpressing
RAW264.7 macrophages (control=13 and alpha=14 independent cell
lines) are presented in Table 10. The statistical significance was
determined by two tail Student's t-test where * represents
P<0.01 and .sctn. represents P<0.05, versus the control.
TABLE-US-00011 TABLE 10 Relative expression of Mmp9 and Cx3cr1
enhancer RNA Cx3cr1 Mmp9 eRNA eRNA WT 0.67 0.33 DKO 1.38*
1.75.sctn. Control 1.37 1.37 Rev-Erb 0.65 0.66.sctn.
[0426] To investigate mechanisms by which Rev-Erbs regulate eRNA
expression, the effects of gain and loss of Rev-Erb function on
enhancer assembly and histone modification were evaluated. ChIP-Seq
experiments demonstrated increased H3K9 acetylation (H3K9ac) at
Rev-Erb-occupied enhancers in DKO macrophages and reduced H3K9ac
enrichment in macrophages with constitutively expressed Rev-Erba.
H3K9ac enrichment was not changed at the global set of
PU.1-enhancers, consistent with Rev-Erb-mediated recruitment of
NCoR/HDAC3 complexes mediating local deacetylation of H3K9 (Yin, L.
and Lazar, M. A. Mol. Endocrinol. 2005. 19: 1452-1459). The assay
measured the average distribution of H3K9ac ChIP-Seq signal
flanking 53 Rev-Erb bound enhancers or the top 500 enriched PU.1
bound enhancers for WT and Rev-Erb DKO macrophages. The assay also
measured the same parameters for 266 Rev-Erb bound enhancer which
have repressed eRNA expression or the top 500 enriched PU.1 bound
enhancer for control and Rev-Erb.alpha. overexpressing RAW264.7
macrophages.
[0427] In contrast, constitutive expression of Rev-Erb.alpha. had
no significant effect on H3K4me1 or PU.1 enrichment at Rev-Erb
bound enhancer elements, despite the profound changes in eRNA
initiation. The assay measured the average distribution of PI.1 and
H3K4me1 and ChIP-Seq signal flanking the 266 Rev-Erb bound
enhancers with repressed eRNA level upon overexpression of
Rev-Erba.
[0428] Collectively, these results raise the possibility that
Rev-Erbs repressed gene expression at a distance by regulating
enhancer-directed transcription. Consistent with this possibility,
changes in eRNA expression at Rev-Erb-bound sites due to gain or
loss of Rev-Erb function were correlated with changes in expression
of the nearest mRNA.
Example 5: Determination of the Role of eRNA Activity In Vitro
[0429] Even though levels of eRNA are low at steady state (Kim,
T.-K. et al., Nature. 2010. 465: 182), transcriptional initiation
from enhancers, as measured by 5' GRO-Seq, was often comparable to
that at promoters of protein-coding genes, as exemplified by Cx3cr1
andMmp9, suggesting robust production of short-lived transcripts.
Three experimental approaches were used to investigate whether the
synthesis of enhancer-directed RNA transcripts contributed to
enhancer activity.
[0430] First, RNA interference (RNAi) was utilized to target eRNA
transcripts of Mmp9 and Cx3cr1. Non-targeting siRNA oligos or siRNA
directed against Mmp9 and Cxcr1 eRNA (Dharmacon) were transfected
using DeliverX (Affymetrix) or LipofectAMINE2000.RTM. (Invitrogen)
into ThioMac or BMDM, respectively. siRNAs were identified that
specifically reduced expression of eRNAs associated with the Mmp9
or Cx3cr1 enhancers in primary WT macrophages. Q-PCR analysis of
Mmp9 eRNA, Mmp9 mRNA and NCoA5 (negative control) for WT and
Rev-Erb DKO ThioMac transfected with control or Mmp9 eRNA siRNA
(WT=4 and DKO=4 in number) was conducted. The results are presented
in Table 11. Q-PCR analysis was also conducted of Cx3cr1 eRNA,
Cxc3cr1 mRNA and Csrnp1 (negative control) for WT and Rev-Erb DKO
BMDM transfected with siRNA targeting Cx3cr1 eRNA (WT=6 and DKO=5
in number). The results are presented in Table 12. The results
demonstrate the reduction in eRNA expression was associated with a
corresponding reduction of Mmp9 and Cx3cr1 mRNAs, but not mRNAs
from the nearest expressing genes such as NCoA5 and Csrnp1,
respectively. Furthermore, these siRNAs reversed the de-repression
phenotype associated with increased eRNA expression in Rev-Erb DKO
macrophages.
TABLE-US-00012 TABLE 11 Relative expression of Mmp9 eRNA and mRNA
after treatment with siRNA Mmp9 eRNA Mmp9 mRNA NCoA5 Control siRNA
WT 0.4 1.1 0.8 siRNA to Mmp9 WT 0.3 0.4 0.8 eRNA Control siRNA DKO
1.3 2.0 0.8 siRNA to Mmp9 DKO 0.5 0.4 1.0 eRNA
TABLE-US-00013 TABLE 12 Relative expression of Cx3cr1 eRNA and mRNA
after treatment with siRNA Cx3cr1 eRNA Cx3cr1 mRNA CsrnpI Control
siRNA WT 0.8 0.3 0.9 siRNA to Cx3cr1 WT 0.2 0.1 0.9 eRNA Control
siRNA DKO 2.1 2.5 1.0 siRNA to Cx3cr1 DKO 0.9 1.4 1.2 eRNA
[0431] As a second approach, chemically modified antisense
oligonucleotides (ASO) were utilized to knock down the plus strand
Mmp9-5 kb eRNA. Seventy seven overlapping ASOs targeting the
proximal 450 bp of the plus-strand Mmp9-5 kb eRNA were
systematically screened and the most effective ASOs were selected
for detailed analysis.
[0432] ISIS 566237 is an oligonucleotide with deoxy, MOE and
(S)-cEthyl units with a sequence 5'-ATTGTGTGACCCCAGC-3' (SEQ ID
NO:3) and a chemistry notation 5'-Aes Tes Tks Gds Tds Gds Tds Gds
Ads mCds mCds mCds mCds Aks Gks mCe-3' (e=2'-O-methoxyethyl ribose;
s=thioate ester; k=(S)-cEt; d=2'-deoxyribose). ISIS 566237 is
targeted to an Mmp9 eRNA sequence, SEQ ID NO: 1 (GENBANK Accession
No. NT_039207.7 truncated from 105809972 to 105810309). ISIS 566237
targets SEQ ID NO: 1 at nucleotides 247 to 262.
[0433] ISIS 566241 is an oligonucleotide with deoxy, MOE and
(S)-cEthyl units with a sequence 5'-CAAGCTTCAGCTCATT-3' (SEQ ID
NO:4) and a chemistry notation 5'-mCes Aes Aks Gds mCds Tds Tds
mCds Ads Gds mCds Tds mCds Aks Tks Te-3' (e=2'-O-methoxyethyl
ribose; s=thioate ester; k=(S)-cEt; d=2'-deoxyribose). ISIS 566241
is targeted to an Mmp9 eRNA sequence, SEQ ID NO: 1 at nucleotides
260 to 275.
[0434] ISIS 129700 is a 5-10-5 MOE gapmer and is 20 nucleosides in
length, wherein the central gap segment comprises often
2'-deoxynucleosides and is flanked by wing segments on the 5'
direction and the 3' direction comprising five nucleosides each.
Each nucleoside in the 5' wing segment and each nucleoside in the
3' wing segment has a 2'-MOE modification. The internucleoside
linkages throughout the gapmer are phosphorothioate (P.dbd.S)
linkages. All cytosine residues throughout the gapmer are
5-methylcytosines. ISIS 129700 has the sequence
5'-TAGTGCGGACCTACCCACGA-3' (SEQ ID NO: 5) and does not target any
known murine target. Hence, it was used as a negative control.
[0435] ISIS 535522 is a 5-10-5 MOE gapmer with a sequence
5'-GCACCTTTCCCTCGGATGGG-3' (SEQ ID NO: 6) and is targeted to the
murine Mmp9 mRNA sequence (GENBANK Accession No. NM_013599.2) (SEQ
ID NO:203) at nucleotides 2275 to 2294. ISIS 535522 also served as
a control in the assay.
[0436] The ASOs were transfected into ThioMac using Cytofectin
(Gene Therapy System). The results of the Q-PCR analysis of Mmp9
eRNA expression in thioglycollate-elicited primary macrophages
transfected with ASOs are presented in Table 13. Both ISIS 566237
and ISIS 566241 reduced eRNA expression. Statistical significance
was determined by one-way ANOVA with Tukey HSD test. In case of the
P value, * represents P<0.05 and .sctn. represents P<0.005,
versus the control.
TABLE-US-00014 TABLE 13 Relative expression of Mmp9 eRNA and mRNA
after treatment with ASOs % inhibition ISIS 129700 0 ISIS 566237
15* ISIS 566241 42.sctn.
[0437] Furthermore, titrating the concentration of ASO resulted in
dose dependent reduction of the corresponding Mmp9 mRNA. Table 14
presents the Q-PCR analysis of Mmp9 mRNA expression in ThioMac
transfected with titrated concentration of ASO (n=3 per
condition).
TABLE-US-00015 TABLE 14 Dose-dependent inhibition of Mmp9 mRNA
after treatment with ASOs % ISIS No Dose (nM) inhibition ASO
targeting 566237 12.5 0 Mmp9 eRNA 566237 25 0 566237 50 10 566237
100 45 566237 200 54 ASO targeting 566241 12.5 0 Mmp9 eRNA 566241
25 0 566241 50 9 566241 100 55 566241 200 49 ASO targeting 535522
100 88 Mmp9 mRNA
[0438] As a third approach, the functional significance of the
Mmp9-5 kb eRNAs was examined using the enhancer reporter assay
guided by the definition of eRNA start sites provided by 5'GRO-Seq.
The 983 bp sequence upstream of Mmp9 that conferred
Rev-Erb-regulated enhancer activity in RAW264.7 cells encompassed a
388 bp central region of open chromatin containing the binding
sites for PU.1, C/EBPs, AP-1 and Rev-Erbs, as well as start sites
of the plus and minus-strand eRNAs. The 983 bp of the Mmp9 enhancer
was cloned downstream of the luciferase reporter gene driven by the
Mmp9 promoter. The luciferase activity of the enhancer reporter
driven by Mmp9 promoter containing the indicated DNA fragments and
transfected in RAW264.7 macrophages (n=8) was measured and is
presented in Table 15. The 388 bp core was significantly less
active than the 983 bp sequence, which encoded the eRNAs.
Statistical significance was determined by one-way ANOVA followed
by Tukey HSD test. In case of the P value, .sctn. represents
P<0.005 versus all other indicated conditions.
TABLE-US-00016 TABLE 15 Relative promoter activity of the Mmp9
enhancer activity Random 1kb 0.14 Mmp9 enhancer 983 bp 1.96.sctn.
Mmp9 enhancer 388 bp 0.90
[0439] Expression of the plus-strand eRNA from the 983 bp enhancer
was confirmed by RT-PCR of Mmp9 plus eRNA normalized to the copy
number of the transfected plasmid DNA using reporter-specific
primer for first strand cDNA synthesis. Enhancer reporter assays
were performed as described above with different DNA fragments
cloned in the luciferase reporter and the data is presented in
Table 16. Addition of DNA encoding the plus-strand eRNA to the core
enhancer, but not the DNA encoding the minus strand eRNA, restored
transcriptional activity. Statistical significance was determined
by one-way ANOVA followed by Tukey HSD test. In case of the P
value, .sctn. represents P<0.005 versus all other indicated
conditions.
[0440] In another experiment, 983 bp of the Mmp9 enhancer was
cloned downstream of the luciferase reporter gene driven by the
Mmp9 promoter in the opposite orientation from that used in the
study above. Enhancer reporter constructs driven by Mmp9 promoter
containing the DNA fragments were transfected into RAW264.7
macrophages. A similar activity of the plus strand eRNA was
observed when the 1 kb or core enhancer elements were inserted in
the reverse orientation.
TABLE-US-00017 TABLE 16 Relative promoter activity of the Mmp9
enhancer Activity Mmp9 enhancer 388 bp 0.77 Plus eRNA WT 1.91.sctn.
Flipped 0.70 Minus eRNA WT 0.84 Flipped 0.79
[0441] These observations were consistent with the finding that
siRNAs and ASOs directed against the plus-strand eRNA resulted in
reduction of Mmp9 mRNA expression. These findings also suggested
that either the eRNA sequence is an important determinant of
enhancer function, or the sequences encoding the plus strand eRNA
contain binding sites for additional transcription factors that
contribute to enhancer activity.
[0442] To address this question, the orientation of the sequences
encoding the plus strand eRNA enhancer was inverted relative to the
388 bp-core. This strategy would retain any putative transcription
factor binding sites but completely change the sequence of any
potential eRNA product. In the "flipped" construct, enhancer
activity was reduced to a level comparable to the 388 bp-enhancer
construct despite production of eRNA from an alternative start
site. Collectively, these data suggest that the DNA element
encoding the plus eRNA contributes to Mmp9 enhancer activity.
Example 6: Determination of the Role of eRNA Activity In Vivo
[0443] The findings of the studies described above raised the
question of whether enhancers might be considered as targets for
cell-specific manipulation of gene expression in vivo. To explore
this possibility, sterile peritonitis was induced in mice and the
ability of siRNAs directed against the Mmp9-5 kb plus strand eRNA
to alter Mmp9 mRNA expression was investigated.
Thioglycollate-elicicted sterile peritonitis and in vivo RNAi
assays were performed as described in previous studies (Huang, W.
et al., Nature. 2011. 470: 414-418). Briefly, 2 ml thioglycollate
medium was delivered to each animal by intra-peritoneal injection
on day 1. On day 2, 100 .mu.g scrambled control siRNAs or Mmp9
eRNA-specific siRNA was complexed in LipofectAMINE2000.RTM. and
serum-depleted medium (in 1 ml final volume) and delivered to
animals by intraperitoneal injection. Elicited macrophages in the
peritoneal cavities were collected with 10 ml of PBS on day 4 for
RNA analysis (n=8 per condition). Values were normalized to the
average of 36B4 and Cyclophilin A mRNA. Statistical significance
was determined by two tail Student's t-test. In case of the P
value, * represents P<0.05 versus the control siRNA. The results
are presented in Table 17 and indicate that the eRNA-specific
siRNA, but not a control siRNA, reduced expression of the .about.5
kb plus strand eRNA and the Mmp9 primary transcript, but not the
NCoA5 mRNA, as was observed in primary macrophages in vitro. Cx3cr1
mRNA was also measured as a negative control.
TABLE-US-00018 TABLE 17 Relative RNA expression in mice control
siRNA to siRNA Mmp9 eRNA Mmp9 eRNA 1.17 0.83 Mmp9 pre-mRNA 1.21
0.79 NcoA5 1.07 0.93 Cx3cr1 1.05 0.95
Example 7: Role of eRNAs in Enhancer-Dependent Activation of Coding
Genes Regulated by Sex Steroid Receptors
[0444] The role of eRNAs in the enhancer-dependent activation of
coding genes regulated by sex steroid receptors was studied by
performing experiments designed to determine whether liganded
estrogen receptors induce eRNA transcription on ER.alpha.-bound
enhancers.
[0445] MCF-7 cells were initially obtained from ATCC and were
incubated in .alpha.-MEM media supplemented with 10% FBS in a 7%
CO.sub.2 humidified incubator. Once the cells reached 60%
confluency, they were hormone-stripped for 3 days by culturing in
phenol-free media plus charcoal-depleted FBS. The cells were
treated or not with 100 nM Estradiol (E.sub.2) for 1 hr to induce
estrogen signaling (Prasanth, K. V. and Spector, D. L. Genes Dev.
2007.21: 11-42).
[0446] A ChIP-seq analysis (>100.times.10.sup.6 uniquely mapped
reads) of ER.alpha. binding sites was performed, as previously
described (Wang, D. et al., Nature. 2011. 474: 390-394). Briefly,
approximately 10.sup.7 treated cells were cross-linked with 1%
formaldehyde at room temperature for 10 min. After sonication, the
soluble chromatin was incubated with 1-5 .mu.g of antibody (HC-20
and H-184, Santa Cruz Biotechnology) at 40.degree. C. overnight.
Immunoprecipitated complexes were collected using Dynabeads A/G
(Invitrogen). Subsequently, immunocomplexes were washed, DNA
extracted and purified by QIAquick Spin columns (Qiagen). The
extracted DNA was ligated to specific adaptors, followed by deep
sequencing with the Illumina HiSeq 2000 system, according to the
manufacturer's instructions. The first 48 bp for each sequence tag
returned by the Illumina pipeline was aligned to the hg18 assembly
(National Center for Biotechnology Information, build 36.1), using
BFast, allowing up to two mismatches. Only uniquely mapped tags
were selected for further analysis.
[0447] The data was visualized by preparing custom tracks on the
University of California, Santa Cruz genome browser, using HOMER
(biowhat.ucsd.edu/homer) (Heinz, S. et al., Mol. Cell. 2010. 38:
576-589). Given that the peak distribution of transcription factors
and histone marks were markedly different, parameters were
optimized for the narrow tag distribution characteristic of
transcription factors by searching for high read density regions
with a 200 bp sliding window. Regions of maximal density exceeding
a given threshold were called `peaks`, and it was required for
adjacent peaks to be at least 500 bp away to avoid redundant
detection. The common artifacts derived from clonal amplification
were circumvented by considering only one tag from each unique
genomic position, as determined from the mapping data. The
threshold for the number of tags that determined a valid peak was
selected at a false discovery rate of 0.001, determined by peak
finding using randomized tag positions in a genome with an
effective size of 2.times.10.sup.9 bp. It was also required for
peaks to have at least four-fold more tags (normalized to total
count) than input control samples. In addition, it was required to
obtain four-fold more tags relative to the local background region
(10 kb) to avoid identifying regions with genomic duplications or
non-localized binding.
[0448] In the case of histone marks, the parameters were modified
to search for enrichment in wide genomic segments as, unlike
transcription factors, they can occupy large segments in the
magnitude of several kb. Seed regions were initially found using a
peak size of 500 bp at a false discovery rate of 0.001 to identify
enriched loci. Enriched regions separated by 1 kb were merged and
considered as blocks of variable lengths. All called peaks meeting
the criteria established for transcription factors and histone
marks were then associated with genes by cross-referencing the
RefSeq TSS database as available in the UCSC genome browser. Peaks
from individual experiments were considered equivalent if their
peak centers were located within 200 bp.
[0449] The analysis (>100.times.10.sup.6 uniquely mapped reads)
of ER.alpha. binding sites using vehicle or E.sub.2-treated MCF-7
breast cancer cells increased the number of known genomic ER.alpha.
binding sites three-fold, to 23,255, genome-wide. In this robust
analysis, ER.alpha. was found to preferentially bind distal
intergenic (53%) and intronic sites (39%), with only 3% being bound
to promoters, suggesting that ER.alpha. is able to exert
transcriptional effects based on binding to genomic elements other
than the regulated coding gene promoters. A corresponding `deep`
ChIP-seq analysis was done for H3K4me (Newman J. J. and Young, R.
A. Cold Spring Harb. Symp. Quant. Biol. 2011. 75: 227-235), a
histone modification considered to mark enhancers (Heintzman, et
al., Nat. Genet. 2007. 39: 311-318). Analysis was also done for
H3K27ac, a modification considered to mark potentially active
enhancers (Creyghton, M. P. et al., Proc. Natl. Acad. Sci. USA.
2010. 107: 21931-6). Analysis of these two markers was used to
identify 7,797 potential estrogen-responsive enhancers.
Example 8: GRO-Seq Analysis of Genome-Wide Transcription Units
Regulated by ER.alpha.
[0450] The transcriptional consequences of a one hour E.sub.2
treatment at 100 nM, compared to the vehicle, was determined by
GRO-Seq (Core, L. J. et al., Science. 2008. 322: 1845-8) to provide
a genome-wide catalogue of transcription units regulated by
ER.alpha..
[0451] GRO-sequencing of nascent RNAQ was achieved using MCF-7
cells hormone-stripped for 3 days and treated or not with 100 nM
Estradiol (E.sub.2) for 1 hr to induce estrogen signaling. The
cells were then washed three times with cold PBS buffer and then
swelled in swelling buffer (10 mM Tris-HCl, pH 7.5, 2 mM
MgCl.sub.2, 3 mM CaCl.sub.2) for 5 min on ice, and harvested. Cells
were re-suspended and lysed in lysis buffer (swelling buffer with
0.5% IGEPAL and 10% glycerol). Nuclei were washed once with 10 mM
lysis buffer and re-suspended in 100 .mu.L freezing buffer (50 mM
Tris-HCl, pH 8.3, 40% glycerol, 5 mM MgCl.sub.2, 0.1 mM EDTA). For
the run-on assay, resuspended nuclei were mixed with an equal
volume of reaction buffer (10 mM Tris-HCl, pH 8.0, 5 mM MgCl.sub.2,
1 mM DTT, 300 mM KCl, 20 units SUPERase-In.TM., 1% sarkosyl, 500 M
ATP, GTP, Br-UTP, 2 M CTP), and incubated for 5 min at 30.degree.
C. The nuclear run-on RNA (NRO-RNA) was then extracted with TRIzol
LS reagent (Invitrogen), following the manufacturer's instructions.
NRO-RNA was then subjected to base hydrolysis on ice for 40 min,
followed by treatment with DNase I and Antarctic phosphatase. To
purify the Br-UTP labeled RNA, the NRO-RNA was immunoprecipitated
with anti-BrdU agarose beads (Santa Cruz Biotech) in binding buffer
(0.5.times.SSPE, 1 mM EDTA, 0.05% Tween-20) for 1 hour at
40.degree. C. with rotation. To repair the end, the
immunoprecipitated BrU-RNA was re-suspended in 50 .mu.L reaction
(45 .mu.L DEPC water, 5.2 .mu.L T4 PNK buffer, 1 .mu.L SUPERase-In
and 1 .mu.L T4 PNK [NEB]) and incubated at 37.degree. C. for 1 hr.
The RNA was extracted and precipitated using acidic
phenol-chloroform.
[0452] cDNA synthesis was performed, as described previously (Tsai,
M. C. et al., Science. 2010. 329: 689-93), with some modifications.
The RNA fragments were subjected to poly-A tailing reaction by
poly-A polymerase (NEB) for 30 min at 37.degree. C. Subsequently,
reverse transcription was performed using oNTI223 primer, the
sequence of which is presented in Table 18. Tailed RNA (8.0 .mu.L)
was subjected to reverse transcription using Superscript III
(Invitrogen). The cDNA products were separated on a 10%
polyacrylamide TBE-urea gel. The extended first-strand product
(100-500 bp) was excised and recovered by gel extraction. The
first-strand cDNA was then circularized by CircLigase.TM.
(Epicentre) and re-linearized by Apel (NEB). Re-linearized single
strand cDNA (sscDNA) was separated in a 10% polyacrylamide TBE gel
and the product of needed size was excised (.about.120-320 bp) for
gel extraction. Finally, sscDNA template was amplified by PCR using
the Phusion High-Fidelity enzyme (NEB), according to the
manufacturer's instructions. The oligonucleotide primers oNTI200
and oNTI201 were used to generate DNA for deep sequencing (Table
18). `;` indicated an abasic dSpacer furan; `N` indicates
degenerate nucleotides.
TABLE-US-00019 TABLE 18 Oligos used in the Gro-Seq protocol SEQ ID
Name Sequence 5' to 3' NO oNTI223 GATCGTCGGACTGTAGAACTCT; 7
CAAGCAGAAGACGGCATACGATTTTTTTTTTT TTTTTTTTTN oNTI200
CAAGCAGAAGACGGCATA 8 oNTI201 AATGATACGGCGACCACCGACAGGTTCAGAGT 9
TCTACAGTCCGACG Illumina CGACAGGTTCAGAGTTCTACAGTCCGACGATC 10 small
RNA- seq
[0453] Transcript identification and assignment to genomic regions,
including annotated genes was accomplished using HOMER. GRO-Seq
read densities were analyzed in a similar manner to ChIP-Seq,
except that in this case, all the GRO-Seq libraries corresponding
to the same experiment were merged in order to maximize read
density for transcript identification. Provided GRO-Seq generated
strand-specific data, separate tracks were uploaded onto the UCSC
genome browser, once tag-enriched sites were identified using a
sliding window of 250 bp. The portion of GRO-Seq tags that mapped
to repeat regions was excluded and instead, the read density for
these regions was approximated with values from flanking regions to
avoid having to end transcripts prematurely. Transcript initiation
sites were identified as regions where the GRO-Seq read density
increased three-fold relative to the preceding 1 kb region.
Transcript termination sites were defined by either a reduction in
reads below 10% of the start of the transcript or when another
transcript's start site was identified on the same strand.
Individual high-density peaks spanning a region less than 250 bp
were considered as artifacts, and thus removed from the analysis.
Transcripts were defined as putative eRNAs if their TSS was located
distal to RefSeq TSS (>3 kb) and were associated with ER.alpha.
and H3K4me1 regions. To identify differentially regulated
transcripts, strand-specific read counts from each GRO-Seq
experiment were determined for each transcript using HOMER. EdgeR
(bioconductor.org/) was then used to calculate differential genomic
and non-genic expression (>1.5-fold, <0.01 false discovery
rate).
[0454] The sequencing resulted in the finding of 1,033 up-regulated
genes that exhibited E.sub.2/ER.alpha.-binding in one or in
multiple adjacent enhancers, while only 112 of these ER.alpha.
up-regulated coding genes exhibited ER.alpha. binding to their
promoters, consistent with initial suggestions (Jin, V. X. et al.,
Nucleic Acids Res. 2004. 32: 6627-35; Carroll, J. S. et al., Nat.
Genet. 2006. 38: 1289-97; Kwon, Y. S. et al., Proc. Natl. Acad.
Sci. USA 2007. 104: 4852-7; Lin, C. Y. et al., PLoS Genet. 2007. 3:
e87; Welboren, W. J. et al., EMBO J. 2009. 28: 1418-28) that
ER.alpha. occupancy on enhancers is likely to be the key strategy
underlying estrogen-induced gene expression.
[0455] The E.sub.2-regulated enhancers generally displayed a basal
expression of bidirectional eRNAs and those in proximity to
up-regulated coding genes displayed a characteristic bidirectional
activation of eRNAs, exemplified by the FOXC1 locus, in general
agreement with recent findings (Hah, N. et al., Cell. 2011. 145:
622-34). In contrast to the more 1:1 enhancer:promoter ratio for
AR-regulated genes (Prasanth, K. V. and Spector, D. L. Genes Dev.
2007. 21: 11-42), there was often more than one ER.alpha.-bound
enhancer adjacent to up-regulated coding genes. This raised the
possibility that for many estrogen-regulated coding genes, more
than one enhancer might be involved in up-regulation events and
might even cross-regulate. The eRNA transcripts varied in apparent
length but were generally .about.1.5 kb, although .about.10%
exhibited an apparent predominance of unidirectional eRNA
transcripts. Analysis of the GRO-Seq data confirmed the overall
up-regulation of eRNAs in response to ligand, generally with
bidirectional transcription, robust at 1 h after E.sub.2, and
subsequently diminishing, and being highly diminished by 24 hr.
Overall, >83% of ER.alpha.-bound enhancers adjacent to
up-regulated coding genes exhibited Ez_induced eRNA transcription
by GRO-Seq. The median distance between enhancers exhibiting
E.sub.2-dependent up-regulation of their eRNAs and their closest
up-regulated coding gene was .about.52 kb, with most <215 kb
from the coding gene cap site, compared with a median distance of
>270 kb for enhancers exhibiting ligand-insensitive enhancer
eRNAs with corresponding non-responsive coding genes.
[0456] Examining the strength of ER.alpha. binding, based on
normalized ChIP-seq data on these cohorts of enhancers with
upregulation of the eRNAs, exhibited significantly stronger binding
than on enhancers not exhibiting eRNA upregulation.
[0457] Based on these GRO-seq data analyses, ten robustly
up-regulated transcription units were selected for further
experimentation, each associated with enhancers exhibiting clearly
increased eRNAs--CA12, FOXC1, GREB1, P2RY2, SMAD7, PGR, SIAH2,
NRIP1, TFF1 and KCNK5. For these transcription units, there was a
.about.2-5-fold increase in coding gene expression, with a
corresponding .about.2.5-5-fold increase in eRNA expression on
associated enhancers, assessed 1 hr following addition of E.sub.2
to MCF-7 cell cultures.
Example 9: Investigation of the Potential Role of Ligand-Induced
eRNAs on Gene Activation Events Using Transcription Inhibition
Assays
[0458] To investigate the potential roles, if any, of
ligand-induced eRNAs on gene activation events, two different
technologies were employed to down-regulate eRNAs: siRNAs and
locked nucleic acid antisense oligonucleotides (LNAs).
[0459] Specific siRNAs directed at several regions of each
transcript were used to assess possible effects on gene expression
(Table 19). Similarly, LNAs were utilized by placing the
LNA-modified bases at key positions to ensure target specificity as
well as stability of the oligonucleotides (Table 20). The LNAs were
designed for this purpose with complete phosphorothioate backbones
to trigger RNAse H cleavage of the targeted sequences (Vester, B.
et al., Bioorg. Med. Chem. Lett. 2008. 18: 2296-300) (Table 20). In
both cases, the siRNAs or LNAs were designed based on the location
of the eRNA CAP sites .about.200 bp 5' of ER.alpha. binding sites,
determined using the modified GRO-seq protocol described above. For
both LNAs and siRNAs, scrambled sequences were used as controls.
For all transcription units examined, experiments were performed
with two different LNAs or siRNAs, with similar knock-down
efficacy, to exclude any off-target effects.
TABLE-US-00020 TABLE 19 siRNA sequences SEQ Name SEQ Name ID (Anti-
Sequence (Antisense) ID Over- (Sense) Sequence (Sense) 5' to 3' NO:
sense) 5' to 3' NO: hangs TFF1e_1 CAGAGUCAGAGAGUCAGAGAGAGAU 11
TFF1e_1 AUCUCUCUCUGACUCUCUGACUCUG 12 None TFF1e_2
GAGUUUGGACCUGUGACCUUCCUAA 13 TFF1e_2 UUAGGAAGGUCACAGGUCCAAACUC 14
None TFF1e_3 AAUCUCCUGGGAGGAUGAAGCUGUU 15 TFF1e_3
AACAGCUUCAUCCUCCCAGGAGAUU 16 None GREB1e1_1
ACCACUGUUUCUGACUGCUUUCUCA 17 GREB1e1_1 UGAGAAAGCAGUCAGAAACAGUGGU 18
None GREB1e1_2 GGAUUGAGAGUGACCAGGACAUUUA 19 GREB1e1_2
UAAAUGUCCUGGUCACUCUCAAUCC 20 None GREB1e1_3
CGCCCAGCCUAAUUGUAGUACUUUA 21 GREB1e1_3 UAAAGUACUACAAUUAGGCUGGGCG 22
None PGRe_1 GCAAAUUCUUUCAUGACAA 23 PGRe_1 UUGUCAUGAAAGAAUUUGC 24 UU
PGRe_2 GCAAAGAUGGAUAGAGAUA 25 PGRe_2 UAUCUCUAUCCAUCUUUGC 26 UU
SIAH2e1_1 GCACAUACCUCAUUAGAGA 27 SIAH2e1_1 UCUCUAAUGAGGUAUGUGC 28
UU SIAH2e2_2 GGUAUUAAUAGCUCUGAAA 29 SIAH2e2_2 UUUCAGAGCUAUUAAUACC
30 UU NRIP1e1_1 GGGAGAGGGUCUACAAUUA 31 NRIP1e1_1
UAAUUGUCGACCCUCUCCC 32 UU NRIP1e3_2 GGCCAGAUCUCCUGUGAUA 33
NRIP1e3_2 UAUCACAGGAGAUCUGGCC 34 UU FOXC1e_1 GCUCCAUUCUGCUGCUCAA 35
FOXC1e_1 UUGAGCAGCAGAAUGGAGC 36 UU FOXC1e_2 CUAACGUGACAGUGACAUA 37
FOXC1e_2 UAUGUCACUGUCACGUUAG 38 UU P2RY2e_1 GCAAAAGGUAGGAGGGUUU 39
P2RY2e_1 AAACCCUCCUACCUUUUGC 40 UU P2RY2e_2 GGAGAUGAAUUGAUAGAGA 41
P2RY2e_2 UCUCUAUCAAUUCAUCUCC 42 UU CA12e_1 CAGAAGAGCUAUUUGGUAU 43
CA12e_1 AUACCAAAUAGCUCUUCUG 44 UU CA12e_2 GAGUGGACUUCACAAGAAA 45
CA12e_2 UUUCUUGUGAAGUCCACUC 46 UU SMAD7e1_1 AGAGAAGAAUGAAGGUGAA 47
SMAD7e1_1 UUCACCUUCAUUCUUCUCU 48 UU SMAD7e2_2 CCACAGGUGAGCAGAAAUU
49 SMAD7e2_2 AAUUUCUGCUCACCUGUGG 50 UU SMAD7e3_3
CCUAAUUCCCAGAAGCAGA 51 SMAD7e3_3 UCUGCUUCUGGGAAUUAGG 52 UU
KCNK5e1_1 CGAAAUGGCCUAAAGAUGA 53 KCNK5e1_1 UCAUCUUUAGGCCAUUUCG 54
UU KCNK5e2_2 ACACAAAGGUGGAAGGAAA 55 KCNK5e2_2 UUUCCUUCCACCUUUGUGU
56 UU KCNK5e3_3 GGAAGAACCUGCAGAGAUG 57 KCNK5e3_3
CAUCUCUGCAGGUUCUUCC 58 UU
TABLE-US-00021 TABLE 20 LNA sequences LNA name Sequence SEQ ID NO:
LNA_Ctrl CACGTCTATACACCAC 59 TFF1E_1 GAATTAACGCCTGAGG 60 TFF1E_2
GAACTGACAAAGGTGG 61 TFF1E_3 ATCTCCCCACTCAAGG 62 TFF1E_4
CATTTTTCTGCTGACC 63 CA12E_1 ACAAGACAGAGGCAGA 64 CA12E_2
TCAGTTGGAGGACAGT 65 FOXC1E_1 GAAGGAGCAGGTGAAA 66 FOXC1E_2
GGTATTTCCGCTTCAC 67 NRIP1E3_1 AGGATACCAGGACACA 68 NRIP1E3_2
TGATAAAAGCAGGGTC 69
[0460] Twenty four hours after cell seeding, MCF-7 cells were
hormone-stripped for one day, followed by siRNA transfection (40
nM) using LipofectAMINE2000.RTM.. Cells were washed twice with PBS
and maintained in hormone-deprived phenol-free supplemented
stripped media for 2 days, and then treated with EtOH or E2 for 1
hr. LNA transfections (40 nM) were performed 2 days after
starvation in stripped media and the LNA treatment lasted 6 or 24
hrs, after which cells were treated as described above.
[0461] For RT-QPCR, RNA was isolated using TRIzol reagent
(Invitrogen), and total RNA was reverse-transcribed using
SuperScript III Reverse Transcriptase (Invitrogen), as per the
manufacturer's instructions. Quantitative PCRs were performed in
MX3000P (Stratagene), using Q-PCR master mix (Agilent Inc.). For
normalization, .DELTA.Ct values were calculated using the formula:
.DELTA.Ct=(Ct Target-Ct input) where input corresponds to the level
of ACTB transcript. Fold differences in normalized gene expression
were calculated by dividing the level of expression of the treated
sample with the untreated sample or between siRNA/LNA and Control
siRNA/control-LNA transfected cells. A list of primers used for
Q-PCR is provided in Tables 21 and 22. `F` and `R` indicate the
forward and reverse primers, respectively.
TABLE-US-00022 TABLE 21 List of primers used to measure eRNA SEQ ID
Name Sequence 5' to 3' NO: TFF1e_F TCAGTTCCCAGCATTCTCATC 70 TFF1e_R
TTGAGCCTTGGAGACAGAAAG 71 GREB1e1_F TCCAAAGCATCCCATTCCTG 72
GREB1e1_R TGAGCAAAACAAGACAAACCG 73 PGRe_F TTATGTTGCTCTTGATAGACTCCC
74 PGRe_R GCTAGGTGCTGTCTGAGATTC 75 SIAH2e1_F
TTCAAGCAAAGATTATAGCCATGTG 76 SIAH2e1_R ATCCAGTGCAGAGTAACATCAG 77
SIAH2e2_F AGATGCCTCTGCATACTGGTT 78 SIAH2e2_R CAGACCATATTGGGCCACAG
79 NRIP1e1_F CCACAGCAGAAAACCACTGA 80 NRIP1e1_R TTCCCTCTGCACTGACTCCT
81 NRIP1e3_F CGTCTTTTCCCACTGACACA 82 NRIP1e3_R CCCCTCCCCAGAAGAAAATA
83 FOXC1e_F CTGAGGAACACAAGACTAGCC 84 FOXC1e_R
ACTGGACTCATTTTGGGACATC 85 P2RY2e_F ATTGTGCATGGCTCTTACCC 86 P2RY2e_R
CTTGGTGCATGTGAGCTTGT 87 P2RY2e_F AGCTTCTGGTTCCAAGGTCA 88 P2RY2e_R
CATGTGCTGTTGTTGCTGTG 89 CA12e_F TGAAAGGGAAGACGCAGATG 90 CA12e_R
TTGTATCCTTTGACTGGGCAG 91 SMAD7e1_F AAAGAAGGCAGGGGAACAAT 92
SMAD7e1_R CACTTGGGCAATCCAGAAAT 93 SMAD7e2_F TCACCTGTGGAAAGAGACAAC
94 SMAD7e2_R AGAACCTTTTGCTCCCTAGTG 95 SMAD7e3_F
TTAAACGAGCCTGGAGTTGG 96 SMAD7e3_R AAATTCCTCAGAGCCCAGTG 97 KCNK5e1_F
GGCTCAGAGAGGCCAAAA 98 KCNK5e1_R TGGACCCTATCATCTCCTTTAACT 99
KCNK5e2_F GGAAAGGAATTGCTGGATCA 100 KCNK5e2_S_R GTGCAACCACTTGGGAAACT
101 KCNK5e3_S_F CAGAGATGAGGAAAGGTTTGC 102 KCNK5e3_S_R
ATCTGCTTCACGGTCTCATG 103
TABLE-US-00023 TABLE 22 List of primers used to measure mRNA SEQ ID
Name Sequence 5' to 3' NO: FOXC1_F AGTAGCTGTCAAATGGCCTTC 104
FOXC1_R TTAGTTCGGCTTTGAGGGTG 105 P2RY2_F GGGGACCTGTTTTTCCTGTT 106
P2RY2_R GACTTGGATCTGGACCTGGA 107 CA12_F TCTGTCTGCCAACAAGCAGT 108
CA12_R GCACTGTAGCGAGACTGGAG 109 SMAD7_F TCCTGCTGTGCAAAGTGTTC 110
SMAD7_R AAATCCATCGGGTATCTGGA 111 KCNK5_F TGCCAAGAGACTAGGGCAGT 112
KCNK5_R GAATACGAAGGGTGGGATCA 113 PGR_F CATCACAGGGAACCAGACCT 114
PGR_R CACCCCGAAGAGACCATAGA 115 SIAH2_F TCAGGAACCTGGCTATGGAG 116
SIAH2_R GGCAGGAGTAGGGACGGTAT 117 NRIP1_F GCCAGAAGATGCACACTTGA 118
NRIP1_R CAAGCTCTGAGCCTCTGCTT 119 TFF1_F CACCATGGAGAACAAGGTGA 120
TFF1_R TGACACCAGGAAAACCACAA 121 GREB1_F GGCAGGACCAGCTTCTGA 122
GREB1_R CTGTTCCCACCACCTTGG 123
[0462] Both siRNA knockdown and LNA treatment of the TFF1, FOXC1,
CA12 and NRIP1 enhancers revealed that, for each transcription
unit, the induction of both the eRNA and of the adjacent coding
gene transcript, as assessed by Q-PCR and GRO-seq, respectively,
was significantly inhibited or fully abolished. In contrast, these
LNAs or siRNAs caused no inhibitory effects on housekeeping genes
tested or on E.sub.2-regulated or non-E2-regulated adjacent
transcription units located distal to the regulated coding genes,
as exemplified by measuring levels of RSPH1 (TFF1e), APH1b (CA12e),
and USP25 (NRIP1e). Ligand-induced increase of ER.alpha. binding
occurred even after eRNA knockdown. Similar eRNA requirements for
coding genes were observed based on knockdown of the eRNAs for PGR,
SIAH2, KCNK5, P2RY2 and SMAD7, using either of two LNAs or siRNAs
designed for each targeted enhancer. GRO-Seq analysis of effects of
siRNAs or LNAs on Ez-regulated coding transcription units gave
similar results as those quantitated by QPCR.
Example 10: Investigation of the Potential Role eRNA in Enhancer:
Promoter Looping Events
[0463] To investigate whether eRNAs might be required for
enhancer:promoter looping events, generally considered to be part
of the E.sub.2-activation process, an open-ended (3D-DSL) approach
was employed for studying the spatial organization of genomes
(Harismendy, O. et al., Nature. 2011. 470: 264-8), conceptually
analogous to 5C methodology (Fullwood, M. J. et al., Nature. 2009.
462: 58-64).
[0464] In the 3D-DSL method, oligonucleotides corresponding to
genomic sites that are to be analyzed for participation in a
network contain a 5'-phosphate (referred to as acceptors), while
oligonucleotides corresponding to genomic sites of potential
interaction have a 5'-OH (referred to as donors). This method
permits interrogation of both short (<10 kb), as well as
long-distance, genomic interactions with specific genomic regions
including promoters and enhancers. Therefore, "donor" pools of
oligonucleotides spanning .about.200 kb flanking the promoter of
four up-regulated ER.alpha. target genes were designed based on the
HindIII restriction site. The "acceptor" pool constituted all
ER.alpha. binding sites and promoters in the interval. The
housekeeping gene GAPDH was used as a control (data not shown).
3D-DSL was performed as described previously (Fullwood, M. J. et
al., Nature 2009. 462: 58-64).
[0465] Briefly, equal amount of 3C chromatin was biotinylated using
the Photoprobe Kit (Vector Lab). Donor and acceptor probe pools
(2.5 fmol per probe) were annealed to the biotinylated 3C samples
at 45.degree. C. for 2 hrs, followed by 10 min at 95.degree. C. The
biotinylated DNA was immunoprecipitated with magnetic beads
conjugated to streptavidin. During this process, unbound
oligonucleotides were removed by stringent washes. The 5'-phosphate
of acceptor probes and 3'-OH of donor probes were ligated using Taq
DNA ligase at 45.degree. C. for 1 hr. These ligated products were
washed and eluted from beads and then amplified by PCR using
primers A and B-AD (or Primer B-BC1 and -BC2 if bar coding was
used) for deep sequencing on the Illumina HiSeq 2000, using Primer
A as sequencing primer.
[0466] For data analysis, a virtual library was first built of all
possible donor-acceptor sequences by in silico concatenating all
acceptor sequences with all donor sequences. These reads were then
aligned to the virtual library of DSL donors-acceptors sequences,
using NOVOALIGN (-t 248 -r None), and the number of reads that are
mapped to every interaction with no mismatches were counted, by
using custom Perl scripts. Next, from each sample the counts given
by the ligations of donors to acceptors on the identical
restriction sites (the "spot" ligations) was subtracted, and the
counts of the interactions were normalized to the remaining number
of total reads, after subtraction. Finally, from each interaction,
the counts that are present in unligated controls were subtracted,
after normalization.
[0467] 3D-DSL plots were generated using Matlabs where a 10 kb
window was set to bundle the interaction intensities, except for a
20 kb windown for NRIP1. The interactions were plotted using a
Bezier curve between the two positions with the third point in the
middle of the positions with the y-axis corresponding to the log 10
intensity. The peak locations were then added on the bottom of the
plot.
[0468] Two E.sub.2-regulated transcription units, P2RY2 and KCNK5,
were first examined. In the case of the P2RY2 transcription unit,
E.sub.2 caused an increase in the specific promoter: enhancer
interaction approximately 1,000-fold compared to that observed in
the control cultures. In addition to promoter: enhancer loops, a
new interaction between enhancer and gene terminator was also
observed, as compared to the--E.sub.2 condition. The P2RY2 promoter
locus exhibited three additional loops, one of which did not change
upon E.sub.2 treatment, but two other low intensity loops
disappeared upon gene activation, consistent with the dynamic
nature of gene topology. Based on results of ER.alpha. knock-down,
it was noted that even after 3 days in stripped-serum medium, MCF-7
cells still exhibited some ER.alpha.-dependent basal activation of
a significant cohort of coding gene targets, and hence both siRNAs
and LNAs against enhancer eRNAs caused a decrease in basal
transcription for some E.sub.2-regulated genes, in addition to
their more robust effects on E.sub.2-stimulated gene expression.
Similarly, for the KCNK5 gene locus, E.sub.2 treatment caused a
>300-fold increase in promoter: enhancer interactions. Two more
loops arising from enhancer in response to E.sub.2 were detected,
one of them around the terminator region of gene and the other
around that might represent enhancer-specific loops. These
observations indicate that a major effect of the ligand was to
enhance specific promoter: enhancer interactions and, in some
cases, enhancer: gene terminator interactions, in parallel to
induction of eRNA. For some loci, new enhancer:promoter
interactions were actually established and additional interactions
were also observed. This raised the question whether the induced
eRNAs exert any roles in the dynamic regulation of short-range and
long-range induced interactions.
Example 11: Investigation of the Regulation of E.sub.2-Induced
Enhancer: Promoter Interactions by Specific eRNAs
[0469] The effect of loss of specific eRNAs on E2-induced
enhancer:promoter interactions was investigated.
[0470] LNAs that were highly effective against two
estrogen-regulated enhancers, NRIP1 and GREB1, were characterized.
Chromatin conformation capture (3C) was performed. Briefly,
25.times.10.sup.6 MCF-7 cells were fixed by adding 1% formaldehyde
at room temperature for 10 min, and the reaction stopped by adding
glycine. Lysis buffer (500 .mu.l 10 mM Tris-HCl pH 8.0, 10 mM NaCl,
0.2% IGEPAL CA-630, protease inhibitors [Sigma]) was added and
cells were incubated on ice. Next, cells were lysed with a Dounce
homogenizer, and the suspension spun down at 5,000 rpm at 4.degree.
C. The supernatant was discarded and the pellet was washed twice
with 500 .mu.l ice-cold 1.times. NEBuffer 2 (NEB, Ipswich, Mass.).
The pellet was then resuspended in 1.times. NEBuffer 2 and split
into five separate 50 .mu.l aliquots. The extracted chromatin was
then digested overnight by adding 400 units HindIII (NEB). Each
digested chromatin mixture was ligated by adding T4 DNA Ligase (800
units) in 20 times of initial volume for 4 hrs at 16.degree. C. The
ligase step was omitted in one chromatin aliquot from the five
mentioned above to use the sample as the unligated control. After
incubation at 16.degree. C., the chromatin was de-cross-linked
overnight at 65.degree. C. and purified twice with phenol and then
with phenol:chloroform:IAA (25:24:1). DNA was precipitated and
pellets were air-dried before re-suspending in 250 .mu.l 1.times.TE
buffer. To degrade any carryover RNA, 1 .mu.l RNAse A (1 mg/ml) was
added to each tube and incubated at 37.degree. C. for 15 min. DNA
was further purified using Phenol:Chloroform:IAA and precipitated.
This enriched fraction was used for the DSL part of the protocol or
subjected to PCR using unique primers, and was electrophoresed on
Agarose gel.
[0471] In the case of the NRIP1 locus, which was shown to exhibit a
ligand-induced enhancer:promoter loop by conventional 3C assay,
treatment with LNA against eRNA caused a .about.200-fold inhibition
of the coding gene expression and also inhibited both
enhancer:promoter and enhancer:terminator interactions in
E.sub.2-treated MCF-7 cells, assessed using conventional 3C assays
and 3D-DSL. An interaction between a different upstream
ER.alpha.-binding site and the promoter was not affected. In the
case of the GREB1 locus, siRNA-mediated eRNA knockdown inhibited
GREB1 coding gene induction and also inhibited the specific
enhancer:promoter interaction induced by E.sub.2. The
enhancer:terminator loop was also reduced upon siRNA-mediated
knockdown of eRNA, suggesting that eRNAs are required for
interactions between enhancer and adjacent regulatory elements.
Additional interactions of the GREB1 promoter with a non-enhancer
region were also diminished by eRNA knockdown, indicating that
these loops were altered by interruption of enhancer:promoter
interaction, licensing other interactions.
[0472] Together these experiments indicate that estrogen causes
quantitative, as well as some qualitative, alterations in the
interactions between enhancers and coding gene promoters and even
between enhancers, terminators and other ER.alpha.-bound regions,
which are highly diminished or abolished with down-regulation of
the targeted eRNAs. For these gene targets, the eRNA was,
therefore, of functional importance for robust enhancer:promoter
interactions, with knock-down by either siRNA or LNA treatment
invariantly diminishing, or even abolishing, these putatively
activating enhancer:promoter interactions, consistent with eRNA
function, even under unstimulated conditions.
Example 12: Investigation of Enhancer and Promoter Interactions
[0473] The interaction between an enhancer and promoter that spans
a distance of >250 kb permitting FISH analysis, was
investigated.
[0474] Cells were processed for DNA ImmunoFISH. BAC probes were
commercially obtained from Empire Genomics and are listed in Table
23.
TABLE-US-00024 TABLE 23 BAS probes Coordinates (including Gene
eRNA/s) FISH BAC FOXC1 chr6: 1,548,833-1,590,281 RP11-13F18 P2RY2
chr11: 72,568,712-72,653,158 RP11-352115 STARD10 chr11:
71,986,844-72,178,371 RP11-610C10 NRIP1 chr21:
15,228,005-15,513,603 RP11-22D1 GREB1 chr2: 11,530,334-11,710,942
RP11-50E1
[0475] MCF-7 cells were grown onto acid-washed polylysine-coated
coverslips. Cells were treated with vehicle (EtOH) or E2 for 1
hour, washed with PBS and immediately fixed with freshly made 4%
paraformaldehyde/PBS for 10 min. Permeabilization was achieved by
incubating in ice-cold cytoskeletal buffer (10 mM PIPES, pH 6.8;
300 mM sucrose; 100 mM NaCl; 3 mM MgCl.sub.2; 1 mM EGTA; 20 mM
vanadyl ribonucleoside complex and 1 mM 4-(2-aminoethyl)
benzenesulfonyl fluoride) containing 0.5% Triton X-100 for 10 min.
FISH pre-hybridization treatments included incubating the
coverslips in 0.1N HCl for 5 min at room temperature, followed by
digestion with 0.01N HCl/0.002% pepsin for 5 min at 37.degree. C.,
stopped by 50 mM MgCl.sub.2/PBS and equilibrated in 50%
formamide/2.times.SSC 2 hrs prior to hybridization. Five
microliters of probe/hybridization buffer mix (Empire Genomics) was
used per coverslip, with a hybridization program of 76.degree. C.
for 3 min followed by overnight hybridization at 37.degree. C. in a
humidified dark chamber. The coverslips were then washed with
pre-warmed WS1 (0.4.times.SSC/0.3% NP-40) buffer to 72.degree. C.
for 2 min, and then transferred to WS2 (2.times.SSC/0.1% NP-40)
buffer at room temperature for 1 min. A final wash with 1.times.PBS
was performed, excess liquid was aspirated and the coverslips were
then mounted with prolong gold-DAPI antifade mounting reagent
(Invitrogen).
[0476] One known interaction suitable for study was chosen: the
interaction between two E.sub.2-regulated P2RY2 and
STARD10-transcription units at a distance of .about.428 kb
(Fullwood, M. J. et al., Nature. 2009. 462: 58-64). Knockdown of
the P2RY2 enhancer by specific siRNAs caused downregulation of the
two E.sub.2-regulated target-coding genes, P2RY2 and STAR 10, both
of which are upregulated following E.sub.2 treatment. These two
genomic loci exhibited E.sub.2-dependent enhanced colocalization
when treated with E.sub.2, for 1 hr prior to fixation and
examination using FISH. When cells were transfected with siRNAs
against P2RY2e, the P2RY2e knockdown blocked the previously
observed P2RY2:STARD10 co-localization. Therefore, together, these
data suggest that ligand-dependent induction of eRNAs initiates
processes, including enhancer:promoter looping, in concert with the
requirement for the resultant coding gene activation observed after
hormone treatment.
[0477] Additional data supporting the suggestion that eRNAs are
required for tight control of ER.alpha.-regulated genes was
provided by evidence of its role in the "switch" from association
with corepressors to coactivators. The methylation status of Pc2
present on growth control gene regulatory regions regulates its
association with two abundant ncRNAs, TUG1 and NEAT2, located
primarily with markers of distinct subnuclear individual
structures-polycomb bodies (PcGs) and interchromatin granules
(ICGs), respectively (Yang, L. et al., Cell. 2011. 147: 773-88).
Studies were conducted to test if similar interactions might be
regulated by eRNAs induced by liganded ER.alpha.. ImmunoFISH was
performed using antibodies against RING1a (H-110, Santa Cruz
Biotechnology), and the interchromatin granule marker, SC35
(ab88720, Abcam), and with specific BAC probes for three genomic
loci interrogated (NRIP1, FOXC1, and SIAH2). This revealed that
there was a reproducible E.sub.2-dependent switch in the
predominant colocalization of each transcription unit from RING1a-
to SC35-stained structures. When LNA transfections were used to
deplete eRNA transcripts for two genes, FOXC1 and NRIP1, immunoFISH
data from each locus showed a clear inhibition of their
ligand-dependent-enhanced association with SC35, directly
implicating the eRNA transcripts in these altered target gene
co-localization events. Similar effects were observed for
siRNA-mediated knock-down of the GREB-1 eRNA.
[0478] While it is quite likely that a series of complexes
combinatorially contribute to these interactions, several studies
have established a role for Cohesin in enhancer:promoter looping
events (Hadjur, S. et al., Nature. 2009. 460: 410-3; Mishiro, T. et
al., EMBO J. 2009. 28: 1234-45; Nativio, R. et al., PLoS Genet.
2009. 5: e1000739; Hou, C. et al., Proc. Natl. Acad. Sci. USA 2010.
107: 3651-6), and protein: protein interactions between Cohesin and
the mediator complex protein, Med12, have been reported (Kagey, M.
H. et al., Nature. 2010. 467: 430-5). Therefore, the levels of
Cohesin recruitment to regulated ER.alpha.-regulated enhancers were
assessed after ligand addition. An increased occupancy was observed
of the Cohesin subunit Rad21 on ER.alpha. target genes enhancers
adjacent to up-regulated coding genes after E.sub.2 treatment, as
studied by conventional ChIP and metanalysis of ChIP-seq data.
Based on fractionation studies, Rad21 association with chromatin
was diminished following RNaseA treatment. Depletion of specific
NRIP1e eRNA by siRNA or LNA or FOXCle eRNA by LNA, resulted in a
decrease of Cohesin recruitment to enhancers in response to
E.sub.2, with essentially no significant alteration of the H3K4me
enhancer mark, or in ligand-dependent increase of ER.alpha.
recruitment. Therefore, eRNAs may help to stabilize the
ER.alpha.-dependent recruitment of Cohesin to the regulatory
enhancers, perhaps by recruiting some common or related complexes
that contribute to this event.
[0479] Possible interactions between the Cohesin complex and
regulated eRNAs were explored using RNA immunoprecipitation (RIP)
with an anti-Rad21-specific antibody (ab922, Abcam). RNA
immunopreciptations were performed as described previously (Chen,
J. et al., Mol. Endocrinol. 2006. 20: 1-13). Briefly, cells were
washed in PBS, cross-linked by 1% paraformaldehyde for 10 min at
room temperature, and 125 mM glycine was added to quench the
cross-linking. The cell pellet was then lysed in Buffer A and then
Buffer B. IP was performed overnight using 1-5 .mu.g antibody.
Thirty microliters of Dynabeads were used per IP or in a
beads-alone reaction. IP complexes were washed and de-cross-linked
at 65.degree. C. DNase I treatment was given to get rid of genomic
DNA. RNA was isolated and cDNA synthesis was performed.
[0480] This assay revealed that the eRNAs of FOXC1, PGR and TFF1,
while highly divergent in primary sequence, exhibited interactions
with Rad21 that were further enhanced after ligand treatment.
siRNA-mediated depletion of Rad21 caused loss of enhancer:promoter
interactions, both basal and E.sub.2-induced, when assessed by 3C
assay for the NRIP1 and GREB1 gene loci. In addition, these data
suggest that eRNAs might be required for effective additional
recruitment of the Cohesin complex to the enhancer in response to
E.sub.2, and their subsequent role in stabilizing enhancer:promoter
interactions. This implies that the specific eRNA sequences
participate in coding gene activation events.
[0481] The effects of E.sub.2-dependent coding gene stimulation in
MCF-7 cells treated with SMC3 (Cohesin subunit) siRNA (chosen for
its more effective knock-down compared to Rad21 siRNA) vs. control
siRNA was also assessed. Inhibition of most of the E.sub.2-induced
coding gene transcriptional program, with loss of .about.50% of
coding gene activation program by E.sub.2, was observed with
significant inactivation for the remaining E.sub.2-activated
transcription units. Using SMC3-specific siRNAs, inhibition of
ER.alpha. target genes was confirmed by Q-PCR. Indeed, analysis of
GRO-Seq data and MA analyses further confirmed the broad inhibition
of E.sub.2-dependent activating transcriptional effects following
SMC3 knockdown in MCF-7 cells.
Example 13: Design of Antisense Oligonucleotides Targeting Murine
Mmp9 eRNA
[0482] Antisense oligonucleotides were designed targeting a Mmp9
eRNA. The newly designed oligonucleotides in Table 24 were designed
as uniform deoxy oligonucleotides with phosphate backbones, or as
oligonucleotides containing deoxy, MOE and (S)-cEt units and a
phosphorothioate backbone. "Start site" indicates the 5'-most
nucleoside to which the oligonucleotide is targeted in the murine
eRNA sequence. "Stop site" indicates the 3'-most nucleoside to
which the oligonucleotide is targeted murine eRNA sequence. Each
gapmer listed in Table 24 is targeted to SEQ ID NO: 202 (GENBANK
Accession number NT_039207.7 truncated from 105809967 to
105810417). The Chemistry column describes the chemistry of each
oligonucleotide, where `d` indicates 2' deoxyribose; `o` indicates
phosphate ester; `e` indicates 2'-O-methyoxyethyl ribose (MOE); `s`
indicates thioate ester; `m` indicates 5' methyl group; `k`
indicates (S)-cEt. The SEQ ID NO for each antisense oligonucleotide
is associated with its sequence and is not intended to require the
chemistry indicated in Table 24.
TABLE-US-00025 TABLE 24 Antisense oligonucleotides targeted
targeted to SEQ ID NO: 202 (GENBANK Accession number NT_039207.7
truncated from 105809967 to 105810417). SEQ ISIS Start Stop ID No
Site Site Sequence Chemistry Notation NO 566188 14 29
TCCATTGCCACCCCCA Tes mCes mCks Ads Tds Tds Gds mCds 124 mCds Ads
mCds mCds mCds mCks mCks Ae 566189 17 32 TCCTCCATTGCCACCC Tes mCes
mCks Tds mCds mCds Ads 125 Tds Tds Gds mCds mCds Ads mCks mCks mCe
566190 20 35 ACTTCCTCCATTGCCA Aes mCes Tks Tds mCds mCds Tds 126
mCds mCds Ads Tds Tds Gds mCks mCks Ae 566191 23 38
CCAACTTCCTCCATTG mCes mCes Aks Ads mCds Tds Tds 127 mCds mCds Tds
mCds mCds Ads Tks Tks Ge 566192 41 56 ACACTTCTCTCCCTAC Aes mCes Aks
mCds Tds Tds mCds Tds 128 mCds Tds mCds mCds mCds Tks Aks mCe
566193 65 80 GGCTTGGAATCCATCA Ges Ges mCks Tds Tds Gds Gds Ads 129
Ads Tds mCds mCds Ads Tks mCks Ae 566194 91 106 CAACTGCGGAGGGAGG
mCes Aes Aks mCds Tds Gds mCds Gds 130 Gds Ads Gds Gds Gds Aks Gks
Ge 566195 94 109 TACCAACTGCGGAGGG Tes Aes mCks mCds Ads Ads mCds
Tds 131 Gds mCds Gds Gds Ads Gks Gks Ge 566196 97 112
TCTTACCAACTGCGGA Tes mCes Tks Tds Ads mCds mCds Ads 132 Ads mCds
Tds Gds mCds Gks Gks Ae 566197 100 115 CTTTCTTACCAACTGC mCes Tes
Tks Tds mCds Tds Tds Ads 133 mCds mCds Ads Ads mCds Tks Gks mCe
566198 103 118 GTTCTTTCTTACCAAC Ges Tes Tks mCds Tds Tds Tds mCds
134 Tds Tds Ads mCds mCds Aks Aks mCe 566199 114 129
GATTGCTGCTGGTTCT Ges Aes Tks Tds Gds mCds Tds Gds 135 mCds Tds Gds
Gds Tds Tks mCks Te 566200 117 132 CAGGATTGCTGCTGGT mCes Aes Gks
Gds Ads Tds Tds Gds 136 mCds Tds Gds mCds Tds Gks Gks Te 566201 120
135 CTTCAGGATTGCTGCT mCes Tes Tks mCds Ads Gds Gds Ads 137 Tds Tds
Gds mCds Tds Gks mCks Te 566202 123 138 CGCCTTCAGGATTGCT mCes Ges
mCks mCds Tds Tds mCds 138 Ads Gds Gds Ads Tds Tds Gks mCks Te
562914 126 147 CACTTCACTCGCCTTCAGGATT Cdo Ado Cdo Tdo Tdo Cdo Ado
Cdo 139 Tdo Cdo Gdo Cdo Cdo Tdo Tdo Cdo Ado Gdo Gdo Ado Tdo Td
566203 126 141 ACTCGCCTTCAGGATT Aes mCes Tks mCds Gds mCds mCds 140
Tds Tds mCds Ads Gds Gds Aks Tks Te 566204 129 144 TTCACTCGCCTTCAGG
Tes Tes mCks Ads mCds Tds mCds Gds 141 mCds mCds Tds Tds mCds Aks
Gks Ge 566205 132 147 CACTTCACTCGCCTTC mCes Aes mCks Tds Tds mCds
Ads 142 mCds Tds mCds Gds mCds mCds Tks Tks mCe 566206 135 150
TACCACTTCACTCGCC Tes Aes mCks mCds Ads mCds Tds Tds 143 mCds Ads
mCds Tds mCds Gks mCks mCe 566207 138 153 GGGTACCACTTCACTC Ges Ges
Gks Tds Ads mCds mCds Ads 144 mCds Tds Tds mCds Ads mCks Tks mCe
566208 141 156 AGTGGGTACCACTTCA Aes Ges Tks Gds Gds Gds Tds Ads 145
mCds mCds Ads mCds Tds Tks mCks Ae 566209 144 159 AGCAGTGGGTACCACT
Aes Ges mCks Ads Gds Tds Gds Gds 146 Gds Tds Ads mCds mCds Aks mCks
Te 566210 147 162 GTAAGCAGTGGGTACC Ges Tes Aks Ads Gds mCds Ads Gds
147 Tds Gds Gds Gds Tds Aks mCks mCe 566211 152 167
AGTGGGTAAGCAGTGG Aes Ges Tks Gds Gds Gds Tds Ads Ads 148 Gds mCds
Ads Gds Tks Gks Ge 566212 155 170 AACAGTGGGTAAGCAG Aes Aes mCks Ads
Gds Tds Gds Gds 149 Gds Tds Ads Ads Gds mCks Aks Ge 566213 159 174
CTGGAACAGTGGGTAA mCes Tes Gks Gds Ads Ads mCds Ads 150 Gds Tds Gds
Gds Gds Tks Aks Ae 566214 162 177 TGCCTGGAACAGTGGG Tes Ges mCks
mCds Tds Gds Gds Ads 151 Ads mCds Ads Gds Tds Gks Gks Ge 566215 165
180 AGGTGCCTGGAACAGT Aes Ges Gks Tds Gds mCds mCds Tds 152 Gds Gds
Ads Ads mCds Aks Gks Te 566216 171 186 TTACAGAGGTGCCTGG Tes Tes Aks
mCds Ads Gds Ads Gds 153 Gds Tds Gds mCds mCds Tks Gks Ge 566217
174 189 CTGTTACAGAGGTGCC mCes Tes Gks Tds Tds Ads mCds Ads 154 Gds
Ads Gds Gds Tds Gks mCks mCe 566218 177 192 GGCCTGTTACAGAGGT Ges
Ges mCks mCds Tds Gds Tds Tds 155 Ads mCds Ads Gds Ads Gks Gks Te
566219 180 195 GTGGGCCTGTTACAGA Ges Tes Gks Gds Gds mCds mCds Tds
156 Gds Tds Tds Ads mCds Aks Gks Ae 566220 183 198 CATGTGGGCCTGTTAC
mCes Aes Tks Gds Tds Gds Gds Gds 157 mCds mCds Tds Gds Tds Tks Aks
mCe 566221 186 201 TCCCATGTGGGCCTGT Tes mCes mCks mCds Ads Tds Gds
Tds 158 Gds Gds Gds mCds mCds Tks Gks Te 566222 189 204
GTTTCCCATGTGGGCC Ges Tes Tks Tds mCds mCds mCds Ads 159 Tds Gds Tds
Gds Gds Gks mCks mCe 566223 192 207 AGTGTTTCCCATGTGG Aes Ges Tks
Gds Tds Tds Tds mCds 160 mCds mCds Ads Tds Gds Tks Gks Ge 566224
201 216 GCTAATAACAGTGTTT Ges mCes Tks Ads Ads Tds Ads Ads 161 mCds
Ads Gds Tds Gds Tks Tks Te 566225 204 219 AGTGCTAATAACAGTG Aes Ges
Tks Gds mCds Tds Ads Ads 162 Tds Ads Ads mCds Ads Gks Tks Ge 566226
207 222 ACAAGTGCTAATAACA Aes mCes Aks Ads Gds Tds Gds mCds 163 Tds
Ads Ads Tds Ads Aks mCks Ae 562911 218 241 CATTTCCCCCATCTTAAAAACAAG
Cdo Ado Tdo Tdo Tdo Cdo Cdo Cdo 164 Cdo Cdo Ado Tdo Cdo Tdo Tdo Ado
Ado Ado Ado Ado Cdo Ado Ado Gd 566227 224 239 TTTCCCCCATCTTAAA Tes
Tes Tks mCds mCds mCds mCds 165 mCds Ads Tds mCds Tds Tds Aks Aks
Ae 566228 231 246 CCTACCATTTCCCCCA mCes mCes Tks Ads mCds mCds Ads
166 Tds Tds Tds mCds mCds mCds mCks mCks Ae 566229 234 249
CAACCTACCATTTCCC mCes Aes Aks mCds mCds Tds Ads 167 mCds mCds Ads
Tds Tds Tds mCks mCks mCe 566230 237 252 ACACAACCTACCATTT Aes mCes
Aks mCds Ads Ads mCds 168 mCds Tds Ads mCds mCds Ads Tks Tks Te
566231 240 255 TCGACACAACCTACCA Tes mCes Gks Ads mCds Ads mCds Ads
169 Ads mCds mCds Tds Ads mCks mCks Ae 566232 243 258
CTATCGACACAACCTA mCes Tes Aks Tds mCds Gds Ads mCds 170 Ads mCds
Ads Ads mCds mCks Tks Ae 566233 246 261 CAGCTATCGACACAAC mCes Aes
Gks mCds Tds Ads Tds mCds 171 Gds Ads mCds Ads mCds Aks Aks mCe
566234 249 264 CCCCAGCTATCGACAC mCes mCes mCks mCds Ads Gds mCds
172 Tds Ads Tds mCds Gds Ads mCks Aks mCe 566235 252 267
TGACCCCAGCTATCGA Tes Ges Aks mCds mCds mCds mCds 173 Ads Gds mCds
Tds Ads Tds mCks Gks Ae 566236 255 270 GTGTGACCCCAGCTAT Ges Tes Gks
Tds Gds Ads mCds mCds 174 mCds mCds Ads Gds mCds Tks Aks Te 566237
258 273 ATTGTGTGACCCCAGC Aes Tes Tks Gds Tds Gds Tds Gds Ads 2 mCds
mCds mCds mCds Aks Gks mCe 566238 261 276 CTCATTGTGTGACCCC mCes Tes
mCks Ads Tds Tds Gds Tds 175 Gds Tds Gds Ads mCds mCks mCks mCe
566239 264 279 CAGCTCATTGTGTGAC mCes Aes Gks mCds Tds mCds Ads Tds
176 Tds Gds Tds Gds Tds Gks Aks mCe 566240 268 283 GCTTCAGCTCATTGTG
Ges mCes Tks Tds mCds Ads Gds mCds 177 Tds mCds Ads Tds Tds Gks Tks
Ge 566241 271 286 CAAGCTTCAGCTCATT mCes Aes Aks Gds mCds Tds Tds
mCds 3 Ads Gds mCds Tds mCds Aks Tks Te 566242 274 289
ATCCAAGCTTCAGCTC Aes Tes mCks mCds Ads Ads Gds mCds 178 Tds Tds
mCds Ads Gds mCks Tks mCe 566243 280 295 GCCGAAATCCAAGCTT Ges mCes
mCks Gds Ads Ads Ads Tds 179 mCds mCds Ads Ads Gds mCks Tks Te
566244 283 298 ACTGCCGAAATCCAAG Aes mCes Tks Gds mCds mCds Gds Ads
180 Ads Ads Tds mCds mCds Aks Aks Ge 566245 286 301
TGGACTGCCGAAATCC Tes Ges Gks Ads mCds Tds Gds mCds 181 mCds Gds Ads
Ads Ads Tks mCks mCe 566246 289 304 GATTGGACTGCCGAAA Ges Aes Tks
Tds Gds Gds Ads mCds 182 Tds Gds mCds mCds Gds Aks Aks Ae 566247
292 307 TGGGATTGGACTGCCG Tes Ges Gks Gds Ads Tds Tds Gds Gds 183
Ads mCds Tds Gds mCks mCks Ge 566248 295 310 CTCTGGGATTGGACTG mCes
Tes mCks Tds Gds Gds Gds Ads 184 Tds Tds Gds Gds Ads mCks Tks Ge
566249 298 313 CCACTCTGGGATTGGA mCes mCes Aks mCds Tds mCds Tds 185
Gds Gds Gds Ads Tds Tds Gks Gks Ae 566250 302 317 GCTCCCACTCTGGGAT
Ges mCes Tks mCds mCds mCds Ads 186 mCds Tds mCds Tds Gds Gds Gks
Aks Te 566251 319 334 TGAGTAGGCCAATGGG Tes Ges Aks Gds Tds Ads Gds
Gds 187 mCds mCds Ads Ads Tds Gks Gks Ge 566252 322 337
GAGTGAGTAGGCCAAT Ges Aes Gks Tds Gds Ads Gds Tds Ads 188 Gds Gds
mCds mCds Aks Aks Te 566253 325 340 GCAGAGTGAGTAGGCC Ges mCes Aks
Gds Ads Gds Tds Gds 189 Ads Gds Tds Ads Gds Gks mCks mCe 566254 343
358 GAGGCCAGGACTTGGC Ges Aes Gks Gds mCds mCds Ads Gds 190 Gds Ads
mCds Tds Tds Gks Gks mCe 566255 353 368 AAGTTCAGCAGAGGCC Aes Aes
Gks Tds Tds mCds Ads Gds 191 mCds Ads Gds Ads Gds Gks mCks mCe
566256 356 371 AACAAGTTCAGCAGAG Aes Aes mCks Ads Ads Gds Tds Tds
192 mCds Ads Gds mCds Ads Gks Aks Ge 566257 365 380
AGATGTGGAAACAAGT Aes Ges Aks Tds Gds Tds Gds Gds Ads 193 Ads Ads
mCds Ads Aks Gks Te 566258 387 402 ATTCTAATTTCCTTCG Aes Tes Tks
mCds Tds Ads Ads Tds Tds 194 Tds mCds mCds Tds Tks mCks Ge
566259 392 407 CATCTATTCTAATTTC mCes Aes Tks mCds Tds Ads Tds Tds
195 mCds Tds Ads Ads Tds Tks Tks mCe 566260 395 410
CCCCATCTATTCTAAT mCes mCes mCks mCds Ads Tds mCds 196 Tds Ads Tds
Tds mCds Tds Aks Aks Te 566261 398 413 TGTCCCCATCTATTCT Tes Ges Tks
mCds mCds mCds mCds 197 Ads Tds mCds Tds Ads Tds Tks mCks Te 566262
401 416 AGGTGTCCCCATCTAT Aes Ges Gks Tds Gds Tds mCds mCds 198 mCds
mCds Ads Tds mCds Tks Aks Te 566263 404 419 TGGAGGTGTCCCCATC Tes
Ges Gks Ads Gds Gds Tds Gds Tds 199 mCds mCds mCds mCds Aks Tks mCe
566264 410 425 CACACATGGAGGTGTC mCes Aes mCks Ads mCds Ads Tds Gds
200 Gds Ads Gds Gds Tds Gks Tks mCe 566265 432 447 GAGTCAACAGAAATAC
Ges Aes Gks Tds mCds Ads Ads mCds 201 Ads Gds Ads Ads Ads Tks Aks
mCe
Sequence CWU 1
1
2031338DNAMus musculus 1tgtgggggtg gcaatggagg aagttggggg tagggagaga
agtgttcttg ctttgatgga 60ttccaagccc tgggttctcc ctccctccgc agttggtaag
aaagaaccag cagcaatcct 120gaaggcgagt gaagtggtac ccactgctta
cccactgttc caggcacctc tgtaacaggc 180ccacatggga aacactgtta
ttagcacttg tttttaagat gggggaaatg gtaggttgtg 240tcgatagctg
gggtcacaca atgagctgaa gcttggattt cggcagtcca atcccagagt
300gggagccccc attggcctac tcactctgcc tgccaagt 338216DNAArtificial
SequenceSynthetic oligonucleotide 2attgtgtgac cccagc
16316DNAArtificial SequenceSynthetic oligonucleotide 3caagcttcag
ctcatt 16427001DNAMus musculus 4tccttccttc cttccttcct tccttccttt
cttccttcct tcccacctgt tctctctctc 60tctctctctc tctctctctc tgttattgtt
cttttggttt tgttttgggg tttttttggt 120ttttttggtt ttttggtttt
ttggtttttt ttttttttgg tttttcaaga cagggcttct 180ctgtatatcc
ctggctgtcc tggaactcac tctgtagacc aggctggcct cgaactcaga
240aatccgcctg cctctgcctc ccaagtgcta ggattaaagg tgtgtgccac
cacacccagc 300tttttgtttc attcttttga gacacagttt ctctgtgatt
ctgtgtagct ttgactgtcc 360tggaactcac tatgtacaca ggctagcctg
gagctcagag gtccacccgt ctctgcctcc 420taagtgctgg gatcacaggc
gggtgccacc acctcccatc ctaagtacat tcgtttcttg 480tttttaaatt
tattttttac actccatatt ctatccccca ccccaccccc atgcaccctc
540cgactgctct acatcccaca cctccacccc accccacccc gcttccaagt
ggatgttccc 600aacccccaag cccacctgac ctaatctccc tggggcctcc
agtctcttga gggttagatg 660catcatctct tactaaagta cgttctcaaa
tgcataaatg gttgttcttt aggaagccat 720gggaaatcct cactttgtca
atagcaaatc tagagatgta cattgggaat ctgactggtc 780ccaggtcctc
tgggccctga gttcacttct gctccctaat gtgtggcaca cctgagaatg
840tgcagctcat aagctgatgg gtggagccca gatgacaccc cggcccgcag
gtgcacaggg 900cagacttaga ttgtctggtt ctcagctctg gctctttgac
ctgctgccca gcctgtctca 960gcccaggcct caggcagcag ttcacctcat
tgcctcaaga gggagctcca aggttgccaa 1020gataggaaat tgttggaagc
gggtgactga ccaggccagc cttttcctgt ccccagctgc 1080agctgccccc
ttggagaagc agtggtggcc acttactctg cctgtgggcc ctgagggcac
1140ctgctctggg ctctagaacc ttacagaagc caccttgttt ccaaggccag
atgttgcaca 1200tgtaaatctc tgatgtgagt ggcaggtagc ctcaagttgt
ccctttaact tccttcagct 1260tcagtctcct cacctgaaag gaaagactga
aaattcaaac acaggtgcca accagggaga 1320aaggaggaga ggcagggagg
gtgggggatg ggatgggaac ctgagtaaga tacaaagata 1380caacaaaaac
tccaaaccgt tcttctgagt gggcaaaccg ccatacacgt aacctcagca
1440cttgggaggt ggaaacggga ggatcaggag tcaaggccat cctcagctcc
atactgagct 1500cctggataac ctgataaatt aacatctgac tttatatctc
aatctccagg gctactgtga 1560taactgtgac aatctggggc ctttgttttg
tttctgatga ttttggagcc tggaagacca 1620agctccaagt gtcagtggat
tcgttctgag gattcaatct gtgggttgca ggcagccatg 1680gctcactgtg
tcctctgtgt ccccgtcccc cccccccgcc cccaggttgg tctcaaactt
1740ggatgagctt ggagtcctcg tcctccacct ctgagtgctg ggatggtagt
tgtgcctcgc 1800ctcactggct tgcaggtgca ggagatcaac ccagagcaag
cactgtactt accaagccac 1860accccaagtc atcattttca gaggagaccc
tcacatgtga gtgaaggcta agtgtagctt 1920gggagagagg gtggactgtg
aggggggcag ggggggcagc ctttggaaca ccagcagctc 1980tgtccttggt
ctggtgccgt ttccctgttc tggtaaattc tgacttcact actgcttcct
2040aacatagggc acaactgaga acataacaga tgcccaacct ggaccatttc
cccttattta 2100tctacgtaaa actgagtctc ggtacattcg agttgcagga
tccaccttag cctctgggta 2160gtggggagag ggcacacagc tgggtgctcc
cccattagaa tttaagatga tttttttttc 2220ctagtaaaca gagctttcag
aaaagcagag agagaagcct gtctgacagg gttgggtggt 2280aatggggatg
ggctgcagag aatgcggaga gttctaaagg accctggatg tcagcaaagc
2340ccagggaagg gggcagctct acttggctcc ctgacagtga agcatgttct
ctgccacctg 2400gtccctctcc tggagccgtc cctgcaaaag tgaagcctgg
atccctaggc agacattgct 2460ccttcttctg tgagccccca gctttttaat
ctcttactta tcctgcctgg gtagaaggtg 2520tttttgccac tgctacaact
tacaccaacc tggcctcaac tatgtcgggg ttgttgctgc 2580tgtttcgaga
taagacctcc ctctgtagct caggctggcc tcctagtcgc agcaatcctc
2640tggcctccaa gtcgcagcaa tcctctggcc tccaagtcac agccgtcctc
tggcctcggc 2700ctcccaagtg ctgggatccc agggatgagt catatcaccc
tccaaggggg cagtgattag 2760tggtggtgat caataattat taaatagtta
agggctgtgg tggtaggaat ggaaatggct 2820atcccacagc tcatgtgttg
gttaactgtt tggaaagaat tggtgggtgt ggccttgttg 2880gagggggtgt
gtcactgggg atttaaaaaa ccattcccag tgtgtctctc tgcttccttc
2940ttttggatca agatgaggat tctcagctgt tccttctgcc gtgcctttac
tccaccacca 3000tgggccctaa ctctctgaag ccataagctc aacatttcct
tcttttataa gttgccttgg 3060gtttagctga gtatcacagc gtgttgtcct
gggagcttgt cctggggtaa cagaagagct 3120cagaagttct agcttggagg
gctgaggtga gaacttagat ctagaatagg ctggccacag 3180agcaagagcc
tgtctcagaa gcaagggaaa ccttaggcaa catctgatgg tttattttgg
3240aataaaaaag aacttttgct tccatttgtt ttgtttattt tgggtttttt
tttggggggg 3300ggttcttcat tatttagaga atactttatt agtttttgta
atcaaaccca cgtagataag 3360accttacata tttaacacag tgcattgccc
ctgtacaaat ggggaaaaaa ttaagtccaa 3420catttctaga ccaatatggc
tgtccatttc tgttcaatgc caactcaaca cagtaaactg 3480gatacttttt
tccaaagttg acagcacttt tgcttccatt tgtaatgcac cgtagttcag
3540ccacctccaa atgctactgc ttagaaatac tttaattggg agctcggtag
ttaaaagcac 3600tggctgctct ggaagagggc ctggatttga ttcccgcccc
actatgtgac tcacaaccct 3660agtctcaggg gacctgggat gccctcttct
ggcctctttg ggtccaagca tgcatgtggc 3720agtggccata cagacaaaca
cttatatcca taaaataaca aaaataggtc tcgaaagaaa 3780tagtttaata
ggaggctgga aagatggctc agtggttagg agtgctcact gccttctaga
3840ggtcagtgtg ggtcccagca cccacgtcag atggctcaca cccacatata
gctccagagc 3900cagggatcag tgctctattc tggacttcat ttatgctata
tagactgtac acacacacac 3960acatgcacac acatacatgc ccacacacac
ttgcacacac acatgtgcat acatacatgc 4020ccacacatac atgcacacac
acttgtgcac acatacatgc ccacacacac ttgcacacat 4080acatacccac
acatacatac ccacacacac ttgcacacac atgcacagat ggatgaggta
4140cagtctgtgg ccttcaggtc catagagcag gcttgctgcc tcctcaccct
gaaatgggat 4200gtcctgcaag ctcaggcgag ctcagtgccc tcggtgtgtg
cagccgtcca tctgggaaca 4260aggataccag cgtgagttac tgacactcgt
cacagagctc acctgctgcg gcatccatga 4320gcaggacagg ctggcttgtc
agcccacagc aggtgaggca gggaggaaag gcatgcacag 4380gccaggggat
gtgtgtgctg gagaagagga agcggataga atgcagtggg aagtaaaaag
4440aagccatggt gctgagaaca tgctcaccag acagaagaga ggagcctccg
agagtgctaa 4500gtctgtgatg ctacgactcg gggtcctctc tggcacatgg
gtagatggcc ggatggtgag 4560atgaataaga tggatgggaa gggagtggtg
ggcacagggt accctcaggc cccagctgaa 4620ggtggagttg tgtgggaaac
agacacggat gagattggtt gacagcaaca gtaggagatt 4680ctcagccaga
ttccagacag gaacacgagg aagagcttga atgccctggg gatacagctc
4740agatggcaaa atgttagact agcctgagtt ccatccccag cccctcataa
acggtggagc 4800atcccagact tgggcagtgg aggcaggagg atgaaaggct
caaggtcttt ttaaccccat 4860agctatttaa agtccagccc aggatgtgtg
ggacctatct caacaacaaa acaaacaaaa 4920acaaagccag ggggctgaag
aaatggctcg gtggctaaga gcacacactg ctcttgcaga 4980ggacacaagt
tcgactccca gcacctatag tgatgggcaa ctcacgactg ccacagggag
5040atctgagttc tctagcctcc ctgggcacat atacataatt aaaaagaaag
ctcgaaaaca 5100aaaagtttag cagaaatgaa taaggacacg gagtcggtga
gctggaatag gatgggggtg 5160gttctgggag gagaggggta gaggagggat
tgtgatcgaa atacatgtga agttcccaag 5220gaattcatac aaataaaagc
caaaaaaaca agagctgaag tggggacagg atcggggtga 5280ggagctgagc
cccaggggaa gctgagtagc ccctgactta gctgctgggg caacgggaaa
5340gggccaatgt ctgcgagcct gtgaggatct gctggctctc tgtgaatctc
tcctgcaggg 5400aaagaagaac agacagggag gccagaagga aggagaaagg
gaactaaccg aggcttcctc 5460aaatgtgaac agctggagag caactggagc
ttttagttcc tacctcactg gacaaagcag 5520gctcctgaga actcccaaga
gttgtgatat ggtcagtggt cagcgaacct gggcccagtg 5580ctgcacaggg
ggtaccagag gcttcctaag aacactggaa agcagagggg ccctcacagc
5640ttgcctgaga cccctattaa ggagagcttg agacctgact tgtgtgctgc
tggactccga 5700ggctacagac tgccatctca ctaggaataa ataatatcca
tccaccccca ggtctgccaa 5760cccacagccc cctgtaaacc ttaggtctca
gtaattccta ggtcagccac cacacagtct 5820ccagcaatcc ccaggtctgc
cacccaacag tccccagtag tccccagcag tccccagcaa 5880tctccaggtt
tgccccagtc tcaagtcccc tagatttgaa atgcaggctc tcttgcggtc
5940agctggttcc cagcctggag cgttgagccc gttgagcttg cttgtcacag
catctaaaga 6000tagggtacca cacaggaaac cagatgctat tggctaactt
cgaaaataaa gatgccctca 6060tagagaggga agcacttgcc tctggtggag
tctgcgtgag actgggtgag tgactggcac 6120ttcctgcaga agttcccttc
ccatctgctc aggtaagtac cacggactcc agactcctcc 6180catacctggg
cgtggggtca atcaggcaca gtcacagggt ttctgatgct gtttgccttc
6240cgtgtctatt ttcctgagga tactgcagat aaatcaggag agtaaaggac
cttttgcacg 6300ctcgtaactt gaggagttag taattacatt ttagggatgt
gaaaaaaaag gtttatatta 6360gatgttacca aaaaaggcct tgatataaaa
tcacatctgg gtaattggaa atattgatat 6420tcttaaagat cacaattcag
attgccagtc agactttttt gatccatgcc tctaatccca 6480gcacttggga
aggtgaagca ggaggatcga tacaagtttg agaccagcct aggctagcta
6540atgagctcta ggccagttta ggcttctgtg tgagaccgcc ttaaacaaac
agcaccaacc 6600ataaaaacta gtgattgtgg ttttcatttc tttttaaaag
gagcttttat cttcagagac 6660tcatacttga atgtctatag aaacagaata
atctaattca gccatgaaat aggacataga 6720tgaaatatta actgggagtt
gataattcct ggagctgagt ggcgggtgcc aggtgtttcc 6780tttgatttcc
cccccccccc ccccggtttt ttgagacagg gtttttctgt gtaactgtga
6840ctatcctgga actcattctg tagaccaggc ttgccttgaa cttatagaga
tccacctgcc 6900tctgccccct cagtactggg attaaaggcg tgcgcctcca
ttgcctggct cccctgattg 6960tatataggct tgtgaatata aagagaataa
tgttatataa atagagttgc ttgcctagca 7020cacaaggagc cctgggccct
gggcacaatc ttcagcatct aataaaattg gacttggtgg 7080cacacactgt
gatcacagca ccctggaggt aaaaggcggg aggtcggaag tgcaagactc
7140ttctcagtga agcagaattt tgaggccagc ctggacttta tgggatcctg
cctctaaaaa 7200caacaataat gatgatggtg acggtggtgg tgatgacggt
ggtggtggta gtggtggtgc 7260tggtggtggt ggtggtggtg gtggtggtgg
tggtgataaa tgttcaaaac gatgttagca 7320tttttactat aaatataaat
ttatgtgtca aaaaagctaa gagtgctatg ctaaacctgc 7380agagttggat
agttttaagg attcctcttc ccctccccct cttttaaatg cttttttggt
7440accatcttca atagtcataa tgaacattta ttacatttat aataaacttg
tcacaaactc 7500attcttcagt tttataaatg ctcagaacca tggctcagac
acttgggcac agacatctga 7560gctaggagtc gtggtcttag ggaggaaacg
ataagaacag gccaggaggg ctggagaggt 7620ggctcagtgg ttaagagcac
cgactgctct tccgaaggtc ctgagttcaa atcccagcag 7680ccacatgatg
gctcacgacc atccgtaatg agatccgacg ccctcttctg gtgtgtctga
7740agacagctac agtgtactta gatataataa ataaatcttt aaaaaaatat
ttaaaaaaaa 7800aaaacgaaca ggccaggagg agatacaccc ctgcttgaca
cagacaagcc cctattcaga 7860ggaccctgca gcctcgctca ctctgtgcct
gatcatttat aaccatgtgc gagaaaagct 7920gggaacttgg gattctcctg
ccttctgtct ttccaattct gccatttttt ttcttttaat 7980tttttcccaa
ctgcttgaaa tacaatactt gaggtaggaa gaaattcagt caaatgtgaa
8040gatacgcagg tcataagaag accctgttca ggcccaggtc ataagagggc
cccagcctac 8100tgagaggaga caagctcaga gtgagacctg gcctgctgag
ccttgggaac ctatgagggt 8160cagcagggta ggtgcagtgg ctgaactgga
atggggtttt cctggacaac agaaatggcc 8220ccaggaagct gttcggtggc
ttttcccaga gaaatgtgaa ccaagttatc caccaacgct 8280atgactcctg
gggcaagcag gaacgacccc acacccaagt ttaggctgga gaatcagcaa
8340gtcttttggg gttactcata gcaacatgcc ctagggttag tcacagctta
tctcagtggg 8400gtgcccactc atgagagctg tgttcctggg actccttagc
ctcctgagag ggaaccttgt 8460aagttagctg aatcctgtga gcctctatcc
cctttcctgg aggccatcgt ggcttcttta 8520ccctctatcc tgttcacctt
tgtttttatc aaaggatgct ggagcagaaa atagtcccag 8580cccagttcag
tctggctagc ctggcccttc acacacccct ttttttctgg gaagaagaac
8640ccgaccaatg ctaatctctt tgaaatatat cctccgccct ttgcttctgc
cgaccccatt 8700gcacagggag ggctggaggg tggtgggaga tgctgttcaa
cttagggaca cagtacacac 8760tgcccctgcc aacacttctg gcaaagtcag
cttcctgctt ttcctatggc agtaggcttc 8820ggagtgcacc gttagagtgt
ggtatgcaaa gtcccaaaca cacattggac gtctttagtg 8880cctaaaacaa
tacgggccag caaagtggat tcaggcacct gttgctgatg tgttagaatg
8940gcggtcgcat ctcagcagca ctctgggcca aggcagttcc acgtggaaga
ggttttattg 9000gggaaagaga gagaaggtgg ctgaataaac agaacaggca
aggagagaga gtgcgagcag 9060tgttctcctt atttatatgg agaatgacat
aacgcaggta aaggtggaag gtgagccaag 9120tggatgttgg gaatatggtg
cctgttgcct tggcaacctg tctgcaggtc gcaagtcatg 9180ctgttgccta
tgtgatgtcc tgatgccaac agttgccaag cttgaccacc tgagtttgat
9240ccctgggaca tgcgcagtag aaggacagaa ctgactccct caagatgtaa
tctgaccacg 9300tgttgtggca tgtgcgaaag tgtgtgtggg gaggagcgtg
ggcccccccc cacacacaca 9360cacacacaaa tgatcaaggt gtactctaac
ctgcatcgtg gctagtccaa gtgtgtgcac 9420acatacatat aaataaatgt
aattttaaaa accatgcatg tctattactt cagggaaagt 9480taagctctgt
gaccttaggg ctttaaaatg acagcctgct ttcagaggtt actaaggatc
9540ccaggtcgtg ggaacgggag cgaagaaggc atgctagggc tgatccagat
caaaaccaac 9600tctagttcct tcttctcccg agccagctgt gcaggggtgg
ccatgtcagg catggcctgg 9660ggactgcatg agctgcaggg ggggaactca
ggctgttgcg ggggggagga gggggtcggg 9720gtggggagac cctcgctgac
tttgatgagc cacagctcag gagctctcag aagctgggac 9780cttgtgtgac
tcaggtcatt gcctgccaag gaaaaccaaa ggaaggctaa ggcttgtgac
9840caaatctgtg gtctgccttt cctcctggag gttcagggca aactgccctg
agggtggaat 9900ctccctgaac tctgaatgga gagcgcttta accaactcat
ctggtcaaat tgttttgaat 9960tatgagtatt aatagaaaaa agcaaatctg
tattgctttt ccttaaatgc ctttccagaa 10020cattgctaag ctaaacctac
tgactatgta gcacagtacg ctgagagaca tgaaaggtca 10080tcagcaatat
aggccaggct attggagaga ggcaggagga agtcagtgag tttgaggcca
10140tcttggagac ccaggacaac ataaagagac cctgtctcaa caacaacaac
aaaaaacttc 10200attatataaa accttgcaaa cagttttttt aaatctcaca
tcagaattaa tcagctccaa 10260tgtcaatgca ccataatgaa cgtatagttt
gaattggcat ttgaatttcc tccaggctct 10320ctggggtgga gtctgcagct
ctcctgtccc cctcttctgc tacacagcca gcttggctct 10380ctgtaaacca
ggctgcccct gaaatctccc aaacaagtag gctcttcccc acccccaccc
10440ccacatcccc tcttgtctgc tgttttgggt actttctctc acatcctctc
tacttgacca 10500ggaaacccca gactcagccc ctctgagcct acctcacctc
attccctgat acctccctct 10560gtctgcaagt ttcctcccac ctttaaaagt
ttcttttaaa atatttattt atttttagtt 10620tacatgcatt gatgttttgt
ctgcatgtat gtctgtgtga gggtgtcaga tcccctggaa 10680ctggagtcac
agactgtcgt gagctgccat gtgggtgctg ggaattgaac ccaggtcttc
10740tgggagtgct agtagccagt gctcttagtt gctgagccat ctctccagac
ctaaaggtga 10800ctttttatga caccctttta tgcccctcct tcagtcctaa
aggagacaga aatagagacc 10860caagcctgag tctattattt aaccttccct
gtatttggtg ataaacattt atagagctgc 10920ttctgtgttt ctttctcagc
aggttcttgt acagcactca tccagtacag tacttgtctt 10980agttagggtt
ttactgctgt gaacagacac catgaccaag gcaagtctta taaaaaacaa
11040catttaactg gggctgcctt acaggttcag aggttcagtc cattatcatc
aaggtgggag 11100catggcagta tccaggcagg catggtgcag gcagagctga
gagttctaca tcttcatcca 11160aaggctgcta gtggaagact gacttccagg
caactagtgt gaggatctta tacccacacc 11220cacagtgaca cacccattcc
aactaggtca cacctattcc aacaaagcca caccttcaga 11280tggtgccact
ccctggtcca aggatataca aaccatcaca ctccactccc tggtccccac
11340agacttgttc aaaaacatga gtctatgggg gccatactta aacatagcat
aatgcaaaat 11400gcatttagtc caactttcaa agtcctcata gtctatagca
gtcgcaacaa tgttaaaagt 11460ccaaagttca agggctcttc tgagattcat
ccaactaatt aactgtaatc cccaaagcaa 11520ggcaggaaac cagctgtgca
aactccaaac tctgcatctc catggctgat gtcaaagcgg 11580tcttcagatc
tcctctcctt tttcatcttt gttgactgca acaaactgct ttctcctggg
11640ctggttccac tccctgttag cagctttcct cagcatgtat cccatggctc
tggtatcttt 11700aacatctttg agtctccaag gcaatttcaa tgttacagct
tcttgtttca gtgtctggga 11760ttctacttga tcttttggac tcctccatca
cttttccagc tctgccctct gtagcactct 11820aagctcaggt tgttcactcc
actacggctg ctgttctctt ggtgatcatc ttactgacat 11880ctccaataca
ctggggtgtt ccactccaac taagcttcac caatagcctc tcataggctc
11940tcttcagggt gccaagcctc aaatcctttg catgacccct tcagtcctgg
gccatcaact 12000acagctgagg cttcaccttc tccagtggcc ttccctggcc
tctcacagtg ctaagcctca 12060gcttctctcc atgatccctt cattccttca
caagcatact gcctgagtca cctgagtgac 12120tcttacacat taccaagtcc
agtcgcagca tgaggtacaa ccttgggtat ctctggaaca 12180cagctacttt
gtgctctcag aaaacaattt ccagaagatt ttacctcagt gatgctggta
12240tcttcttaat cactactaat tccttagctc cagctaacca gcatcaattg
ccccagtagt 12300tccttccatt cttaactcta gagccagagc ctcatggctg
aagctgccga gttctgctgc 12360ttacaggaac tagaacatga tccccttgta
ctattattac attatcacta gctttatgtt 12420ttctaaatcc ttcactgcct
aagcttggct atcctggttc ttgctctgta gattgacctt 12480gaatgcagag
atcagcatgc ctgtctcatg ggattaaagg tgtataccac catgcctggt
12540tctaaattca gctgggtagg gtcttgcccc aaggtcccac tcccttaatc
tgttatttcc 12600tagaacacag gatttttctt catttcactt cctggtatgc
ctttaatact cgaaccatat 12660attttatatt ttgcctttct aagcttgcta
tgcttgttca aacttctctt tgtgagactt 12720aaccagagaa caaagtctct
gctgggcttt tttgaaactt cctttgtcag tgcaattaat 12780gcaattaatc
caagtctctt caccttagcc tcaggcagac ttttcagaca agggtaaaaa
12840gtaaccacat tcttcaccaa aataccacaa aaacagtctt tatgccacat
tctgaaattc 12900ttctcctttc ttgggccagg tcaatacagt tcaaattact
cccagcaaca aagtcttcca 12960taatcctact aggatgacca attaaacccc
atttaaagca ttccactgct tcccaaatcc 13020aaagtcccaa aatccacatt
ctttcaaata aagcatggtc aggcctatca cagcaatacc 13080ccactcctgg
taccaacttt tgtcttagtt agggttttac tgctgtgaac agtaaaccca
13140tgaccaaggc aagtcttcta aaaaaacaac atttaattgg ggctgcctta
caggttcaga 13200ggttcaatcc attatcatca aggtgggagc atggcagtat
ccaggcaggc atggcgcagg 13260aggagctgag agttctatat cttcatctaa
aggctgctag tggaagactg acttccaggc 13320aactagggtg aggatcttat
acccacactc acagtgacac acccattcca accaggtcac 13380acctattcca
acaaggccat accttcagat ggtgccactc cctggtccaa agatataaaa
13440accatcacag tactctagag cagaatgaaa atcaaaagct tcttgtagca
cagaatcttc 13500ccggacagag atcaaagaga aaggaagccc tccccttacc
tgctcaataa accagagtgt 13560gttatcctag acaatctact aggaatctga
gacaggaatc cttcctccct tcccatttca 13620catacaatca aatgcatcag
tccttaaggt gatcaacaac tgtgcatgaa gcaagaggac 13680ctgacagcgt
atacatacat acatgcatgt gtgagagcat gtgtgcacgt gtgtatatgt
13740gtgtgtgtat gcatgcatga gtgcatgcct gcatttgtga atgtatgtgt
gtatgcatgc 13800atgcttgtgt gtgtgcatgt gtgtatacat gagtgtgtgt
gcatgtgtgt gtgtgtgtgt 13860gtgtgtgttt acgtgtgtaa aaccaacatc
cagtgccctt ctcagtcatt tccaccttgt 13920cttttcagag agggtctctt
ctttttcttt agaactcacc catttggttg ggtcaactgg 13980tgagagagct
ccaaagatcc ctctgcattt tccaaatgct ggggttatat catgcctagc
14040atcttatatt tttggttgtg agcctagtct ttaataactg agccatctct
ccagccccat 14100gtttagcttc cttttttttt tctttctttt tttttttttt
tttttttttg gtttttcgag 14160acagggtttc tttatatagc cctggctgtc
ctgaaactca ctctgtagac caggctggcc 14220tcagactcag aaatccacct
gcctctgcct cctaggtgct ggaattaaag gcatgcgcca 14280ccactgccca
gcccatgttt agcttcttaa tatgggttca gaggctagaa ctctcatctt
14340ggagtttgca aaataagtaa tttgctgact gagccattcc acccacccaa
gacccctgga 14400tgttggtttt acacacaaaa acgagtgggc ttggtggctc
atatttttgg ttgtgagcct 14460agcctttaac ggctgagcca tctctccagc
ccggtggctc atatttttaa tcacagtact 14520gaggaggctc aagcagtgcg
atttcagtga atttgaggct agcctaggct aacctagaga 14580agtctgggtt
agagatgggc aatagcatga gatctaatct caaaaacccc tacagtgact
14640agaattctaa tattaaaaaa gtccttctgt ttctccatta cttaaaaaaa
agtaataaaa 14700catttgcttg ttcacagttt gtttgtatag aaataaacaa
atgccacaaa gtgctttaaa 14760gaggaagagg gagggagagg tatcaaacct
cagataatgg tgtgctttag aaaggaggta 14820actctgttac ccacagggag
gttcctatag cttgggtttg ggtttctctt agcattcatt 14880gtttttttgg
cttggtggtg tgcctttggt ctgggctaaa ccctgctgcg caacactctc
14940actctacttt acctgagctc atagctatag gaacagaggg tccgctaact
tgcacaggaa 15000actgggcgga aattgtaaaa ataaacagaa aaatagatag
atagatagat agatagatag 15060atagatagat agatagatag atagatagat
agatagatag atagacagat aggactgtca 15120gacactggag acatcgctcc
gtcagtaaag tgtttataat acctggagac cagagctctg 15180tcctcagaat
gaactaaaag gctgtgctca gcaactcagg agaatgaaaa cctaaaggca
15240gacaccaagt ttagaaatca ataagcagaa tctggagcca aaggagaggg
ggaaacacca 15300taatgaggat gccaacacga ggagaagcca tcttagaaga
agggaagtaa agaaacagga 15360agctggctgg aagctgtggg caacggtgcc
ccatccctgg tacaaaagaa aggagtggac 15420cccaaaaaag gaagtggcca
gaggaagtgg accaggatgg gcagtgagag tgaggaggga 15480attttataaa
gtgggtcaca caggagtcat ttctgtttgg atttagaaca agtgtttctc
15540aatcttccta atgctgcaac ccttaaatac agttcctcct gctgtggtga
ctcccaacca 15600tccaattact tcattactac ttcgtaactg tgatcttgct
actgttgtga atagtaatgc 15660acccgtctgt gttttctgat ggtcttagat
gacccctgcc aaaaggctac tgggctccca 15720aagggtcagg acccacaggt
tgagaaccgc tgatgtagac cattccaatc tctgcttcta 15780ggttcaactc
agattcccca gctgaatatc agttagtgga accacaagct aatgctggag
15840aatggagacc tgagagataa gggaggtttc cgtggacata gttgggtgga
agtaggaagg 15900gtatttgtgc ctacatgagt gtgcgtgcgt gtgtgtgtgt
gtaggtgcag ctgtgcacac 15960atgtatgtgt atgcgtgtgt gcttgtgcag
gtgtacctgt gcacacatgt gcatgcatgt 16020gtgtgtgcaa gtgcacacgt
gtatgtgcat gtgtgtgtgt ataggtacag ctgtgcaaac 16080atgtattgca
tgcatgtgtg tgtgtgtgtg tgtgcgtgtg tgtgcaggtg caggtgcagc
16140tgtgcacaca tgtatgtgta tgcatgtgga ggccagaggt caaccttatg
tgtcatttct 16200caggtacccc ccacattatg tttgtagact gtctctcaat
gacatctgag gcttatggtt 16260cagatgcaag ccagtgagcc ttccgtgtgg
ttccggatac cttcatgtct tcacagcagg 16320catctcactg actgggtcca
tcaggatttg tgttctcccc tgagctatgt aatgcacagc 16380tgccactgtt
ggctgatggt tcaatgccca cacaaaccag cccccagata tgcttcctgg
16440aagcccccct aagagtgaaa gacagctgag ggagtcctgc agagagattc
cttgtcagat 16500ttttaccttt ccttttcgag tgtcctctgc ttcggtagaa
tgccagcact ggggcaggtc 16560aatgatctca ggctgcctca ctatgtagcc
caggctagcc ccaaactaaa gattaccctg 16620gattcctggc tgctctccat
ctgctgccag gaaggaagcc ctgcctttag gttcatttcc 16680cagtctaaac
atctcagagt acccagagat caaggcttgc tcaggtcaga ccagaaagtt
16740catttgctgg gcttatcggg ttggaggacg tcttgggagg gagcacgctt
tgctgacctg 16800aggtttctaa ctctagtgga atccccgtgc tctggggctc
atcgatgatg ctgggtttga 16860accaacacag cgtgctagca tcttccaagt
agatataaac cttgtgtcat tctcactcac 16920agcggaggca gtgtggtttc
tcagcatcgg gctagaagac tcggcacaaa ttgctggcac 16980aggtgtctgt
ctgtccgcca gtagccatgg ccagtgtgat gggtgagaat gcatgctgag
17040atgatgacga gtctttcccg cactggtttc tgattgtgga gccacggtga
gctcctactg 17100ggaccccacg tgtgagactt atcttcccct gccaggtctt
acttttaccc agtcactcac 17160tcatttagca cagcagatac ctgcagagct
gtcaagtgta agggcccagg gcccacagcc 17220ataaaagata tgtgcacacc
ctgtgcagct ctccaggaag aggccgcgcg gaaggtgtca 17280ccatcacttt
ctcggaacct gtcattgcat tgctatttat tttagttttc catcaaaatt
17340catatctttt tcttgatttt taaaattgaa aaatccaaca attaatagat
tttccaaatg 17400gagaatactt acgtggctaa gaaagaatcc aagcaaatat
agtaaaacta aacctccttt 17460tctgggtcct tcggtcctca gaatcgccct
ccggcactgt tgctcccagg gattcagata 17520cacacacaca cacacacaca
cacacacaca cacacatgca cacatacaca tacacacaca 17580cacatatata
cacacataca cacacacaca tacacacaca cacatacaca cacatacaca
17640cacatacaca catacacaca catacacaca tacacacaca tacacacaca
cacacacaga 17700aagagaggga gagggagagg gagacggagg gagagagaga
accttttcca accttctctc 17760aaatggaagc ggtctatgtc catgggacct
cacacgggcc ctgtggtttt gccttgaagc 17820gtttagtgtt ctgtcattca
gattcacagt agttagctct gtcaagactg atcagagctc 17880aataacgggc
atcatactct cctccacttt caaaataagc caagaaaggt acatttcttg
17940cgtcagtgga aaaaaaaata ccatctttac tatgcaaatt ttccacagtg
ctcagggtcc 18000agtaaaacga gttccacggg ctgtctaaca gtcagacggt
ctctgcaagg gcctgctgta 18060acccacaggt taacagatgg tctctgcaag
agcctgctgt aacccatggg ctgtctaaca 18120gtcagacggt ctctgcaagg
gcctgctgta atccatgggc tgtctaacag tcagacggtc 18180tctgcaaggg
cctgctgtaa cccatgggct gtctaacagt cagacggtct ctgcaaaggt
18240ctgctgtaac ccacgggctg tctaacagtc agacagtctc tgcaagggcc
tgctgtaacc 18300ttggactagg ctctctcctt agactagctc gtggtcaatc
aggagactga accccagact 18360tgcagaggga cccagcaagc ccaaagtctc
ctagctcatt ctctggctag agggctccat 18420cctccacaga agtccacaga
agctgttgga ctggaggaca gatccccagc caaagagctt 18480ttcctagctt
tgacctcctc ttgggggtca gcactgctaa ctcttcacac tgggagaagg
18540aggaagactg tggctaccct ggggtctccc acttatgacc tccacaggtc
atattgctgc 18600atggcatgtc ttcccgcacc tgggaagata atccactctg
catacaagtc tctcaggata 18660agcaacaatt cctgtttgct cgtctgtcaa
ctatagatat atgaaatatc acattttagg 18720ggatacttat ttatttactt
atttatttgt aagacaaagt ctgaaatatc ccaaattgga 18780ctgaagcttg
ctgaagcttg ctgtgtagcc aagaatgagg taaccttgaa ctctgccagt
18840tctcctgtct ccacctcctg attgctggga ttacacatgc atactaatat
gcctggtttg 18900tgtgacgctg aggtccaagc ccaaggcttc atgctcccta
ggcaagtact cacaccgcag 18960ttacatcctc agccctgaat gacacccgtt
gggtccagcg agtgctgtca gccagcagtc 19020tggtactgac cagcttgaac
gctcctgagt aagatcacca caaaggccct ctgcagagaa 19080aggggccccg
tggcctgaag cagagactgc ctatgcaatc cccgcagcct gaactccatc
19140acagcccgag gtggtccaga gcagacagcc tcagcccagt ccactagggg
agagattggc 19200tggctggctg gctgacatgc aaattcacag acaggcaatg
caggaagaag ccatggctgg 19260gtgggtgggc tgcggtgaga ccattgtgag
ctgggtgcgc tgggtgtgga aactccctgt 19320taaaacccgt gagctttgct
ttccattgca atggggaagg aggcaaaggc agccaggaag 19380tgcactctga
gatgacttta gacttctgaa gggtctgtct gtggtttcaa gaggcagagg
19440aggaagccca gagcagcttg acagagtggc caaccaacac atcctgcctg
gagcgtgagg 19500ggaaggggac aggtgttatt acccaacttg tggggaaaga
atagggatag gctaggggtg 19560agaatatccc aatagatgag ccactgaaag
caagagcagc aggctggctg agcccatcct 19620ctgcctggtg tcagctgatg
cttctctggc tacagagccc atgctacaac aatgcttcct 19680ttccacctag
agctgccaga tggccaaccc agtgcgattg ggatggagga actttccaca
19740cagaattaac cctgacaaaa tcctgggtac tatgagacaa gagtgtaggg
actacactgg 19800ttattttcct cacaccagtg accaaattcc aggctagaag
caactaagga tgaaagaagt 19860tacagcttct tctatgatag cctgggctga
ggctgaggct gaggctctgg accacctcgg 19920gccatgatgg aggtcaggct
gcaggacaag catagcagtc tttgcttcag gctgcaggac 19980cttctttttt
ttttaattag gtattttctt catttacatt tcaaatgcta tcccaaaagt
20040ccccccgtac tgcccccccc cattccccta cccacccact cccacttctt
ggccctggcg 20100ttcccctgta ctgaggcata taaagtttac aagaccaagg
ggcctctctt cccaatgatg 20160gcctactaag ccatcttctg atacatatgc
agctagagac atgaactcgg ggggtactgg 20220ttagttcata ctgttgttcc
acctataggg ttgcagttcc cttcagctcc ttgggtactt 20280tctctagctc
ctccattggg gaccctgtgt tccatccaat agctgactgt gagcatccac
20340ttctgtgttt gctaggcccc agcatagtct cacaagagac agctatatca
gggtcctttc 20400agcaaaatct tgcttgtgta tgcaatggtg tcagtgtttg
gaggctgatt atgggatgga 20460tccccgggtg tggcagtctc tagatggtcc
atccttttgt ctcagctcca aactttgtct 20520ctgtaactcc ttccatgggt
gttttgttcc caattctaag aaggggcaag gtgtccacac 20580tttggtcttc
cttcttcttg agtttcatgt gttttgcaaa ttgtatcttg tatcttgggt
20640attctaaagg accttcttct ctgagcacct ctgctgtgat cttagtaagc
tggtcagtaa 20700gctgcctcac agctggtgtg tccttcctcc ccgaaaggaa
gtggcatact gactggtggg 20760atcactctgg tgtgaagtgg tgtgaagtcc
tggcaggcgt gggaggcagc aggttcctat 20820gtgcctgtaa atgggaaagc
tcactcactc cttttctagg aggtttggga ccctaaccta 20880tgcaatggtt
ccatccacgt ttagagtgtt ttggttttgt ttttgtttta ccaagacaga
20940atttcactgt gtagccctgg atggcctgta actcactctt gtagaccagg
ctggcctcag 21000actcagaaat ctgccagcct ctgcctacca agtgctaaga
ttaaaggcgt gtactaccag 21060gcccctggct acagtgggtc tccctacctt
attaactcaa tatttaaaat ccctcccatg 21120gggctggaga gatggctcag
gagtttagag cattagctgc tcttccagag gacttaggtt 21180caattcccag
aacctacatg gtggctccca accatctgtt ttcaaaggtt ccaacaccct
21240cttctggtct gggcaccagg cacaaccatg gtgctggcca gtcatgcaca
catgtaaata 21300aataaatctt tgtaaaaatt ataaataaat taggcccctc
acagatgtgc tgagatgtgc 21360atttccatgg agattctaaa ttccatcaaa
gagctgagag atgcaaatgc tattctcaaa 21420gaggaatcag tccgggtggc
tcccatgtca gggtggcccc catgtcaggg tggcctacaa 21480acacctgtaa
gtccaactct aggggatcca ttgccccctt caggactcaa caaacacctg
21540cactccatgt gccttcccac acacaaaccc acatgcacat aattttaaat
aaaatcatat 21600ttaaaaaaaa aagaaccagc gtagtatggg ctcatatctt
tgatcccagc attcaggaga 21660cagagacaga cagatctctg tgagttgcag
accaacaggg ttccaagcaa gtcagggttt 21720cacaatgaga ccctgttgca
aaaataaaaa taaaaacaga aatgttttaa aagataggat 21780gagtgaagac
aaaatctagt tccaattgtt caccctttca gtgttttctc ccgcttgctg
21840catgcagcca gtgagaaccg cgatcctcta agactcacgt gatctggttt
gctgcataca 21900gccagtgaga actgcgatcc tctaagactc acgtggacct
gcttactgca tgcagccagt 21960gagaactaca atcctttaag gctcacgtga
tctggtttct ccttcccctc caggacctca 22020ccatgtccac ctccttccct
gaactggatc tagagaattt tgagtatgac gattctgctg 22080aggcctgtta
tttgggcgac attgtggcct ttggaaccat cttcctgtcc gtcttctacg
22140ccctcgtctt cacgttcggt ctggtgggaa atctgttggt ggtcctcgct
ctcaccaaca 22200gccggaagcc caagagcatc actgacatct acctcctgaa
cctggccttg agcgacctgc 22260tctttgtggc caccttgccc ttctggactc
actacctcat cagccatgag ggcctccaca 22320atgccatgtg caagctcacg
actgccttct tcttcattgg cttctttggg ggcatattct 22380tcatcaccgt
catcagcatc gaccggtacc ttgccatcgt cctggccgcc aactccatga
22440acaaccggac agtgcagcac ggtgtcacca ttagtctggg cgtctgggcg
gcggccatct 22500tagtggcgtc accccagttc atgttcacaa agagaaagga
caacgagtgt ctgggtgact 22560accccgaggt cctgcaggaa atgtggcccg
tgctccgcaa ctcggaagtc aacatcctgg 22620gcttcgccct gcccttgctt
atcatgagct tttgctactt ccgcatcatc cagacgctgt 22680tttcctgcaa
gaatcgcaag aaggccagag ccgtcagact catcctcctg gtggtctttg
22740ccttcttcct cttctggaca ccatacaaca tcatgatttt cctggagact
ctcaagttct 22800acaacttctt ccccagttgt gacatgaaga gggacctgag
gttggccctc agtgtgacgg 22860agacagtggc gttcagccac tgttgcctca
acccctttat ctacgccttt gccggggaaa 22920agttcagaag atacctggga
cacctgtata ggaagtgcct ggccgtcctg tgcggtcatc 22980ctgtccacac
cggcttctcg ccagagtccc agaggagcag gcaggacagc attctgagca
23040gtttcactca ctacacaagc gagggagatg ggtctctcct gctctgaagg
ggtctccccg 23100accctagctc cactaggaac ccagagttct tgcatcagat
ttccctgccg ctccccctgc 23160atcttatgtg caagaaatat ggaccagatg
cctgcaaacc aaccccgtgg tgtttttttg 23220aaaaatttat gttcaatgtg
tgaaaaacac acgtatctct tactgcaaat gttgaacatt 23280ggggcttact
ggtgacaaaa attctaacca gattagtgca attacaaagg ggtttggtga
23340gtcctggttg catgatcatg tgataaagga caactaagtc ctcagactga
gtggaaacca 23400aggcttggct ccaatgtccc ctctctgacc ttcagatcct
tcatagtgac agatcatcca 23460ggttctatca tcagagaagg accacatctc
tctgatttca aaattggtat tcctagggaa 23520cacctccgtt ggccgagtgt
gtcgggtgtc cattccttga ctaggtggtg ttattgaaat 23580agaagggata
cctaagatgc tgttggaatc tcaaggttag cggttgagag agacacatct
23640ctcagaagct ggggggtggg agctactctg acagcaagaa ctgctgactc
gccttaccat 23700ggagctcatt caggctcccc ttcagtaact agcagtatct
gttgctagct tctttaatct 23760tctgttgaga atgtcctgaa ctctccaagg
gttagaattt gggttactgc tcacagcatc 23820aaattcaatc ccaaggccct
gtcctccaag accaggaaga taggatgcag ttctaacaag 23880agactccacg
ctgactcctc attccacagg actccgtcca cccagttggc catgtccctt
23940tttcttgtct tgacccacat ccctccactc ttctcagccc aggggaagaa
atagaaagag 24000ccatgcccca gagtgaaggg atcgattcat atcccaactc
tgttgcttgc acattgggga 24060gactggagcc aacagagctt cagtcccttc
aatatagaaa ggggactgtg gtgccttcat 24120ccattctagc atagtacctc
agcaaggact ttagcattcc ctggatcagg aactgttacc 24180ctgcctctga
gaaatggagc tggtggagtg ggaggaacct gcaggctttg ctgcaggaca
24240cagccagaca agaggagacc tattcctaca gcatccccca acatgtgcct
agatctacaa 24300agccattccc atgtccccgc tgtcagggca agacccaggc
cacgagagca gcttgctttc 24360tcccctgacc ctgcaagcat cacgtaggat
gtagccacaa gaatgtcttc atgcattcac 24420tgactccggt ctcatttgca
ggcttacatt gaaagttcca gttctgcaac ttgcttttta 24480aaaaacactg
gatttcaggg gctggagaga tggctcagtg gttaagagca cagtctgctc
24540ctacagaggt cccaagttca attcccatgt catgtctgaa gacaaggaca
gtgtagtcaa 24600aaaaaacact ggaattcaaa tagctccctg ttcctgtgtt
ggttgtgata accatttcag 24660aagtctctcc cagcctgttg ctcacggcgg
catgtctgat atctccttgg cagtctgtat 24720gtttgtgtcg aggatgacag
acagactgag tcatatcccc cacaggcata tccaaccctt 24780tgttattgca
acaccatgct gtcatattca aaggtcacaa atgagaacct caaaattgag
24840ttaccaaagt gggagcctgg agagatggct cagtggttaa tagcactggc
tgctcttcca 24900gaggtctggg gttggattcc cagcaagcat agtagcttac
aatggtctat aatataactc 24960tagttccagg tgacccaaca ccctcttcta
atttgtgagg gtagcagaca tgtgcattgt 25020gaacattcag gcaaacaccc
atacatacaa aataagtaaa aaagaaaaag aaaggaagga 25080atggagagag
agaaagaggg ggagagagag agggagaggg agagggagag ggagagggag
25140ggagggagag ggagggaggg agggagggag ggagggaggg agggagggaa
aggaaagaaa 25200gaaagaaaga aaggaaggaa ggaaggaagg aaggaaggaa
ggaagaaaga aagaaagagg 25260gagagagaga aagagagaaa gagagaaaga
gaaagagaga aagagagaaa gagaaagaga 25320gaaagagaga aagaagaaag
aaagacagaa aattggtttt tcaagatagg ttctctctat 25380gtagcctcgg
ctgtcctgaa actctctgtg tagaccaggc tggcctagag ctcaaagaaa
25440tccacctgcc tctgcctcct gagtactggg atcgaaggtc tgtggcacca
tggcaggctt 25500agtcaataaa tgttttattt tcaaaagtat cctataatgt
tttaagtaag tttatgcttt 25560ggtgttggtc tgtatttccc gctgtctcgg
gtcacatggt taagcgtgcc tagagtgtgt 25620ctatcccact tgtaattctg
tcaataaaca ttggtttcct tccagctctt ggcaagtacg 25680agtctcaggg
aactttaatc tgtgcacgtt tcctctccct gctcacttat ttccatcaga
25740ttaattcttt gccatggggg tagctgggtc aaagggcaca ggaatgtttc
agctctgttc 25800tccagtacat acaattttat caaaaagcaa agcctggcca
ggcatgctaa cctacatcct 25860taacgacagc attcacgagg cagagggagg
tatctctgcc agcccaagac cagcctggta 25920acattgtaag actgaaaaaa
aaacctagga aaacaaaaaa ccaaaaaaac cctaaagctc 25980tctagggaag
gccagccgct cctcagcacc taaagcatcg ttgtcttgac caacctggaa
26040gtaatggggc tgacaaggct gtcacaggca gccatcttgg cagggctgct
ttgactgcca 26100agctcagtaa gatccagtgc agcttgcttg aaaattttta
atattgattg atccgttgtt 26160tgtacatgta tgtgtgtgta tgcacatgta
tgtatgttta tgcatgtgtg tatgtgtgtg 26220tgtgtttatg catgtgtgta
catgtgtgta tatatgcatg tgtatatatg tgtgcatgtg 26280tatgtgtgca
catgagtgta tgcatgtgca tgcacatgaa cacacatgaa gaaactcaga
26340ggacaaattg cagaagtcag ggctcccttt ccaccacata ggtcccagga
tcaaactccg 26400gttgaggggc ttggtggcaa ttgtctttac ctgatgaacc
atctctccag gcccgcttta 26460gtttttgcat acacatgacc ttcatttgat
aatgacaatt tgttacaagt ctttacgaag 26520cacatatcct agcgggctcc
agagatgttt ccacagcagt gagaccacac ctctgttctc 26580agaggttttg
atttattttt tgagatagag tctcactttg tagaccaggc tgccctggaa
26640ctcggaaatc tgcctgcctc ttcccctgga gtgttgggat taaaggtgtg
cgccaccacc 26700ctgggcttga tatctgtgga cagaaaaggc ctggctgtgt
ttaacttgct tgctgtaaga 26760cagagcagag gtaataagat ctgacccaag
acttcaggga tatgagcttc tccaggagaa 26820gcaggggctg tttgctagga
ggcagggatg tggaattcgt gtgagagagc acgaggttcc 26880ttcagtgtca
gtccctcatt ccaactgatg agcctgagag ttgtcatcaa aggttaatct
26940gttcctggac tcccatgtag agaagaaaga cttctggcct gagaagcaaa
catagggaag 27000c 27001520DNAArtificial SequenceSynthetic
oligonucleotide 5tagtgcggac ctacccacga 20620DNAArtificial
SequenceSynthetic oligonucleotide 6gcacctttcc ctcggatggg
20764DNAArtificial SequenceSynthetic
oligonucleotidemisc_feature(64)..(64)n = A,T,C or G 7gatcgtcgga
ctgtagaact ctcaagcaga agacggcata cgattttttt tttttttttt 60tttn
64818DNAArtificial SequenceSynthetic oligonucleotide 8caagcagaag
acggcata 18946DNAArtificial SequenceSynthetic oligonucleotide
9aatgatacgg cgaccaccga caggttcaga gttctacagt ccgacg
461032DNAArtificial SequenceSynthetic oligonucleotide 10cgacaggttc
agagttctac agtccgacga tc 321125RNAArtificial SequenceSynthetic
oligonucleotide 11cagagucaga gagucagaga gagau 251225RNAArtificial
SequenceSynthetic oligonucleotide 12aucucucucu gacucucuga cucug
251325RNAArtificial SequenceSynthetic oligonucleotide 13gaguuuggac
cugugaccuu ccuaa 251425RNAArtificial SequenceSynthetic
oligonucleotide 14uuaggaaggu cacaggucca aacuc 251525RNAArtificial
SequenceSynthetic oligonucleotide 15aaucuccugg gaggaugaag cuguu
251625RNAArtificial SequenceSynthetic oligonucleotide 16aacagcuuca
uccucccagg agauu 251725RNAArtificial SequenceSynthetic
oligonucleotide 17accacuguuu cugacugcuu ucuca 251825RNAArtificial
SequenceSynthetic oligonucleotide 18ugagaaagca gucagaaaca guggu
251925RNAArtificial SequenceSynthetic oligonucleotide 19ggauugagag
ugaccaggac auuua 252025RNAArtificial SequenceSynthetic
oligonucleotide 20uaaauguccu ggucacucuc aaucc 252125RNAArtificial
SequenceSynthetic oligonucleotide 21cgcccagccu aauuguagua cuuua
252225RNAArtificial SequenceSynthetic oligonucleotide 22uaaaguacua
caauuaggcu gggcg 252319RNAArtificial SequenceSynthetic
oligonucleotide 23gcaaauucuu ucaugacaa 192419RNAArtificial
SequenceSynthetic oligonucleotide 24uugucaugaa agaauuugc
192519RNAArtificial SequenceSynthetic oligonucleotide 25gcaaagaugg
auagagaua 192619RNAArtificial SequenceSynthetic oligonucleotide
26uaucucuauc caucuuugc 192719RNAArtificial SequenceSynthetic
oligonucleotide 27gcacauaccu cauuagaga 192819RNAArtificial
SequenceSynthetic oligonucleotide 28ucucuaauga gguaugugc
192919RNAArtificial SequenceSynthetic oligonucleotide 29gguauuaaua
gcucugaaa 193019RNAArtificial SequenceSynthetic oligonucleotide
30uuucagagcu auuaauacc 193119RNAArtificial SequenceSynthetic
oligonucleotide 31gggagagggu cuacaauua 193219RNAArtificial
SequenceSynthetic oligonucleotide 32uaauugucga cccucuccc
193319RNAArtificial SequenceSynthetic oligonucleotide 33ggccagaucu
ccugugaua 193419RNAArtificial SequenceSynthetic oligonucleotide
34uaucacagga gaucuggcc 193519RNAArtificial SequenceSynthetic
oligonucleotide 35gcuccauucu gcugcucaa 193619RNAArtificial
SequenceSynthetic oligonucleotide 36uugagcagca gaauggagc
193719RNAArtificial SequenceSynthetic oligonucleotide 37cuaacgugac
agugacaua 193819RNAArtificial SequenceSynthetic oligonucleotide
38uaugucacug ucacguuag 193919RNAArtificial SequenceSynthetic
oligonucleotide 39gcaaaaggua ggaggguuu 194019RNAArtificial
SequenceSynthetic oligonucleotide 40aaacccuccu accuuuugc
194119RNAArtificial SequenceSynthetic oligonucleotide 41ggagaugaau
ugauagaga 194219RNAArtificial SequenceSynthetic oligonucleotide
42ucucuaucaa uucaucucc 194319RNAArtificial SequenceSynthetic
oligonucleotide 43cagaagagcu auuugguau 194419RNAArtificial
SequenceSynthetic oligonucleotide 44auaccaaaua gcucuucug
194519RNAArtificial SequenceSynthetic oligonucleotide 45gaguggacuu
cacaagaaa 194619RNAArtificial SequenceSynthetic oligonucleotide
46uuucuuguga aguccacuc 194719RNAArtificial SequenceSynthetic
oligonucleotide 47agagaagaau gaaggugaa 194819RNAArtificial
SequenceSynthetic oligonucleotide 48uucaccuuca uucuucucu
194919RNAArtificial SequenceSynthetic oligonucleotide 49ccacagguga
gcagaaauu 195019RNAArtificial SequenceSynthetic oligonucleotide
50aauuucugcu caccugugg 195119RNAArtificial SequenceSynthetic
oligonucleotide 51ccuaauuccc agaagcaga 195219RNAArtificial
SequenceSynthetic oligonucleotide 52ucugcuucug ggaauuagg
195319RNAArtificial SequenceSynthetic oligonucleotide 53cgaaauggcc
uaaagauga 195419RNAArtificial SequenceSynthetic oligonucleotide
54ucaucuuuag gccauuucg 195519RNAArtificial SequenceSynthetic
oligonucleotide 55acacaaaggu ggaaggaaa 195619RNAArtificial
SequenceSynthetic oligonucleotide 56uuuccuucca ccuuugugu
195719RNAArtificial SequenceSynthetic oligonucleotide 57ggaagaaccu
gcagagaug 195819RNAArtificial SequenceSynthetic oligonucleotide
58caucucugca gguucuucc 195916DNAArtificial SequenceSynthetic
oligonucleotide 59cacgtctata caccac 166016DNAArtificial
SequenceSynthetic oligonucleotide 60gaattaacgc ctgagg
166116DNAArtificial SequenceSynthetic oligonucleotide 61gaactgacaa
aggtgg 166216DNAArtificial SequenceSynthetic oligonucleotide
62atctccccac tcaagg 166316DNAArtificial SequenceSynthetic
oligonucleotide 63catttttctg ctgacc 166416DNAArtificial
SequenceSynthetic oligonucleotide 64acaagacaga ggcaga
166516DNAArtificial SequenceSynthetic oligonucleotide 65tcagttggag
gacagt 166616DNAArtificial SequenceSynthetic oligonucleotide
66gaaggagcag gtgaaa 166716DNAArtificial SequenceSynthetic
oligonucleotide 67ggtatttccg cttcac 166816DNAArtificial
SequenceSynthetic oligonucleotide 68aggataccag gacaca
166916DNAArtificial SequenceSynthetic oligonucleotide 69tgataaaagc
agggtc 167021DNAArtificial SequenceSynthetic oligonucleotide
70tcagttccca gcattctcat c 217121DNAArtificial SequenceSynthetic
oligonucleotide 71ttgagccttg gagacagaaa g 217220DNAArtificial
SequenceSynthetic oligonucleotide 72tccaaagcat cccattcctg
207321DNAArtificial SequenceSynthetic oligonucleotide 73tgagcaaaac
aagacaaacc g 217424DNAArtificial SequenceSynthetic oligonucleotide
74ttatgttgct cttgatagac tccc 247521DNAArtificial SequenceSynthetic
oligonucleotide 75gctaggtgct gtctgagatt c 217625DNAArtificial
SequenceSynthetic oligonucleotide 76ttcaagcaaa gattatagcc atgtg
257722DNAArtificial SequenceSynthetic oligonucleotide 77atccagtgca
gagtaacatc ag 227821DNAArtificial SequenceSynthetic oligonucleotide
78agatgcctct gcatactggt t 217920DNAArtificial SequenceSynthetic
oligonucleotide 79cagaccatat tgggccacag 208020DNAArtificial
SequenceSynthetic oligonucleotide 80ccacagcaga aaaccactga
208120DNAArtificial SequenceSynthetic oligonucleotide 81ttccctctgc
actgactcct 208220DNAArtificial SequenceSynthetic oligonucleotide
82cgtcttttcc cactgacaca 208320DNAArtificial SequenceSynthetic
oligonucleotide 83cccctcccca gaagaaaata 208421DNAArtificial
SequenceSynthetic oligonucleotide 84ctgaggaaca caagactagc c
218522DNAArtificial SequenceSynthetic oligonucleotide 85actggactca
ttttgggaca tc 228620DNAArtificial SequenceSynthetic oligonucleotide
86attgtgcatg gctcttaccc 208720DNAArtificial SequenceSynthetic
oligonucleotide 87cttggtgcat gtgagcttgt 208820DNAArtificial
SequenceSynthetic oligonucleotide 88agcttctggt tccaaggtca
208920DNAArtificial SequenceSynthetic oligonucleotide 89catgtgctgt
tgttgctgtg 209020DNAArtificial SequenceSynthetic oligonucleotide
90tgaaagggaa gacgcagatg 209121DNAArtificial SequenceSynthetic
oligonucleotide 91ttgtatcctt tgactgggca g 219220DNAArtificial
SequenceSynthetic oligonucleotide 92aaagaaggca ggggaacaat
209320DNAArtificial SequenceSynthetic oligonucleotide 93cacttgggca
atccagaaat 209421DNAArtificial SequenceSynthetic oligonucleotide
94tcacctgtgg aaagagacaa c 219521DNAArtificial SequenceSynthetic
oligonucleotide 95agaacctttt gctccctagt g 219620DNAArtificial
SequenceSynthetic oligonucleotide 96ttaaacgagc ctggagttgg
209720DNAArtificial SequenceSynthetic oligonucleotide 97aaattcctca
gagcccagtg 209818DNAArtificial SequenceSynthetic oligonucleotide
98ggctcagaga ggccaaaa 189924DNAArtificial SequenceSynthetic
oligonucleotide 99tggaccctat catctccttt aact 2410020DNAArtificial
SequenceSynthetic oligonucleotide 100ggaaaggaat tgctggatca
2010120DNAArtificial SequenceSynthetic oligonucleotide
101gtgcaaccac ttgggaaact 2010221DNAArtificial SequenceSynthetic
oligonucleotide 102cagagatgag gaaaggtttg c 2110320DNAArtificial
SequenceSynthetic oligonucleotide 103atctgcttca cggtctcatg
2010421DNAArtificial SequenceSynthetic oligonucleotide
104agtagctgtc aaatggcctt c 2110520DNAArtificial SequenceSynthetic
oligonucleotide 105ttagttcggc tttgagggtg 2010620DNAArtificial
SequenceSynthetic oligonucleotide 106ggggacctgt ttttcctgtt
2010720DNAArtificial SequenceSynthetic oligonucleotide
107gacttggatc tggacctgga 2010820DNAArtificial SequenceSynthetic
oligonucleotide 108tctgtctgcc aacaagcagt 2010920DNAArtificial
SequenceSynthetic oligonucleotide 109gcactgtagc gagactggag
2011020DNAArtificial SequenceSynthetic oligonucleotide
110tcctgctgtg caaagtgttc 2011120DNAArtificial SequenceSynthetic
oligonucleotide 111aaatccatcg ggtatctgga 2011220DNAArtificial
SequenceSynthetic oligonucleotide 112tgccaagaga ctagggcagt
2011320DNAArtificial SequenceSynthetic oligonucleotide
113gaatacgaag ggtgggatca 2011420DNAArtificial SequenceSynthetic
oligonucleotide 114catcacaggg aaccagacct 2011520DNAArtificial
SequenceSynthetic oligonucleotide 115caccccgaag agaccataga
2011620DNAArtificial SequenceSynthetic oligonucleotide
116tcaggaacct ggctatggag 2011720DNAArtificial SequenceSynthetic
oligonucleotide 117ggcaggagta gggacggtat 2011820DNAArtificial
SequenceSynthetic oligonucleotide 118gccagaagat gcacacttga
2011920DNAArtificial SequenceSynthetic oligonucleotide
119caagctctga gcctctgctt 2012020DNAArtificial SequenceSynthetic
oligonucleotide 120caccatggag aacaaggtga 2012120DNAArtificial
SequenceSynthetic oligonucleotide 121tgacaccagg aaaaccacaa
2012218DNAArtificial SequenceSynthetic oligonucleotide
122ggcaggacca gcttctga 1812318DNAArtificial SequenceSynthetic
oligonucleotide 123ctgttcccac caccttgg 1812416DNAArtificial
SequenceSynthetic oligonucleotide 124tccattgcca ccccca
1612516DNAArtificial SequenceSynthetic oligonucleotide
125tcctccattg ccaccc 1612616DNAArtificial SequenceSynthetic
oligonucleotide 126acttcctcca ttgcca 1612716DNAArtificial
SequenceSynthetic oligonucleotide 127ccaacttcct ccattg
1612816DNAArtificial SequenceSynthetic oligonucleotide
128acacttctct ccctac 1612916DNAArtificial SequenceSynthetic
oligonucleotide 129ggcttggaat ccatca 1613016DNAArtificial
SequenceSynthetic oligonucleotide 130caactgcgga gggagg
1613116DNAArtificial SequenceSynthetic oligonucleotide
131taccaactgc ggaggg 1613216DNAArtificial SequenceSynthetic
oligonucleotide 132tcttaccaac tgcgga 1613316DNAArtificial
SequenceSynthetic oligonucleotide 133ctttcttacc aactgc
1613416DNAArtificial SequenceSynthetic oligonucleotide
134gttctttctt accaac 1613516DNAArtificial SequenceSynthetic
oligonucleotide 135gattgctgct ggttct 1613616DNAArtificial
SequenceSynthetic oligonucleotide 136caggattgct gctggt
1613716DNAArtificial SequenceSynthetic oligonucleotide
137cttcaggatt gctgct 1613816DNAArtificial SequenceSynthetic
oligonucleotide 138cgccttcagg attgct 1613922DNAArtificial
SequenceSynthetic oligonucleotide 139cacttcactc gccttcagga tt
2214016DNAArtificial SequenceSynthetic oligonucleotide
140actcgccttc aggatt 1614116DNAArtificial SequenceSynthetic
oligonucleotide 141ttcactcgcc ttcagg 1614216DNAArtificial
SequenceSynthetic oligonucleotide 142cacttcactc gccttc
1614316DNAArtificial SequenceSynthetic oligonucleotide
143taccacttca ctcgcc 1614416DNAArtificial SequenceSynthetic
oligonucleotide 144gggtaccact tcactc 1614516DNAArtificial
SequenceSynthetic oligonucleotide 145agtgggtacc acttca
1614616DNAArtificial SequenceSynthetic oligonucleotide
146agcagtgggt accact 1614716DNAArtificial SequenceSynthetic
oligonucleotide 147gtaagcagtg ggtacc 1614816DNAArtificial
SequenceSynthetic oligonucleotide 148agtgggtaag cagtgg
1614916DNAArtificial SequenceSynthetic oligonucleotide
149aacagtgggt aagcag 1615016DNAArtificial SequenceSynthetic
oligonucleotide 150ctggaacagt gggtaa 1615116DNAArtificial
SequenceSynthetic oligonucleotide 151tgcctggaac agtggg
1615216DNAArtificial SequenceSynthetic oligonucleotide
152aggtgcctgg aacagt 1615316DNAArtificial SequenceSynthetic
oligonucleotide 153ttacagaggt gcctgg 1615416DNAArtificial
SequenceSynthetic oligonucleotide 154ctgttacaga ggtgcc
1615516DNAArtificial SequenceSynthetic oligonucleotide
155ggcctgttac agaggt 1615616DNAArtificial SequenceSynthetic
oligonucleotide 156gtgggcctgt tacaga 1615716DNAArtificial
SequenceSynthetic oligonucleotide 157catgtgggcc tgttac
1615816DNAArtificial SequenceSynthetic oligonucleotide
158tcccatgtgg gcctgt 1615916DNAArtificial SequenceSynthetic
oligonucleotide 159gtttcccatg tgggcc 1616016DNAArtificial
SequenceSynthetic oligonucleotide 160agtgtttccc atgtgg
1616116DNAArtificial SequenceSynthetic oligonucleotide
161gctaataaca gtgttt 1616216DNAArtificial SequenceSynthetic
oligonucleotide 162agtgctaata acagtg 1616316DNAArtificial
SequenceSynthetic oligonucleotide 163acaagtgcta ataaca
1616424DNAArtificial SequenceSynthetic oligonucleotide
164catttccccc atcttaaaaa caag 2416516DNAArtificial
SequenceSynthetic oligonucleotide 165tttcccccat cttaaa
1616616DNAArtificial SequenceSynthetic oligonucleotide
166cctaccattt ccccca 1616716DNAArtificial SequenceSynthetic
oligonucleotide 167caacctacca tttccc 1616816DNAArtificial
SequenceSynthetic oligonucleotide 168acacaaccta ccattt
1616916DNAArtificial SequenceSynthetic oligonucleotide
169tcgacacaac ctacca 1617016DNAArtificial SequenceSynthetic
oligonucleotide 170ctatcgacac aaccta 1617116DNAArtificial
SequenceSynthetic oligonucleotide 171cagctatcga cacaac
1617216DNAArtificial SequenceSynthetic oligonucleotide
172ccccagctat cgacac 1617316DNAArtificial SequenceSynthetic
oligonucleotide 173tgaccccagc tatcga 1617416DNAArtificial
SequenceSynthetic oligonucleotide 174gtgtgacccc agctat
1617516DNAArtificial SequenceSynthetic oligonucleotide
175ctcattgtgt gacccc 1617616DNAArtificial SequenceSynthetic
oligonucleotide 176cagctcattg tgtgac 1617716DNAArtificial
SequenceSynthetic oligonucleotide 177gcttcagctc attgtg
1617816DNAArtificial SequenceSynthetic oligonucleotide
178atccaagctt cagctc 1617916DNAArtificial SequenceSynthetic
oligonucleotide 179gccgaaatcc aagctt 1618016DNAArtificial
SequenceSynthetic oligonucleotide 180actgccgaaa tccaag
1618116DNAArtificial SequenceSynthetic oligonucleotide
181tggactgccg aaatcc 1618216DNAArtificial SequenceSynthetic
oligonucleotide 182gattggactg ccgaaa 1618316DNAArtificial
SequenceSynthetic oligonucleotide 183tgggattgga ctgccg
1618416DNAArtificial SequenceSynthetic oligonucleotide
184ctctgggatt ggactg 1618516DNAArtificial SequenceSynthetic
oligonucleotide 185ccactctggg attgga 1618616DNAArtificial
SequenceSynthetic oligonucleotide 186gctcccactc tgggat
1618716DNAArtificial SequenceSynthetic oligonucleotide
187tgagtaggcc aatggg 1618816DNAArtificial SequenceSynthetic
oligonucleotide 188gagtgagtag gccaat 1618916DNAArtificial
SequenceSynthetic oligonucleotide 189gcagagtgag taggcc
1619016DNAArtificial SequenceSynthetic oligonucleotide
190gaggccagga cttggc 1619116DNAArtificial SequenceSynthetic
oligonucleotide 191aagttcagca gaggcc 1619216DNAArtificial
SequenceSynthetic oligonucleotide 192aacaagttca gcagag
1619316DNAArtificial SequenceSynthetic oligonucleotide
193agatgtggaa acaagt 1619416DNAArtificial SequenceSynthetic
oligonucleotide 194attctaattt ccttcg 1619516DNAArtificial
SequenceSynthetic oligonucleotide 195catctattct aatttc
1619616DNAArtificial SequenceSynthetic oligonucleotide
196ccccatctat tctaat 1619716DNAArtificial SequenceSynthetic
oligonucleotide 197tgtccccatc tattct 1619816DNAArtificial
SequenceSynthetic oligonucleotide 198aggtgtcccc atctat
1619916DNAArtificial SequenceSynthetic oligonucleotide
199tggaggtgtc cccatc 1620016DNAArtificial SequenceSynthetic
oligonucleotide 200cacacatgga ggtgtc 1620116DNAArtificial
SequenceSynthetic oligonucleotide 201gagtcaacag aaatac
16202457DNAMus musculus 202cagggtgtat gtgtgggggt ggcaatggag
gaagttgggg gtagggagag aagtgttctt 60gctttgatgg attccaagcc ctgggttctc
cctccctccg cagttggtaa gaaagaacca 120gcagcaatcc tgaaggcgag
tgaagtggta cccactgctt acccactgtt ccaggcacct 180ctgtaacagg
cccacatggg aaacactgtt attagcactt gtttttaaga tgggggaaat
240ggtaggttgt gtcgatagct ggggtcacac aatgagctga agcttggatt
tcggcagtcc 300aatcccagag tgggagcccc cattggccta ctcactctgc
ctgccaagtc ctggcctctg 360ctgaacttgt ttccacatct gcatgacgaa
ggaaattaga atagatgggg acacctccat 420gtgtggtgtt tgtatttctg
ttgactcttt tttttct 4572033185DNAMus musculus 203ctcaccatga
gtccctggca gcccctgctc ctggctctcc tggctttcgg ctgcagctct 60gctgcccctt
accagcgcca gccgactttt gtggtcttcc ccaaagacct gaaaacctcc
120aacctcacgg acacccagct ggcagaggca tacttgtacc gctatggtta
cacccgggcc 180gcccagatga tgggagagaa gcagtctcta cggccggctt
tgctgatgct tcagaagcag 240ctctccctgc cccagactgg tgagctggac
agccagacac taaaggccat tcgaacacca 300cgctgtggtg tcccagacgt
gggtcgattc caaaccttca aaggcctcaa gtgggaccat 360cataacatca
catactggat ccaaaactac tctgaagact tgccgcgaga catgatcgat
420gacgccttcg cgcgcgcctt cgcggtgtgg ggcgaggtgg cacccctcac
cttcacccgc 480gtgtacggac ccgaagcgga cattgtcatc cagtttggtg
tcgcggagca cggagacggg 540tatcccttcg acggcaagga cggccttctg
gcacacgcct ttccccctgg cgccggcgtt 600cagggagatg cccatttcga
cgacgacgag ttgtggtcgc tgggcaaagg cgtcgtgatc 660cccacttact
atggaaactc aaatggtgcc ccatgtcact ttcccttcac cttcgaggga
720cgctcctatt cggcctgcac cacagacggc cgcaacgacg gcacgccttg
gtgtagcaca 780acagctgact acgataagga cggcaaattt ggtttctgcc
ctagtgagag actctacacg 840gagcacggca acggagaagg caaaccctgt
gtgttcccgt tcatctttga gggccgctcc 900tactctgcct gcaccactaa
aggccgctcg gatggttacc gctggtgcgc caccacagcc 960aactatgacc
aggataaact gtatggcttc tgccctaccc gagtggacgc gaccgtagtt
1020gggggcaact cggcaggaga gctgtgcgtc ttccccttcg tcttcctggg
caagcagtac 1080tcttcctgta ccagcgacgg ccgcagggat gggcgcctct
ggtgtgcgac cacatcgaac 1140ttcgacactg acaagaagtg gggtttctgt
ccagaccaag ggtacagcct gttcctggtg 1200gcagcgcacg agttcggcca
tgcactgggc ttagatcatt ccagcgtgcc ggaagcgctc 1260atgtacccgc
tgtatagcta cctcgagggc ttccctctga ataaagacga catagacggc
1320atccagtatc tgtatggtcg tggctctaag cctgacccaa ggcctccagc
caccaccaca 1380actgaaccac agccgacagc acctcccact atgtgtccca
ctatacctcc cacggcctat 1440cccacagtgg gccccacggt tggccctaca
ggcgccccct cacctggccc cacaagcagc 1500ccgtcacctg gccctacagg
cgccccctca cctggcccta cagcgccccc tactgcgggc 1560tcttctgagg
cctctacaga gtctttgagt ccggcagaca atccttgcaa tgtggatgtt
1620tttgatgcta ttgctgagat ccagggcgct ctgcatttct tcaaggacgg
ttggtactgg 1680aagttcctga atcatagagg aagcccatta cagggcccct
tccttactgc ccgcacgtgg 1740ccagccctgc ctgcaacgct ggactccgcc
tttgaggatc cgcagaccaa gagggttttc 1800ttcttctctg gacgtcaaat
gtgggtgtac acaggcaaga ccgtgctggg ccccaggagt 1860ctggataagt
tgggtctagg cccagaggta acccacgtca gcgggcttct cccgcgtcgt
1920ctcgggaagg ctctgctgtt cagcaagggg cgtgtctgga gattcgactt
gaagtctcag 1980aaggtggatc cccagagcgt cattcgcgtg gataaggagt
tctctggtgt gccctggaac 2040tcacacgaca tcttccagta ccaagacaaa
gcctatttct gccatggcaa attcttctgg 2100cgtgtgagtt tccaaaatga
ggtgaacaag gtggaccatg aggtgaacca ggtggacgac 2160gtgggctacg
tgacctacga cctcctgcag tgcccttgaa ctagggctcc ttctttgctt
2220caaccgtgca gtgcaagtct ctagagacca ccaccaccac caccacacac
aaaccccatc 2280cgagggaaag gtgctagctg gccaggtaca gactggtgat
ctcttctaga gactgggaag 2340gagtggaggc aggcagggct ctctctgccc
accgtccttt cttgttggac tgtttctaat 2400aaacacggat ccccaacctt
ttccagctac tttagtcaat cagcttatct gtagttgcag 2460atgcatccga
gcaagaagac aactttgtag ggtggattct gaccttttat ttttgtgtgg
2520cgtctgagaa ttgaatcagc tggcttttgt gacaggcact tcaccggcta
aaccacctct 2580cccgactcca gcccttttat ttattatgta tgaggttatg
ttcacatgca tgtatttaac 2640ccacagaatg cttactgtgt gtcgggcgcg
gctccaaccg ctgcataaat attaaggtat 2700tcagttgccc ctactggaag
gtattatgta actatttctc tcttacattg gagaacacca 2760ccgagctatc
cactcatcaa acatttattg agagcatccc tagggagcca ggctctctac
2820tgggcgttag ggacagaaat gttggttctt ccttcaagga ttgctcagag
attctccgtg 2880tcctgtaaat ctgctgaaac cagaccccag actcctctct
ctcccgagag tccaactcac 2940tcactgtggt tgctggcagc tgcagcatgc
gtatacagca tgtgtgctag agaggtagag 3000ggggtctgtg cgttatggtt
caggtcagac tgtgtcctcc aggtgagatg acccctcagc 3060tggaactgat
ccaggaagga taaccaagtg tcttcctggc agtctttttt aaataaatga
3120ataaatgaat atttacttaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa
aaaaaaaaaa 3180aaaaa 3185
* * * * *