U.S. patent application number 10/916782 was filed with the patent office on 2005-05-05 for vectors for gene mutagenesis and gene discovery.
This patent application is currently assigned to Lexicon Genetics Incorporated. Invention is credited to Friedrich, Glenn A., Lilleberg, Stan, Sands, Arthur T., Zambrowicz, Brian.
Application Number | 20050095713 10/916782 |
Document ID | / |
Family ID | 26806845 |
Filed Date | 2005-05-05 |
United States Patent
Application |
20050095713 |
Kind Code |
A1 |
Zambrowicz, Brian ; et
al. |
May 5, 2005 |
Vectors for gene mutagenesis and gene discovery
Abstract
Novel vectors are described that incorporate, inter alia, a
novel 3' gene trap cassette which can be used to efficiently trap
and identify previously unknown cellular genes. Vectors
incorporating the described 3' gene trap cassette find particular
application in gene discovery and in the production of mutated
cells and animals.
Inventors: |
Zambrowicz, Brian; (The
Woodlands, TX) ; Friedrich, Glenn A.; (The Woodlands,
TX) ; Lilleberg, Stan; (Spring, TX) ; Sands,
Arthur T.; (The Woodlands, TX) |
Correspondence
Address: |
FINNEGAN, HENDERSON, FARABOW, GARRETT & DUNNER
LLP
901 NEW YORK AVENUE, NW
WASHINGTON
DC
20001-4413
US
|
Assignee: |
Lexicon Genetics
Incorporated
|
Family ID: |
26806845 |
Appl. No.: |
10/916782 |
Filed: |
August 11, 2004 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10916782 |
Aug 11, 2004 |
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10158735 |
May 29, 2002 |
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6776988 |
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10158735 |
May 29, 2002 |
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09276533 |
Mar 25, 1999 |
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6436707 |
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60079729 |
Mar 27, 1998 |
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60081727 |
Apr 14, 1998 |
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60109302 |
Nov 20, 1998 |
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Current U.S.
Class: |
435/455 ;
435/320.1 |
Current CPC
Class: |
C12N 2800/30 20130101;
C12N 15/85 20130101; C12N 2840/44 20130101; C12N 15/1034 20130101;
C12N 2840/203 20130101; C12N 2740/13043 20130101; C12N 15/1051
20130101; C40B 40/02 20130101; C12N 15/1037 20130101; C12N
2740/10043 20130101; C12N 15/86 20130101; C12N 2800/60 20130101;
C12N 2840/20 20130101 |
Class at
Publication: |
435/455 ;
435/320.1 |
International
Class: |
C12N 015/85 |
Claims
1-21. (canceled)
22. A vector comprising: a) a 5' gene trap cassette, comprising in
operable combination: 1) a splice acceptor; 2) a first exon located
3' to said splice acceptor, said first exon encoding a marker
enabling the identification of a cell expressing said exon; and 3)
a polyadenylation sequence defining the 3' end of said first exon;
b) a sequence encoding a self-cleaving RNA located 3' to said
polyadenylation sequence; and c) a 3' gene trap cassette located 3'
to said sequence encoding a self-cleaving RNA and comprising in
operable combination: 1) a first promoter; 2) a second exon located
3' from and expressed by said promoter, said second exon not
encoding an activity conferring antibiotic resistance; 3) a splice
donor sequence defining the 3' region of the second exon; and
wherein said vector does not encode a promoter mediating the
expression of said first exon, and wherein said vector does not
encode a sequence that mediates the polyadenylation of an mRNA
transcript encoded by said second exon and expressed by said first
promoter.
23. The vector according to claim 22 wherein said first exon
additionally encodes an internal ribosome entry site operatively
positioned between said splice acceptor and an initiation codon of
said first exon.
24. The vector of claim 22 wherein said second exon and said splice
donor sequence are derived from a naturally occurring eukaryotic
gene.
25. The vector of claim 22 further comprising a mutagenic mini-exon
sequence operatively positioned upstream from said splice acceptor
site.
26. The vector of claim 22 further comprising in the region between
said polyadenylation sequence and said first promoter at least one
mutagenesis enhancer selected from a transcription termination
sequence, a 3' terminal exon, and an exon that changes the reading
frame.
27. The vector of claim 22 wherein said first exon encodes at least
one marker selected from a marker conferring antibiotic resistance,
a marker conferring antibiotic sensitivity, an enzymatic marker, a
recombinase, and a fluorescent marker.
28. The vector of claim 27 wherein the at least one marker confers
neomycin resistance.
29. A vector comprising: a) a first cassette, comprising in
operable combination: 1) a first promoter; and 2) a marker gene
expressed by said first promoter; b) a sequence encoding a
self-cleaving RNA located 3' to said marker gene; and c) a 3' gene
trap cassette, comprising in operable combination: 1) a second
promoter; 2) an exon located 3' from and expressed by said second
promoter, said exon not encoding an activity conferring antibiotic
resistance; 3) a splice donor sequence defining the 3' region of
the exon; and wherein said vector does not encode a sequence that
mediates the polyadenylation of an mRNA transcript encoded by said
exon.
30. A vector comprising: a) a 5' gene trap cassette comprising in
operable combination: 1) a splice acceptor; 2) a first exon located
3' to said splice acceptor, said first exon encoding a marker
enabling the identification of a cell expressing said exon; and 3)
a polyadenylation sequence defining the 3' end of said first exon;
b) a sequence encoding a self-cleaving RNA located 3' to said
polyadenylation sequence; and c) a 3' gene trap cassette located 3'
to said sequence encoding a self-cleaving RNA and comprising in
operable combination: 1) a first promoter; 2) a second exon located
3' from and expressed by said promoter, said second exon being of
non-prokaryotic origin; 3) a splice donor sequence defining the 3'
region of the exon; and wherein said vector does not encode a
promoter mediating the expression of said first exon, and wherein
said vector does not encode a sequence that mediates the
polyadenylation of an mRNA transcript encoded by said second exon
and expressed by said first promoter.
31. An infectious retrovirus comprising a vector according to any
one of claims 22, 29, or 30.
32. A method of trapping a gene in a eukaryotic target cell
comprising introducing a retrovirus according to claim 31 into said
target cell in vitro.
33. A method of trapping a gene in a eukaryotic target cell
comprising introducing a vector according to any one of claims 22,
29, or 30 into said cell in vitro, wherein said vector is
introduced into said target cell by at least one method selected
from electroporation, viral infection, retrotransposition,
microinjection, and transfection.
34. A eukaryotic cell which has a vector according to any one of
claims 22, 29, or 30 incorporated into its genome, wherein the
vector was introduced into the eukaryotic cell or an ancestor of
the eukaryotic cell in vitro.
35. A non-human animal comprising the eukaryotic cell of claim
34.
36. A method of activating the expression of a naturally occurring
gene in a cell comprising introducing a vector according to any one
of claims 22, 29, or 30 into said cell in vitro.
37. The method of claim 36 wherein said cell is a mammalian
cell.
38. The method of claim 37 wherein said mammalian cell is selected
from a human cell and a mouse cell.
39. A method of altering the expression of a cellularly encoded
gene in a eukaryotic cell comprising introducing a vector into said
cell, wherein said vector comprises in operable combination: a) a
sequence encoding a self-cleaving RNA; and b) a 3' gene trap
cassette located 3' to said sequence encoding a self-cleaving RNA
and comprising in operable combination: 1) a promoter; 2) a first
exon located 3' from and expressed by said promoter, said first
exon not encoding an activity conferring antibiotic resistance; and
3) a splice donor sequence defining the 3' region of the first
exon; wherein said vector is non-homologously incorporated into the
genome of the eukaryotic target cell and wherein said splice donor
sequence of the transcript encoded by said first exon is spliced to
a splice acceptor sequence of an exon of said cellularly encoded
gene.
40. The method of claim 39 wherein said non-homologously
incorporated vector is part of a retroviral vector that has
nonspecifically integrated into the genome of the eukaryotic target
cell.
41. The method of claim 40 wherein said first exon is selected from
an exon not encoded by the target cell genome and an exon not
normally expressed by the target cell genome.
42. A method of obtaining novel eukaryotic polynucleotide sequence
information comprising a) introducing into a eukaryotic cell a
vector comprising in operable combination: 1) a sequence encoding a
self-cleaving RNA; and 2) a 3' gene trap cassette located 3' to
said sequence encoding a self-cleaving RNA and comprising in
operable combination: i) a promoter; ii) a first exon located 3'
from and expressed by said promoter, said first exon not encoding
an activity conferring antibiotic resistance; iii) a splice donor
sequence defining the 3' region of the first exon; b) maintaining
the cell under conditions allowing the nontargeted integration of
the vector into the genome of the cell; c) obtaining the chimeric
transcript resulting from the splicing of said first exon from said
3' gene trap cassette to a second exon encoded by the genome of
said eucaryotic cell; and d) reverse transcribing said chimeric
transcript in vitro to produce a cDNA template; and e) determining
the polynucleotide sequence of the cDNA from step d.
Description
[0001] The present application claims priority to U.S. provisional
application. Ser. Nos., 60/079,729, 60/081,727, and 60/109,302,
which are herein incorporated by reference in their entirety.
1.0 FIELD OF THE INVENTION
[0002] The present invention relates to recombinant vectors
incorporating structural elements that, after the vectors have
integrated into the host cell genome, enhance the number of
cellular genes that can be identified as well as effectively
mutated. The described vectors are important tools for both gene
discovery, gene cloning, gene mutation, gene regulation, shuttling
nucleic acid sequences throughout the genome, and gene activation
and over expression.
2.0. BACKGROUND OF THE INVENTION
[0003] Gene trapping provides a powerful approach for
simultaneously mutating and identifying genes. Gene trap vectors
can be nonspecifically inserted into the target cell genome, and
gene trap vectors have consequently been constructed that-select
for events in which the gene trap vector has inserted into and
mutated a gene. By exploiting the cellular splicing machinery, the
selectable nature of these vectors removes the large background of
insertion events where vectors have not integrated into genes.
[0004] Most mammalian genes are divided into exons and introns.
Exons are the portions of the gene that are spliced into mRNA and
encode the protein product of a gene. In genomic DNA, these coding
exons are divided by noncoding intron sequences. Although RNA
polymerase transcribes both intron and exon sequences, the intron
sequences must be removed from the transcript so that the resulting
mRNA can be translated into protein. Accordingly, all mammalian and
most eukaryotic, cells have the machinery to splice exons into
mRNA. Gene trap vectors have been designed to integrate into
introns or genes in a manner that allows the cellular splicing
machinery to splice vector encoded exons to cellular mRNAs. Often,
such gene trap vectors contain selectable marker sequences that are
preceded by strong splice acceptor sequences and are not preceded
by a promoter. Accordingly, when such vectors integrate into a
gene, the cellular splicing machinery splices exons from the
trapped gene onto the 5' end of the selectable marker sequence.
Typically, such selectable marker genes can only be expressed if
the vector encoding the gene has integrated into an intron. The
resulting gene trap events are subsequently identified by selecting
for cells that can survive selective culture.
[0005] Gene trapping has proven to be a very efficient method of
mutating large numbers of genes. The insertion of the gene trap
vector creates a mutation in the trapped gene, and also provides a
molecular tag that can be exploited to identify the trapped gene.
When ROSA.beta.geo was used to trap genes it was demonstrated that
at least 50% of the resulting mutations resulted in a phenotype
when examined in mice. This indicates that the gene trap insertion
vectors are useful mutagens. Although a powerful tool for mutating
genes, the potential of the method had been limited by the
difficulty in identifying the trapped genes. Methods that have been
used to identify trap events rely on the fusion transcripts
resulting from the splicing of exon sequences from the trapped gene
to sequences encoded by the gene trap vector. Common gene
identification-protocols used to obtain sequences from these fusion
transcripts include 5' RACE, cDNA cloning, and cloning of genomic
DNA surrounding the site of vector integration. However, these
methods have proven labor intensive, not readily amenable to
automation, and generally impractical for high-throughput.
3.0. SUMMARY OF THE INVENTION
[0006] Recently, vectors have been developed that rely on a new
strategy of gene trapping that uses a vector that contains a
selectable marker gene preceded by a promoter and followed by a
splice donor sequence instead of a polyadenylation sequence. These
vectors do not provide selection unless they integrate into a gene
and subsequently trap downstream exons that-provide the
polyadenylation sequence required for expression of the selectable
marker. Integration of such vectors into the chromosome results in
the splicing of the selectable marker gene to 3' exons of the
trapped gene. These vectors provide a number of advantages. They
can be used to trap genes regardless of whether the genes are
normally expressed in the cell type in which the vector has
integrated. In addition, cells harboring such vectors can be
screened using automated (e.g., 96-well plate format) gene
identification assays such as 3' RACE (see generally, Frohman,
1994, PCR Methods and Applications, 4:S40-S58). Using these vectors
it is possible to produce large numbers of mutations and rapidly
identify the mutated, or trapped, gene. However, prior to the
present invention, the commercial scale exploitation of such
vectors'has been limited by the number of target genes that can be
trapped using such vectors.
[0007] The relative inefficiency of first generation 3' gene trap
vectors has limited the total number of genes that can be rapidly
and practically trapped, identified, analyzed, and effectively
mutated. This inefficiency prompted the development of more
efficient methods of 3' gene trapping--methods that allow a greater
percentage of genes in the target cell genome to be trapped and
rapidly identified by, for example, DNA sequence analysis.
[0008] The present invention relates to the construction of novel
vectors comprising a 3' gene trap cassette that allows for high
efficiency 3' gene trapping. The presently described 3' gene trap
cassette comprises in operable combination, a promoter region, an
exon (typically characterized by a translation initiation codon and
open reading frame and/or internal ribosome entry site), a splice
donor sequence, and, optionally, intronic sequences. The splice
donor (SD) sequence is operatively positioned such that the exon of
the 3' gene trap cassette is spliced to the splice acceptor (SA)
site of a downstream exon or a cellularly encoded exon. As such,
the described 3' gene trap cassette (or gene trap vector
incorporating the same) shall not incorporate a splice acceptor
(SA) sequence and a polyadenylation site operatively positioned
downstream from the SD sequence of the gene trap cassette. In a
preferred embodiment, the exon component of the 3' gene trap
cassette, which also serves as a sequence acquisition cassette,
will comprise exon sequence and a splice donor sequence derived
from genetic material that naturally occurs in an eukaryotic
cell.
[0009] An additional embodiment of the present invention is the use
of the described vectors to acquire novel DNA sequence information
from gene trapped exons from an infected target cell or a plurality
of target cells.
[0010] Additional embodiments of the present invention include
recombinant vectors, particularly viral vectors, that have been
genetically engineered to incorporate the described 3' gene trap
cassette. Preferably, although not necessarily, these vectors will
additionally incorporate a selectable marker that allows for
maintenance and detection of vector sequence in the target cell.
The selectable marker can be utilized as a 5' gene trap cassette
that is placed upstream from, and in the same orientation as, the
3' gene trap cassette. Optionally, a gene trap cassette
incorporating a selectable marker can be used in conjunction with a
vector encoded mutagenic mini-exon sequence operably positioned,
inter alia, to enhance splicing of cellular transcripts to the
selectable marker of the 5' gene trap cassette.
[0011] Additionally, the vector can include one or more mutagenesis
enhancer sequence(s) such as, but not limited to, a sequence
encoding a self-cleaving RNA, a transcription terminator, an exon
that changes the reading frame (or encodes one or more stop
codons), and/or a terminal exon, or any mixture or combination
thereof., operatively positioned between the 5' gene trap cassette
and the 3' gene trap cassette of the disclosed vectors.
[0012] An additional embodiment of the present invention is the use
of the novel 3' gene trap cassette, or vectors comprising the same,
to mutate and trap genes in a population of target cells, or
tissues, in vitro or in vivo, and/or to obtain the polynucleotide
sequence of unknown genes (i.e., discover new genes). As such,
general methods of gene mutation, identification, and phenotypic
screening are described that use the described 3' gene trap
cassette, and vectors comprising the same.
[0013] Another embodiment of the present invention is the use of
the presently described vectors (e.g., viral vectors comprising a
mini-exon and/or 3' gene trap cassette) to activate gene expression
in target cells. Preferably, the vectors are retroviral vectors
that are nonspecifically integrated (using viral integration
machinery) into the target cell genome. Additionally, assays are
described-that employ the described 3' gene trap cassette, or
vectors incorporating the same, to activate, genetically or
phenotypically select for, and subsequently identify new genes.
[0014] Additional embodiments of the presently described invention
include libraries of eukaryotic cells having genes that have been
simultaneously mutated (by one or more of the described mutagenic
components), and identified (using the described 3' gene trap
cassette) using the described vectors, and/or cDNA libraries
produced by exploiting the targeting frequency and the sequence
acquisition features of the described vectors.
[0015] Another embodiment of the present invention is a method of
obtaining DNA sequence information from a target cell, comprising
the steps of nonspecifically integrating a 3' gene trap cassette
(or mutagenic mini-exon), obtaining the chimeric RNA transcript
produced when the gene trap cassette (or mutagenic mini-exon) is
spliced by the target cell's endogenous splicing machinery to an
endogenous exon encoded within the target cell genome, and
obtaining sequence information from the endogenously encoded exon
from the target cell genome.
4.0. DESCRIPTION OF THE FIGURES
[0016] FIG. 1 presents a diagrammatic representation of how the
presently described 3' gene trap cassette is spliced to cellular
exons after the cassette is incorporated into the target cell
genome.
[0017] FIG. 2 shows a dual (5' and 3') gene trap vector that
incorporates a selectable marker in the 5' trap and the presently
described 3' gene trap. FIG. 2 also shows the positions of
recombinase recognition, e.g. frt or lox, sites that can be
located, for example, 5' to the promoter of the 3' gene trap
cassette and 3' to the SD of the 3' gene trap cassette as well as
the preferable locations of optional features such as a vector
encoded mutagenic mini-exon present upstream from the 5' gene trap
cassette, and mutagenesis enhancer cassettes such as a
unidirectional transcription termination sequence, a mutagenic
terminal exon, and a self-cleaving RNA coding region. The displayed
features are in reverse-orientation relative to the flanking
LTRs.
[0018] FIGS. 3a and 3b show the sequences of two self-cleaving RNAs
that can be used as mutagenesis enhancers.
[0019] FIG. 4 shows a representative example of a mutagenic
mini-exon sequence that can be used in conjunction with the
presently described vectors.
5.0. DETAILED DESCRIPTION OF THE INVENTION
[0020] In the modern age of genomics, gene trapping has proven to
be a powerful approach for both grouping gene sequences into
functional categories, and identifying novel genes. For example,
initial results have shown that about half of the gene trap events
from embryonic stem cells thus far characterized identify gene
sequences that have not been previously discovered by traditional
cDNA library technology.
[0021] Gene trapping (using promoter traps) has been used in a
variety of cell types to genetically screen for genes that are
induced by inductive signals, differentiation events, or phenotypes
of interest (i.e., in gene discovery). Additionally, such screens
have been used to identify tumor suppressor genes, genes induced by
cellular differentiation processes such as hematopoietic and muscle
cell differentiation, genes induced by signals that induce cellular
events such as B cell activation or apoptosis, and genes activated
by small molecules or other compounds. These studies indicate that
gene trapping can be used to group, genes based upon their function
in important cellular and physiological processes. However, the
broader exploitation of these screens has been limited by the
difficulty of identifying the trapped genes.
[0022] Several of the issues that must generally be addressed when
designing gene trap vectors include, but are not limited to: 1) the
percentage of the target cell genome that can be effectively
trapped by a given vector ("target sizee"); 2) the mutagenicity of
the vector after insertion into a gene in a target cell; and 3)
identifying the mutated gene by sequencing the chimeric transcript
produced by gene trap event. The present vectors have been
engineered to address the above concerns by, for example,
incorporating features that optimize the efficiency of the splice
acceptors and splice donors present in the vectors.
[0023] 5.1. The Broad Applicability of the Described Vectors
[0024] The presently described vectors can be used in virtually any
type of eukaryotic cell that can be manipulated to insert a gene
trap vector into the genome of the cell. For example, vectors that
incorporate the presently described 3' gene trap cassette can be
used to trap genes and/or acquire sequence information from primary
animal tissues as well as any other eukaryotic cell or organism
including, but not limited to, yeast, molds, fungi, and plants.
Plants of particular interest include dicots and monocots,
angiosperms (poppies, roses, camellias, etc.), gymnosperms (pine,
etc.), sorghum, grasses, as well as plants of agricultural
significance such as, but not limited to, grains (rice, wheat,
corn, millet, oats, etc.), nuts, lentils, chick peas, tubers
(potatoes, yams, taro, etc.), herbs, cotton, hemp, coffee, cocoa;
tobacco, rye, beets, alfalfa, buckwheat, hay, soy beans, bananas,
sugar cane, fruits (citrus and otherwise), grapes, vegetables, and
fungi (mushrooms, truffles, etc.), palm, maple, redwood, rape seed,
safflower, saffron, coconut yew, oak, and other deciduous and
evergreen trees. Alternatively, linearized 3' gene trap cassettes
can be introduced to target cells using the described conventional
methods of nucleotide delivery.
[0025] Additional examples of suitable animal target cells include,
but are not limited to, mammalian, including human, or avian
endothelial cells, epithelial cells, islets, neurons or neural
tissue, mesothelial cells, osteocytes, lymphocytes, chondrocytes.,
hematopoietic cells, immune cells, cells of the major glands or
organs (e.g., lung, heart, stomach, pancreas, kidney, skin, etc.),
exocrine and/or endocrine cells, embryonic and other totipotent or
pluripotent stem; cells, fibroblasts, and culture adapted and/or
transformed versions of the above can be used in conjunction with
the described vectors. Additionally, tumorigenic or other cell
lines can be targeted by the presently described vectors.
[0026] Preferred target cells for gene trapping using the described
vectors are embryonic stem cells (ES cells). ES cells are
pluripotent or totipotent. Thus, ES cells that have been
genetically engineered in vitro, can subsequently be introduced
into a developing fetus or embryo (e.g., into a morula or a
blastocyst) to result in chimeric animals. These chimeric animals
can subsequently be bred to produce offspring that are heterozygous
or homozygous for the engineered allele. In the case of mammalian
animals, the ES cells are typically microinjected into blastocysts
which are then implanted into pseudopregnant host animals.
[0027] The broad applicability of the described ES cell technology
is shown in the number of different animal systems to which the
technology has been successfully applied. For example, and not by
way of limitation, ES cells and/or transgenic animals have been
described in avian systems (U.S. Pat. No. 5,656,479), swine (U.S.
Pat. No. 5,523,226), non-murine pluripotential cells (U.S. Pat. No.
5,690,926), cattle, sheep, goats, rabbits, and mink (U.S.
Application Ser. No. 60/007,689 or WO1996US0018988 filed by White
et al., and WO1997EP0002323), and human ES Cells (U.S. application
Ser. No. 08/699,040, filed by Robl et al.) all of which are herein
incorporated by reference.
[0028] Typically, vectors incorporating the presently described
features can be introduced into target cells by any of a wide
variety of methods known in the art. Examples of such methods
include, but are not limited to, electroporation, viral infection,
retrotransposition, transposition, microparticle bombardment,
microinjection, lipofection, transfection, as cationic lipid
complexes, or as non-packaged/complexed, or "naked," DNA.
[0029] The vectors described in the present invention can also be
used in conjunction with virtually any type of phenotypic or
genetic screening protocols both in vitro and in vivo, and the
presently described vectors provide the additional advantage of
enabling rapid methods of identifying the DNA sequences of the
trapped genes.
[0030] The structural features of the vectors of the present
invention can be incorporated into any vector backbone so that the
resulting construct is capable of integrating into the genome of a
eukaryotic cell in a substantially non-specific fashion and
preferably in a completely non-specific fashion. A large number of
vectors known in the art may be used. Possible vectors include, but
are not limited to, plasmids or modified viruses, but the vector
system must be compatible with the host cell used. Such vectors
include, but are not limited to, bacteriophages such as lambda
derivatives, or plasmids such as PBR322 or pUC plasmid derivatives
or the Bluescript vector (Stratagene USA, La Jolla, Calif.). The
insertion of the DNA fragments corresponding to the features
described below into a suitable vector can, for example, be
accomplished by ligating the appropriate DNA fragments into the
chosen vector that has complementary cohesive termini. However, if
the complementary restriction sites of the DNA fragments are not
present in the cloning vector, the ends of the DNA molecules may be
enzymatically modified. Alternatively, any site desired may be
produced by ligating nucleotide sequences (linkers) onto the DNA
termini; these ligated linkers may comprise specific chemically
synthesized oligonucleotides encoding restriction endonuclease
recognition sequences.
[0031] 5.2. Structural Features of the Described Vectors
[0032] 5.2.1. Marker Gene
[0033] Vectors contemplated by the present invention can be
engineered to contain selectable marker genes that provide for the
selection, of cells that have incorporated the marker into the
cellular genome. In general, such selectable markers enable facile
methods of identifying and selecting for eukaryotic cells that
incorporate and express the proteins encoded by the selectable
markers. Examples of such selection methods include antibiotic,
calorimetric, enzymatic, and fluorescent selection of cells that
have integrated a gene trap event. One example of such a selectable
marker gene is .beta.geo, but any of a number of other selectable
markers can be employed (for example, see U.S. Pat. No. 5,464,764
herein incorporated by reference). An example of a plant selectable
marker is hygromycin phosphotransferase.
[0034] Accordingly, one embodiment of the present invention
contemplates vectors that are engineered to incorporate, and
optionally express, a marker gene that facilitates the tracking and
identification of target cells that incorporate the presently
described 3' gene trap cassette. Such markers include, but are not
limited to, antibiotic resistance genes, calorimetric marker genes,
enzymes (e.g., O-lactamase), or other marker genes that mediate the
direct or indirect expression of, for example, fluorescent marker
genes such as the gene encoding green fluorescent protein, and
assays for detecting the same, which are described, inter alia, in
U.S. Pat. No. 5,625,048, herein incorporated by reference. For the
purposes of the present disclosure, the term "directly," when used
in a biological or biochemical context, refers to direct causation
of a process that does not require intermediate steps, usually
caused by one molecule contacting or binding to another molecule
(which can be a molecule of the same type or a different type of
molecule). For example, molecule A contacts molecule B, which
causes molecule B to exert effect X that is part of a biological
process. For the purposes of the present invention, the term
"indirectly," when used in a biological or biochemical context,
refers to indirect causation that requires intermediate steps,
usually caused by two or more direct steps. For example, molecule A
contacts molecule B to exert effect X which in turn causes effect
Y. Also for the purposes of the present invention, the term "gene"
shall refer to any and all discrete coding regions of the cell's
genome, as well as associated noncoding and regulatory regions, or
shall refer to the region encoding a specific and functional
protein product or activity. Additionally, the term "operatively
positioned" shall refer to the fact that the control elements or
genes are present in the proper orientation and spacing to provide
the desired or indicated functions of the control elements or
genes. Also for the purposes of the present invention, a gene is
"expressed" when a control element in the cell mediates the
production of functional and/or detectable levels of mRNA encoded
by the gene, or a selectable marker inserted therein, that can
subsequently be spliced/processed and, where applicable, translated
to produce an active product. A gene is not expressed where the
relevant control element in the cell is absent, has been
inactivated, or does not mediate the production of functional
and/or detectable levels of mRNA encoded by the gene, or a
selectable marker inserted therein. For the purposes of the present
invention, a mRNA is produced at "functional" levels if, upon
translation, it produces a protein having the size and activity
normally associated with the corresponding locus.
[0035] The marker gene can be incorporated into the described
vectors as a self-contained expression cassette including, in
operable combination, a marker, promoter for expressing the marker,
ribosome binding/translation start site, and polyadenylation
sequence. Additionally, the marker can be placed in the vector such
that it is expressed from a vector promoter, and can optionally be
engineered to functionally incorporate an independent ribosome
entry site (IRES) that facilitates marker expression.
[0036] 5.2.2. 5' Gene Trap Cassette
[0037] The presently described vectors can be engineered to include
a 5' gene trap cassette that typically contains a splice acceptor
site located 5' to an exon (which can encode a selectable marker
gene) followed by an operatively positioned polyadenylation
sequence. Typically, vectors incorporating 5' gene traps do not
contain promoters that express the exon encoded in the 5' gene trap
cassette, and do not encode a splice donor sequence operatively
positioned 5' to the splice acceptor of the exon of the 5' gene
trap cassette. Consequently, after it is integrated into the
cellular chromosome the 5' gene trap cassette intercepts the normal
splicing of the upstream gene and acts as a terminal exon. The net
effect is that the cellular transcript is disrupted and effectively
mutagenized by the 5' gene trap cassette. The 5' gene trap cassette
can incorporate a marker gene as the exon component, and can thus
be used in lieu of or in addition to the marker gene described in
Section 5.2.1.
[0038] The structural features of the 5' gene trap cassette can
also be manipulated to produce gene trap events that are biased as
to where the 5' gene trap has integrated into the cellar genome
(for purposes of illustration, and not limitation, the following
discussion shall assume that the exon of the 5' gene trap cassette
encodes a selectable marker). For example, given that no promoter
is present, the marker encoded by a 5' gene trap cassette (that has
been engineered without an IRES) can typically only be expressed if
it has been integrated into an intron 5' from the translation start
site of the endogenous gene. Given the absence of an IRES, if the
vector incorporating such a 5' gene trap cassette has integrated
into an intron that is downstream from the translation start site
of the endogenous gene, the marker can only be expressed if it is
present in the correct reading frame to produce a fusion protein
that provides selectable marker activity. Accordingly., vectors
incorporating such 5' gene trap cassettes can selectively increase
the probability that the identified gene trapped sequences begin
with sequences 5' to the start of translation.
[0039] An alternative method of producing a similar effect employs
vectors incorporating a nested set of stop codons present in, or
otherwise engineered into, the region between the SA of 5' gene
trap cassette and the translation initiation codon of the
selectable marker, or such stop codons can located between the end
of the selectable marker coding region and the polyadenylation
sequence. The selectable marker can also be engineered to contain
an independent ribosome entry site (IRES) so that the marker will
be expressed in a manner largely independent of the location in
which the vector has integrated into the target cell genome.
Typically, but not necessarily, an IRES is not used in conjunction
with a nested set of stop codons as described, supra.
[0040] In a particularly preferred embodiment, the described
vectors employ a 5' gene trap cassette that comprises a selectable
marker gene preceded by a splice acceptor sequence and followed a
polyadenylation (pA) sequence (SA.beta.geopA, FIG. 2).
Alternatively, SAIRES.beta.geopA can be used which further
incorporates an internal ribosome entry site upstream from the
.beta.geo gene, or SAneopA can be used (which dispenses with the
.beta.-gal activity). The above 5' gene trap cassettes can
efficiently mutate genes and can be used to follow the expression
of the trapped gene. Optimizing the SA sequence used can further
enhance, or regulate, the efficiency of the 5' gene trap cassette.
Examples of suitable SA sequences include, but are not limited
to:
1 (SEQ ID NO: .sub.----) GCAACCAGTAACCTCTGCCCTTTCTCCTCCATG-
ACAACCAGGT; (SEQ ID NO: .sub.----)
GATGATGTCATACTTATCCTGTCCCTTTTTTTTCCACAGCT; (SEQ ID NO: .sub.----)
GGCGGTCAGGCTGCCCTCTGTTCCCATTGCAGGAA; (SEQ ID NO: .sub.----)
TGTCAGTCTGTCATCCTTGCCCCTTCAGCCGCCCGGATGG- CG; (SEQ ID NO:
.sub.----) TGCTGACACCCCACTGTTCCCTGCAGGACCGCCTTCAAC; (SEQ ID NO:
.sub.----) TAATTGTGTAATTATTGTTTTTCCTCCTTTAGAT; (SEQ ID NO:
.sub.----) CAGAATCTTCTTTTTAATTCCTGATTTTATTTCTATAGGA; (SEQ ID NO:
.sub.----) TACTAACATTGCCTTTTCCTCCT- TCCCTCCCACAGGT; (SEQ ID NO:
.sub.----) TGCTCCACTTTGAAACAGCTGTCTTTCTTTTGCAGAT; (SEQ ID NO:
.sub.----) CTCTCTGCCTATTGGTCTATTTTCCCACCCTTAGGC; and (SEQ ID NO:
.sub.----) ATTAATTACTCTGCCCATTCCTCTCTT- TCAGAGTT.
[0041] Any of the above SA sequences can be used in conjunction
with, for example, SAneopA or SAIRESneopA.
[0042] Optionally, the 5' gene trap cassette can be flanked by
suitable recombinase sites (e.g., lox P, frt, etc.). In one such
embodiment, a recombinase site flanked 5' gene trap cassette is
used in conjunct ion with a second 5' gene trap cassette (present
downstream from the 3' recombinase site) that encodes a detectable
marker, a different selectable marker, or an enzymatic marker (such
as, but not limited to, green fluorescent protein, beta lactamase,
TK, blasticidin, HPRT, etc.), and that is preferably not be flanked
by the same recombinase sites the first 5' gene trap cassette. In
the event that both of the 5' gene trap cassettes are not expressed
at acceptable levels (via alternative splicing), the second 5' gene
trap cassette (that encodes a detectable marker) can be "activated"
by using a suitable recombinase activity (i.e., cre, flp, etc.) in
vitro or in vivo to remove the first (recombinase site flanked) 5'
gene trap cassette.
[0043] 5.2.3. Mutagenesis Enhancers
[0044] To further enhance the splicing and expression of the exon
encoded within a mutagenic 5' gene trap cassette, additional
features can be added to the described vectors. For example, a
mutagenic mini-exon (see FIG. 4), optionally naturally occurring,
can be operatively positioned upstream from the 5' gene trap
cassette. This mutagenic mini-exon minimally comprises, in operable
combination, a splice acceptor (SA) site, a stretch of exon
sequence, and a splice donor (SD). An operative polyadenylation
site is not directly associated with the mutagenic mini-exon since
the exon is not intended to serve as a terminal 3' exon. The
mutagenic mini-exon operates by intercepting the splicing of a
cellularly initiated transcript in the area upstream from and in
proximity to the SA site of the 5' gene trap/selectable marker. By
recruiting the cellular splicing machinery to this region, the SA
of the 5' gene trap cassette is more readily recognized and used
which, inter alia, effectively enhances the mutagenicity and
expression of the 5' gene trap cassette.
[0045] Whether or not the mutagenic mini-exon is used in
conjunction with a 5 gene trap cassette, it will preferably have
3N+1, or 3N+2 bases in order to alter or change the reading frame
of any native gene or exon into which it has been spliced.
Alternatively, but less preferably, the mutagenic mini-exons can
incorporate stop codons in all three reading frames which would
remove the constraint that the exon not contain 3N number of
nucleotides. By introducing frame-shift mutations (i.e., inserts
having 3N+/-1 bases spanning the SA-SD region of the mutagenic
mini-exon), one can also hinder or prevent cellular transcript from
"splicing around" an integrated gene trap construct and producing a
functional protein product. In such cases, varying the SA and/or SD
sequences of the mutagenic mini-exon will produce a corresponding
variation in the efficiency of splice intervention (i.e., effective
mutagenesis). As such, the presently described mutagenic mini-exons
(or mutagenic mini-exons) also provide an effective mechanism for
regulating gene expression in a cell or animal. As with essentially
all of the mutagenic or regulatory features of the described
vectors, the described mutagenic mini-exons can be suitably flanked
by recombinase sites to allow for the expedient, and in some cases
tissue specific, removal of the mutagenic mini-exon sequence.
[0046] Compositional and structural constraints similar to those
discussed above can also be used to design mini-exons for use in
conjunction with 3' gene trap cassettes (described, infra) that
activate cellular gene expression optionally, the mutagenic
mini-exon can be used as a combined mutagenic gene trap cassette
and sequence acquisition component that operates in place of, or in
addition to, the described 5' and 3' gene trap cassettes. In such a
construct, the SA of the mutagenic mini-exon is replaced by a
promoter element, and the mutagenic mini-exon can serve as a
sequence acquisition component that operates independent of the
endogenous expression of the trapped gene (in place of, or in
addition to, the 3' gene trap cassette). Additionally, the
mutagenic mini-exon can be flanked by recombinase sites that allow
for the selective or conditional removal of the mutagenic
mini-exon.
[0047] Additional structural modifications can be employed to
enhance the mutagenic effectiveness of the described gene trap
vectors. Such modifications include, but are not limited to: 1)
modifying/optimizing the sequence at or flanking the branch point
sequence and flanking regions of the SA site of the 5' gene trap
cassette in order to facilitate splicing of the 5' gene-trap
cassette by a given target cell (ideally, the SA region will
naturally occur in the target cell or be a consensus SA region); 2)
placing a terminal 3' exon (SA-exon-polyA/transcription
terminator)., preferably naturally occurring, operatively
positioned upstream from the 3' gene trap cassette (optionally
in-between the described 5' and 3' gene trap cassettes); 3) placing
a unidirectional transcription terminator sequence operatively
positioned upstream from 3' gene trap cassette (optionally
in-between the described 5' and 3' gene trap cassettes, and
preferably downstream from the terminal 3' exon); and 4)
incorporating into the vector in a functional orientation a
self-cleaving RNA sequence upstream from the 3' gene trap cassette
(and preferably downstream from the 5' gene trap cassette and,
optionally, on either side of any naturally occurring terminal 3'
exon or unidirectional transcription terminator that may be present
in one of the described gene trap constructs) that further ablates
the possibility that a cellularly initiated transcript will
"splice-around" a vector encoded gene trap element.
[0048] Cellular splicing of exogenously introduced, or foreign,
exons can also be enhanced by incorporating cassettes encoding
small nuclear RNA and/or small nuclear ribonucleoproteins that have
been engineered to increase the splicing efficiency of an
exogenously introduced gene trap cassette or mutagenic mini-exon
cassette.
[0049] Several of the above features (e.g., the 3' terminal exon
and transcription terminator, etc.) also enhance the efficiency of
sequence acquisition by the 3' gene trap cassette by preventing
run-on transcription/promoter interference that can hinder the
expression of the 3' gene trap cassette. Additionally, particularly
where retroviral vectors are employed, the orientation of several
of the above features is particularly important given that some of
the structural elements would hinder, if not prevent, the
expression and packaging of the retroviral RNA genome.
[0050] Another embodiment of the present invention contemplates the
placement of recombinase sites flanking one or more of the
mutagenesis enhancer regions, or any other gene trap or other
cassette or portion of the described vectors. Using this
arrangement, virtually any portion of the vector that is flanked by
recombinase sites can be conditionally activated, or deactivated,
by exposing a cell harboring such a construct to the corresponding
recombinase activity. Optionally, different mutagenesis enhancer
regions such as the mutagenic mini-exon cassette, transcription
terminator, and the self cleaving RNA cassette can be flanked by
different recombinase sites that will allow the independent
modulation or the function of one or both of these components.
Using such an arrangement in conjunction with a downstream 5' gene
trap cassette mutagenic enhancer sequence, the 5' gene trap can be
"activated" by the recombinase-mediated removal of the mutagenic
enhancer sequence.
[0051] As a rapid means of detecting whether a given integration
locus may allow the cell to efficiently "splice-around" a given 5'
gene trap cassette, a second 5' gene trap cassette incorporating a
different selectable, or enzymatically or fluorescently detectable,
marker can be incorporated in tandem with and downstream from the
first 5' gene trap cassette. By screening or selecting for the
expression of both the first and second 5' gene trap cassettes, one
can rapidly determine the extent to which a cell incorporating such
a vector might "splice-around" the first 5' gene trap cassette. The
second 5' gene trap cassette can also be positioned either upstream
or downstream from any mutagenesis enhancer sequences that are
present in a given vector in order to determine the effectiveness
of the mutagenesis enhancer sequence.
[0052] Alternatively, the exon of the second 5' gene trap cassette
can encode, for example, the thymidine kinase (TK) gene. Using such
constructs, FIAU, for example, can be used to select against cells
that "splice-around" the first, or "mutagenic," 5' gene trap
cassette. Generally, the second 5' gene trap cassettes are
incorporated into the vector downstream from the mutagenesis
enhancer sequences and upstream from the 3' gene trap cassette.
Optionally, one of the two tandem 5' gene trap cassettes can be
flanked by suitably oriented recombinase sites that allow the
subsequent and specific removal of the 5' gene trap cassette. Using
such a strategy, a first 5' gene trap exon (e.g., encoding neo
resistance) may be removed using a suitable recombinase activity to
effectively "activate" the splicing and expression of the second 5'
gene trap cassette which (especially when it encodes a suitable
marker/signal activity such as B-gal, green fluorescent protein,
etc.) can be used to track the expression of the trapped gene in
tissue and in cells and tissue samples using established
methods.
[0053] 5.2.4. Trans-Acting Mutagenic Elements
[0054] Another embodiment of the present invention includes vectors
that have been engineered to encode and express products that
reduce the function or expression of the corresponding unaltered
allele by antisense or ribozyme cleavage. For example, such vectors
could contain an promoter element, preferably inducible or
conditional, that directs an antisense transcript that reads into
the portion of the target cell genome that flanks the integrated
vector. Presumably, such an inducible promoter would engineered to
be present in the integrated provirus in the region 3' of the R
region and 5' of the 3'-terminal inverted repeat of the retroviral
LTR (for example, at the Nhe I site located within 75 bases of the
terminal inverted repeat sequences--this and other restriction
sites in the LTR can also be modified to insert a unique, or rare,
restriction site). Alternatively, such a promoter can be flanked by
recombinase sites and placed in a reverse orientation (relative to
the LTR) and subsequently activated (by recombinase-mediated
"flipping") using a suitable recombinase activity. In general,
antisense strategies or features similar to those described in U.S.
Pat. No. 5,679,523, herein incorporated by reference, can be
incorporated into the presently described vectors. Where the use of
ribozymes or catalytic RNAs are contemplated, ribozymes can be
engineered that are transcribed and appended to (via splicing or
cotranscription), and preferably targeted to, cellularly encoded
transcripts. Ribozyme methods are also adaptable to the recombinase
strategy described above.
[0055] As an alternative means of generating functionally
homozygous mutant cells, the described mutagenic vectors can be
utilized in conjunction with traditional mutagenic methodologies
(i.e., radiation, chemical mutagenesis, UV light, bulky addition
products, deletion mutagenesis, insertional mutagenesis, frame
shift mutagenesis, and transition and transversion mutagens, etc.).
Appropriately mutagenized cells, for example a series of target
cells containing large and preferably overlapping regions of
deleted chromosomal DNA, increase the probability that a given
mutational event obtained with the described vectors will
effectively manifest itself as a homozygous knock out event.
[0056] 5.2.5. 3' Gene Trap Cassette
[0057] The presently described 3' gene trap cassette comprises, in
operative combination, a promoter region that mediates the
expression of an exon, and an operative splice donor (SD) sequence
that defines the 3' end of the exon. After integration into the
target cell chromosome, the transcript expressed by the 3' gene
trap promoter is spliced to a splice acceptor (SA) sequence of a
trapped cellular exon located downstream of the integrated 3' gene
trap cassette. Thus, a fusion transcript is generated comprising
the exon of the 3' gene trap cassette and any downstream cellular
exons the most 3' of which has a polyadenylation signal.
[0058] The fusion transcript can be identified by a variety of
methods known to those of skill in the art at any level of
expression, i.e., as a heterogenous nuclear RNA, as a messenger
RNA, as a protein, etc. For example, one may perform polymerase
chain reaction using a primer pair specific for the exon of the 3'
gene trap cassette and the polyA tail of the transcript. Or, for
example, one may use an exon in the 3' gene trap cassette which
encodes an epitope which can be identified in an antibody screen,
i.e., epitope tagging. Other screening methods known in the art
include, but are not limited to, hybridization (on solid support or
in solution, etc.) with a probe specific for the exon of the 3'
gene trap cassette when screening on the protein level, one may
carry out the screen in any cellular location, e.g., one may screen
for secreted proteins encoded by the fusion transcript. Or, for
example, one may use a first exon which encodes a secretion signal,
thus making the host cells secrete many or all fusion peptides
encoded by the fusion transcripts. All screening methods may also
be modified to render them specific for the trapped exons and the
proteins and polypeptides they encode, i.e., PCR primers,
hybridization probes or antibodies specific for a particular gene
or class of genes may be used to screen. Or, for example, one may
screen based on a posttranslational modification, e.g., one may
screen with an antibody specific for certain or all
glycoproteins.
[0059] As described above, the 3' gene trap cassette contains a
promoter that directs the expression of one or more exons
(optionally encoding one or more open reading frames) that are
followed by a splice donor sequence (FIG. 1). Any number of
transcriptional promoters and enhancers may be incorporated into
the 3' gene trap cassette including, but not limited to, cell or
tissue specific promoters, inducible promoters, the herpes simplex
thymidine kinase promoter, cytomegalovirus (CMV) promoter/enhancer,
SV40 promoters, PGK promoter, regulatable promoters (e.g.,
metallothionein promoter), adenovirus late promoter., vaccinia
virus 7.5K promoter, avian (i.e., chicken, etc.) beta globin
promoter, histone promoters (e.g., mouse histone H3-614, etc.),
beta actin promoter (preferably chicken), metallothionein promoters
(preferably mouse metallothionein I and II), the cauliflower mosaic
virus 35S promoter and the like, as well as any permutations and
variations thereof, which can be produced using well established
molecular biology techniques {see generally, Sambrook et al. (1989)
Molecular Cloning Vols. I-III, Cold Spring Harbor Laboratory Press,
Cold Spring Harbor, N.Y., and Current Protocols in Molecular
Biology (1989) John Wiley & Sons, all Vols. and periodic
updates thereof, herein incorporated by reference).
Promoter/enhancer regions can also be selected to provide
tissue-specific expression or inducible expression.
[0060] Preferably, the exon (or exons) of the 3' gene trap cassette
has been designed to mimic an exon of a gene, preferably a first
exon. Generally, the exon or exons (and part of the intron
following the exon(s)) and splice donor sequence are derived from a
naturally occurring gene; however, synthetic exons designed to
mimic a real exon can also be used. For example, such exons might
be designed and constructed de novo or by modifying existing exons
to incorporate a high efficiency, or consensus, ribosome binding,
site or to add an IRES sequence 5' to the translation initiation
codon of an open reading frame or exon, to create an open reading
frame, to optimize codon usage, to engineer one or more restriction
sites that do not alter the amino acid sequence encoded by the open
reading frame, or to engineer an alternative or consensus splice
donor sequence into the exon.
[0061] Presently described vectors use a 3' gene trap cassette that
employs an exon of non-prokaryotic origin, i.e., an exon obtained
from a eukaryotic organism. Exons useful for the 3' gene trap
cassette of the invention do not encode an antibiotic resistance
activity, or other selectable marker, activity (e.g., an antibiotic
resistance gene). As discussed herein, 3' gene trap cassettes
incorporating open reading frames of noneukaryotic origin typically
display a markedly reduced efficiency of 3' exon trapping.
Consequently, vectors employing the presently described 3' gene
trap cassette greatly increase the number of target genes that can
be trapped and rapidly identified by gene trap sequence
tagging.
[0062] Accordingly, the exon of the 3' gene trap cassette
(including the SD site) is preferably derived from nucleotide
sequence that is similar or homologous to nucleotide sequence that
is native to an eukaryotic cell, or, possibly, an animal or plant
virus, or naturally occurs in, the target cell., or the genome of
cells from a related species, genus, order, class, phylum, or
kingdom. For example, an exon from a human gene may be used in a 3'
gene trap cassette that is used in mouse cells and an exon from a
mouse gene may be used in a 3' gene trap cassette that is used in
human cells. For the purposes of the present invention, a
homologous sequence is defined as a nucleic acid sequence that is
capable of binding to a target sequence under highly stringent
conditions such as, for example, hybridization to filter-bound DNA
in 0.5 M NaHPO.sub.4, 7% sodium dodecyl sulfate (SDS), 1 mM EDTA at
65.degree. C., and washing in 0.1.times.SSC/0.1% SDS at 68.degree.
C. (Ausubel F. M. et al., eds., 1989, Current Protocols in
Molecular Biology, Vol. I, Green Publishing Associates, Inc., and
John Wiley & sons, Inc., New York, at p. 2.10.3), or possibly
under less stringent conditions, such as, for example, moderately
stringent conditions, e.g., washing in 0.2.times.SSC/0.1% SDS at
42.degree. C. (Ausubel et al., 1989, supra). Optionally, the exon
is isogenic to sequence in the target cell genome.
[0063] Exons suitable for the 3' gene trap cassette of the present
invention may also be obtained by combining naturally occurring
exons, or by combining fragments of naturally occurring exons, or
by combining fragments of naturally occurring exons with synthetic
sequences which may be consensus sequences of naturally occurring
exons. For example, when using an exon found in the genome of a
eukaryotic organism that is not the first exon of a gene, one may
render it useful for the 3' gene trap cassette of the present
invention by adding a suitable transcription initiation sequence to
the 5' end of the exon.
[0064] Where the target cell genome encodes a gene identical to (or
corresponding to) the exon of the 3' gene trap cassette, the
naturally occurring gene will preferably not be expressed by the
target cell at levels that substantially interfere with the
amplification and sequencing of the trapped exon sequences in the
target cells. For the purposes of the present disclosure, the term
"substantially interfere with the amplification and sequencing"
shall refer to the fact that the endogenous expression of the
naturally occurring exon may hinder but shall not prevent the
amplification and sequencing of the trapped exon sequence by 3'
RACE protocols, or, optionally, by conventional cloning and
sequencing. Additional methods of circumventing this potential
complication include the incorporation of an unique sequence within
the otherwise naturally occurring exon of the 3' gene trap cassette
that can be used as PCR priming site, or to employ a 3' gene trap
cassette having an exon that does not naturally occur in the target
cell genome. Yet another method of circumventing this potential
complication is to use an exon in the 3' gene trap cassette that is
obtained from an inducible gene, e.g., stress genes. Preferably, in
this embodiment, the cells in which the 3' gene trap cassette is
used would be maintained under conditions so that the gene from
which the exon is obtained is not or barely induced, if the gene is
present in those cells.
[0065] The exon of the presently described 3' gene trap cassette
may or may not contain a translation start site and/or an open
reading frame. Optionally, any open reading frame(s) that may be
present in the exon can be engineered to incorporate codons that
have been optimized to reflect the preferred codon usage of the
host cell.
[0066] Given that the exon of the presently described 3' gene trap
cassette preferably comprises sequence native to an eukaryotic, or
preferably mammalian, cell, the exon will typically not constitute
a marker encoding a protein having an antibiotic resistance
activity (such as neo, amp, e.g., .beta.-lactamase, tet, kan, and
the like) or otherwise confers selectable drug resistance or
sensitivity to the host cell (although such a marker can optionally
be app ended to, for example, the 5' region of the exon). For the
purposes of the present invention, a gene or gene product is
capable of "conferring" antibiotic resistance if a gene encodes a
gene product having an activity that provides a selective growth to
a prokaryotic or eukaryotic cell expressing the antibiotic
resistance gene in media containing appropriate concentrations of
the corresponding antibiotic.
[0067] Alternatively, the exon will generally not encode an
enzymatic activity, or reporter gene, that mediates selectable
detection via a well known conventional chromogenic or fluorescent
assay (e.g., .beta.-galactosidase, alkaline phosphatase, or horse
radish peroxidase) that is not native to the, preferably mammalian,
target cell. Additionally, the presently described vectors shall
preferably not contain regions of targeting DNA sequence (i.e., for
directing gene targeting of the 3' gene trap cassette to a specific
genetic locus via homologous recombination) flanking the described
3' gene trap cassette.
[0068] Moreover, given that splice donor efficiency can be
influenced by intron sequences downstream from the splice donor
site, the presently described 3' gene trap cassette can optionally
be engineered to contain between about one base and about several
thousand bases of intron sequence adjacent and 3' to the
splice-donor sequence.
[0069] 5.3. Applications of the Described Vectors
[0070] Vectors incorporating the described 3' gene trap cassettes
are characterized by a marked improvement in the efficiency of 3'
gene trapping. As such, another embodiment of the present invention
is a 3' gene trap cassette, and vectors incorporating the same,
that are characterized by the capability of trapping 3' exons with
at least about 15 percent of the efficiency with which a similarly
situated SA.beta.geo 5' gene trap cassette (or SAneo 5' gene trap
cassette) traps 5' exons, preferably, at least about 25 percent,
more preferably at least about 40 percent, more preferably at least
about 60 percent, and most preferably at least about 65 percent.
For the purposes of the present invention, a similarly situated
gene trap cassette is a cassette that is present in a similar
orientation within a similar vector. Alternatively, similarly
situated gene trap cassettes may both be present in the same
vector.
[0071] Any of a variety of quantitative measurements ate available
to those skilled in the art and can be used to calculate the
relative efficiency of the respective 3' and 5' gene trap cassettes
as well as the number of genes that can be effectively trapped. For
example, one can determine the percentage of target genes
identified by the presently described 3' gene trap cassette
relative to the percentage of target genes identified by 5' gene
traps such as SA.beta.geo or SAneo and selected-using, for example,
the antibiotic G418. Alternatively, the percentage of identifiable
3' gene trap events can be compared to the percentage of target
cells rendered antibiotic resistant or chromogenically identifiable
by SA.beta.geo-mediated 5' gene trap events.
[0072] The functional efficiency of the presently described 3' gene
trap cassette can-also be quantified by the absolute number of
independent gene trap events characterized using the vector.
Generally, the presently described vectors allow for the expedient
trapping of at least about one to about several hundred genes,
typically at least about 1,000 different genes, more typically at
least about 3,000, preferably at least about 10,000 genes, more
preferably at least about 25,000 genes, more preferably at least
about 50,000 genes, and most preferably at least about 55,000 genes
up to the maximum number of genes present in a given cell or cell
type. For example, murine cells are thought to encode between about
60,000 to 100,000 genes or more.
[0073] Another measure of gene trapping efficiency is the number of
distinct cellular exons that can be trapped. Typically, the
presently described 3' gene trap cassette will trap cellular 3'
exons with sufficient efficiency to enable the facile detection,
screening, and identification of at least about 10,000 distinct 3'
gene trapped cellular exons (generally representing approximately
between about 7,500 to 9,500 different genes--the number is
typically smaller because independent integration events can occur
within different introns/exons within the same gene), preferably at
least about 15,000 distinct 3' gene trapped cellular exons, more
preferably at least about 25,000 distinct 3' gene trapped cellular
exons, and most preferably at least about 50,000 distinct 3' gene
trapped cellular exons up to between about 70 and about 100 percent
of the genes present in the mammalian genome.
[0074] 5.3.1. Gene Trapped Libraries Of Cells
[0075] Given the number of genes that can be rapidly characterized
using the present vectors, additional embodiments of the present
invention include gene trapped libraries of cultured animal cells
that stably incorporate the presently described 3' gene trap
cassette. The presently described libraries may be made by a
process comprising the steps of treating (i.e., infecting,
transfecting, retrotransposing, or virtually any other method of
introducing polynucleotides into a cell) a population of cells to
stably integrate a vector containing the 3' gene trap cassette,
identifying or otherwise selecting for stably transduced cells, and
identifying the trapped 3' cellular exons. In a preferred
embodiment, the animal cell libraries comprise mammalian cells, and
in a particularly preferred embodiment, the mammalian cells are
embryonic stem (ES) cells preferably, such libraries are
constructed such that each mutated cell in the library harbors a
single identifiable 3' gene, trap vector/event (although mutated
cells harboring multiple gene trap vectors are also contemplated by
the present invention).
[0076] In an additional embodiment of the present invention, the
individual mutant cells in the library are separated and clonally
expanded. The isolated and clonally expanded mutant cells are then
analyzed to ascertain the DNA sequence, or partial DNA sequence, of
the insertionally mutated host gene. Thus, the invention further
provides for the sequencing of at least a portion of every gene
mutated in the library. The resulting sequence database
subsequently serves as an index for the library. In essence, every
group of clonally expanded cells in the library is individually
catalogued using the partial sequence information. The resulting
sequence is specific for the mutated gene since the present methods
are designed to obtain sequence information from exons that have
been spliced to the 3' gene trap cassette. The resulting sequence
database can be used to identify the mutated gene of interest, or,
alternatively, represents a, powerful tool for the identification
of novel genes. Once identified, the corresponding mutant cell may
be taken from the library and studied further as described below.,
Generally, indexed libraries of isolated cells, or individual cell
types (e.g., ES cells), that have been mutated using vectors
incorporating the described 3' gene trap cassette will comprise a
collection of at least about 50 different isolated mutant cell
culture lines, typically at least about 100, more typically, at
least about 500, preferably at least about 1,000, more preferably
at least about 5,000, more preferably at least about 10,000, more
preferably at least about 25,000, and even more preferably at least
about 40,000 up to about one to five hundred thousand different
isolated and characterized mutant cell culture lines or more.
Preferably, the genomes of the different mutant cell cultures
present in a given library are essentially identical (e.g., derived
from a common source or inbred strain) except for the location of
the inserted gene trap cassette, or vector incorporating the
same.
[0077] Ideally, the scope of mutagenesis is the entire suet of
genes that can be trapped in the target cell line. By increasing
the redundancy of the library, the resulting sequence database will
ideally contain an essentially complete representation of the genes
that can be trapped in the target cell. For the purposes of the
present invention, the term "essentially complete representation"
shall refer to the statistical situation where there is generally
at least about an 80-95 percent probability that the genomes of the
cells' used to construct the library collectively contain a stably
inserted 3' gene trap cassette in at least about 70 percent of the
genes that can be trapped in the target cell genome, preferably at
least about 85 percent, and most preferably at least about a 95
percent of the genes that can be trapped as determined by a
standard Poisson distribution (and assuming that a given vector
integrates into the genome nonspecifically).
[0078] The broad genomic coverage afforded by the present vectors
also allows for the large-scale mutagenesis of the target cell
genome. Typically, such a library of mutated target cells will
comprise a collection of mutated cells, or isolated cultures
thereof, that collectively represent at least one 3' gene trap
mutation (mediated by the described 3' gene trap cassette or vector
comprising the same) in each chromosome present in the target cell
genome, preferably at least about 2 to 3 independent gene trap
mutations per chromosome will be collectively present in the
library, more preferably at least about 10 independent gene trap
mutations per chromosome are represented, and most preferably at
least about 500 independent gene trap mutations per autosomal
chromosome (minus the sex chromosomes), and/or up to about 70 to 90
percent, or even an essentially complete representation of the
genes in the genome will be collectively represented in the
library.
[0079] The presently described invention allows for large-scale
genetic analysis of the genome of any organism/cell that can be
transduced with the described vectors or for which there exists
cultured cell lines. Accordingly, the described libraries can be
constructed from any type of cell that can be transfected by
standard techniques or transfected with a recombinant vector
harboring the described 3' gene trap cassette. As such the
presently described methods of making, organizing, and indexing
libraries of mutated animal cells are also broadly applicable to
virtually any eukaryotic cells that may be genetically manipulated
and grown in culture.
[0080] Where mouse ES cells are used to construct the library, and
preferably early passage ES cells, the library becomes a genetic
tool for the comprehensive-functional study of the mouse genome.
Since ES cells can be injected back into a blastocyst and
incorporated into normal development and ultimately the germ line,
the mutated ES cells of the library effectively represent a
collection of mutant transgenic mouse strains (see generally, U.S.
Pat. No. 5,464,764 issued Nov. 7, 1995, herein incorporated by
reference).
[0081] A similar methodology can be used to construct virtually any
non-human transgenic animal (or animal capable of being rendered
transgenic), or transgenic plants. Such nonhuman transgenic animals
may include, for example, transgenic pigs, transgenic rats,
transgenic rabbits, transgenic cattle, transgenic goats, and other
transgenic animal species, particularly mammalian species, known in
the art. Additionally, bovine, ovine, and porcine species, other
members of the rodent family, e.g., rat, as well as rabbit and
guinea pig and non-human primates, such as chimpanzee, may be used
to practice the present invention.
[0082] Transgenic animals and cells produced using the presently
described library and/or vectors are useful for the study of basic
biological processes and the development of therapeutics and
diagnostics for diseases including, but not limited to, aging,
cancer, autoimmune disease, immune disorders, alopecia, glandular
disorders, inflammatory disorders, ataxia telangiectasia, diabetes,
arthritis, high blood pressure, atherosclerosis, cardiovascular
disease, pulmonary disease, degenerative diseases of the neural or
skeletal systems, Alzheimer's disease, Parkinsdn's disease, asthma,
developmental disorders or abnormalities, infertility, epithelial
ulcerations, and viral and microbial pathogenesis and infectious
disease (a relatively comprehensive review of such pathogens is
provided, inter alia, in Mandell et al., 1990, "Principles and
Practice of Infectious Disease, 3rd. ed., Churchill Livingstone
Inc., New York, N.Y. 10036, herein incorporated by reference). As
such, the described animals and cells are particularly useful for
the practice of functional genomics (similar libraries, and methods
of making and screening the same, are discussed in U.S. application
Ser. No. 08/942,806, filed Oct. 2, 1997 the disclosure of which is
herein incorporated by reference in its entirety).
[0083] 5.3.2. The Acquisition of DNA Sequence Information
[0084] The sequencing of cDNA libraries has provided many hundreds
of thousands of expressed sequence tags (ESTs). These sequence tags
are typically thought to identify genes or the coding portion of
DNA. Since genes are thought to code for most, if not all,
potential drug targets, there has been a rush to obtain ESTs
identifying all mammalian genes. However, in spite of the wealth of
sequence data generated thus far, many genes have proven difficult
to identify using established cDNA methods because many genes are
not expressed, are expressed at very low levels, are expressed only
in specific cell types, or are only transiently expressed. Given
that gene trapping can identify genes independent of their
endogenous expression levels gene trapping is an important tool for
gene discovery (as demonstrated by the large number of novel
sequences that have been identified using the described vectors).
Like EST technology, one potential limitation of 5' gene trap
vectors (vectors designed to trap 5' exons) is that only expressed
genes are typically trapped. Accordingly, particularly for the
purposes of gene discovery, ES cells are particularly preferred
target cells because ES cells are thought to be generally
promiscuous in the expression of most genes. Given this
promiscuity, then most genes could be trapped in ES cells using the
presently described vectors. To test the percentage of genes that
can be detected as expressed in ES cells, 23 ESTs from the GenBank
dbest database were selected at random, and primers were
synthesized that would identify the genes by PCR. When these
primers were used in RT-PCR assays using ES cell RNA, all 23 sets
of primers produced product. This indicates that transcripts for
all 23 genes could be detected in ES cells. Given that the 23 ESTs
screened were selected at random, it is likely that they are
largely representative of genes in general and indicate that a
majority of genes that are expressed in other cell types at
sufficiently high levels to have been identified by sequencing of
conventional cDNA libraries are also expressed, in ES cells and are
thus presumably identifiable-using SAselectable marker poly A (5'
gene trap) vectors.
[0085] However, in those instances where genes are either not
expressed or only poorly expressed, a 3' gene trap cassette must be
utilized to trap and identify the genes. In addition, 3' gene trap
cassettes enable the rapid procurement of DNA sequence data from
the trapped gene by, automated means.
[0086] Vectors designed to trap 3' exons have made it possible to
produce large numbers of mutations and rapidly identify the genes
that have been mutated. However, a limitation of initial versions
of such vectors is that selectable marker genes used in the 3' gene
trap are inefficiently utilized by the splicing machinery of most
eukaryotic cells. As a consequence, vectors employing a 3' gene
trap cassette that employ an exon encoding an activity conferring
antibiotic resistance only allow the facile and efficient gene
trapping band identification (using 3' RACE) of a relatively small
proportion of the genes in the genome. Additionally, the inherent
inefficiency of selecting for trapped 3' exons limits the total
number of genes that can be analyzed using such methods.
Consequently, prior to the present invention, only a small portion
of the cellular genome had been effectively trapped/mutagenized
using antibiotic selection-mediated 3' exon trapping.
[0087] The presently described vectors incorporate a 3' gene trap
cassette that typically allows several fold to more than an order
of magnitude greater number of genes to be trapped and identified
by exon sequence as compared to initial 3' gene trap vectors that
utilize an exon encoding a selectable marker activity.
[0088] The presently described vectors can also incorporate 3'
and/or 5' gene trap cassettes that are engineered to increase the
probability of identifying the 5' ends of the open reading frames
of genes. This is significant because the 5' ends of genes often
code for the signal sequence that is found in secreted and
transmembrane proteins. This group of genes is highly enriched for
potential protein therapeutics and drug targets. Given that 5'
noncoding sequences average about 100 bp in length and the average
length gene trap sequence is about 500 bp, gene trapped sequences
generated using the presently described vectors will typically
identify the 5' portion of the tagged open reading frame. This is
especially valuable since 5' ends of genes can be difficult to
obtain due to complicating factors such as high GC content,
secondary structure, and reverse transcriptase's lack of
processivity.
[0089] When a large number of gene traps in known genes were made
and identified using the described vectors, 93% of the gene trap
sequence tags that matched cDNA sequences in GenBank contained the
same or additional 5' sequence. This confirms that the described 3'
gene trap cassette can-be used to identify and characterize the 5'
termini of genes. In fact, the gene trap methods of the present
invention identify the 5' end of genes better than or equal to
other methods described to date.
[0090] One of the major challenges in the field of genomics remains
the isolation and cloning of full length cDNAs for all genes. To
date, this has required the production of cDNA from a wide variety
of tissues, followed by the subsequent sequencing of the individual
cDNAs. As described above, using such methods it can be very
difficult to obtain the 5' ends of cDNAs. Additionally there is the
problem that in order to obtain a complete repertoire of cDNAs,
individual cDNA libraries must made from essentially every
differentiated cell type and at every developmental time point
because genes must be expressed in order to be cloned as ESTs.
[0091] As discussed above, the presently described vectors can be
used for the creation of cDNA libraries. When introduced to cells
in culture, the 3' gene trap cassette produces transcripts of genes
independent of whether or not they are normally expressed in that
cell type. The expression levels of the various trapped genes are
normalized by the inserted promoter so that even genes that are
only expressed at very low levels are identified. Using the
presently described methods and vectors, one can obtain broad cDNA
coverage of the target cell genome from a single library without
having to independently produce multiple cDNA libraries from
multiple cell types that were grown under multiple conditions.
[0092] The presently described 3' gene trap cassette can be
inserted into the genome of tissue culture cells, for example, and
methods (e.g., PCR) can be used that only allow cDNA arising from
trapped genes to be subcloned into the cDNA library. These methods
will increase coverage of the cDNAs produced while substantially
decreasing the labor involved to produce the libraries. As
discussed above, the presently described methods are also
particularly useful in obtaining the 5' ends of genes, and thus
optimize the chances of obtaining full length cDNAs. Examples of
variables that can be used to alter the variety and number of
trapped cDNAs produced using the described vectors include, but are
not limited to, adjusting the multiplicity of infection, and
producing cDNAs from infected target cells that have not been
subject to a period of selective culture in order to select for
cells incorporating and expressing an exogenously introduced
selectable marker. The resulting gene trapped cDNA libraries can be
sequenced to produce a multiplicity of gene trapped coding regions
of genes, that can be used for bioinformatics, gene expression
studies both in situ and in vitro (i.e. hybridization studies, gene
chips (which can also use oligonucleotide sequences corresponding
to the trapped gene sequences), etc.), and the production of gene
trap sequence databases from a variety of animals and plants. These
gene trap sequences can be utilized as probes directly, or
oligonucleotide sequences corresponding to the gene trap sequences
can be used screen libraries by hybridization or PCR. Also, gene
trap sequences identified using the disclosed vectors can be
incorporated into cloning vectors that direct the expression of the
gene trap sequences. For the purposes of the present disclosure, an
isolated polynucleotide sequence having, containing, or otherwise
incorporating such a gene trap sequence (or an oligonucleotide
sequence derived therefrom) shall mean any and all isolated
polynucleotides or vectors minimally incorporating, or comprising,
a contiguous stretch of the described cDNA gene trap sequence (or
an oligonucleotide sequence derived therefrom) inclusive of any
additional naturally occurring or recombinant sequences that may
flank the described gene trap sequence present in such isolated
polynucleotides or vectors.
[0093] Given the speed and efficiency with which DNA (and
corresponding amino acid) sequence information can be obtained
using the described methods and vectors, it is clear that they
provide important tools for conducting genetic screens in any cell
(including primary and secondary cells) or cell line that contains
splicing machinery and genes containing introns. The presently
described gene trap vectors represent a particularly important
technological breakthrough because the described 3' gene trap
cassette allows for the rapid identification of roughly 13 fold (as
empirically determined) more genes than can be efficiently obtained
using conventional 3' gene trap vectors that rely upon gene
trapping as detected by antibiotic selection. Combined with the
frequency of obtaining novel gene sequences, the observed increase
in identifiable gene trap targets will provide sequence information
for large numbers of novel genes and gene sequences. Additionally,
when ES cells are targeted, each of these novel sequences represent
both newly identified gene (and potential drug or drug target) and
a "knockout" cell and a potential "knockout" embryo or animal.
[0094] The rapid sequence acquisition features of the presently
described methods, libraries, cells, and animals are well suited
for rapidly identifying the molecular/genetic basis for disease as
well as genetically determined advantages such as prolonged
life-span, low cholesterol, low blood pressure, resistance to
cancer, low incidence of diabetes, lack of obesity, or the
attenuation of, or the prevention of, all inflammatory disorders,
including, but not limited to coronary artery disease, multiple
sclerosis, rheumatoid arthritis, systemic lupus erythematosus, and
inflammatory bowl disease. Given the wide coverage provided by the
large number of target genes, a particularly useful application of
the described techniques involves the characterization and analysis
of coding region single nucleotide polymorphisms (cSNPs).
[0095] 5.4. Methods of Introduction
[0096] The presently described 3' gene trap cassette is preferably
introduced into target cells as a structural component of any of a
wide range of vectors that can be specifically or nonspecifically
inserted into the target cell genome (recombinase systems can also
be used to insert the 3' gene trap cassette). Suitable vectors that
can be used in conjunction with the presently disclosed features
include, but are not limited to, herpes simplex virus vectors,
adenovirus vectors, adeno-associated virus vectors, retroviral
vectors, lentiviral vectors, pseudorabies virus, alpha-herpes virus
vectors, and the like. A thorough review of viral vectors,
particularly viral vectors suitable for modifying nonreplicating
cells, and how to use such vectors in conjunction with the
expression of polynucleotides of interest can be found in the book
Viral Vectors: Gene Therapy and Neuroscience Applications Ed.
Caplitt and Loewy, Academic Press, San Diego (1995).
[0097] Where retroviral vectors are used to deliver the presently
described 3' gene trap cassette, the retroviral vectors can be used
in conjunction with retroviral packaging cell lines such as those
described in U.S. Pat. No. 5,449,614 ('614 patent") issued Sep. 12,
1995, herein incorporated by reference. Where non-mouse animal
cells are to be used as targets for generating the described
libraries, packaging cells producing retrovirus with amphotropic
envelopes will generally be employed to allow infection of a broad
range of host cells. Alternatively, pantropic packaging cell lines
such as, but not limited to, the cell line 293/GPG (Ory et al.,
1996, Proc. Natl. Acad. Sci., USA, 93:11400-11406, and U.S. Applic.
Ser. No. 08/651,050, herein incorporated by reference) can be used
to package the described vectors, or a suitable viral, e.g.,
retroviral, receptor gene can be transfected into the non-murine,
e.g., human, target cells.
[0098] Additionally, the described retroviral vectors can be
packaged in conjunction with chimeric integrase molecules as
described in U.S. application Ser. No. 08/907,598, herein
incorporated by reference. Typically, the LTRs used in the
construction of the packaging cell lines are self-inactivating.
That is, the enhancer element is removed from the 3' U3 sequences
such that the proviruses resulting from infection would not have an
enhancer in either LTR. An enhancer in the provirus may otherwise
affect transcription of the mutated gene or nearby genes.
Typically, the gene trap cassettes of the described retroviral
vectors are present in an orientation opposite the normal
functional orientation of the retroviral LTRs.
[0099] An additional advantage of using viral, and particularly
retroviral, infection (e.g., biological methods) to deliver
recombinant viral vectors incorporating, inter alia, the 3' gene
trap cassette is that viral infection is more efficient than
standard nonbiological methods of delivering genetic material to
target cells. Where recombinant genetic material is delivered by
retroviral infection, the recombinant RNA genome of the retrovirus
is reverse transcribed within the target cell, and the retroviral
integrase packaged within the infecting virus subsequently mediates
the essentially non-specific integration of the vector (and 3' gene
trap cassette) into the target cell genome. Accordingly, additional
embodiments of the present invention include methods of inserting
recombinant vectors incorporating the described 3' gene trap
cassette that are mediated by integrase or recombinase activities
that are either exogenously added to the target cell, or do not
naturally occur within the target cell.
[0100] Representative retroviral vectors that can be adapted to
incorporate the presently described 3' gene trap cassette are
described, inter alia, in U.S. Pat. No. 5,521,076, and U.S.
application Ser. No. 08/942,806, filed Oct. 2, 1997, and Ser. No.
08/907,598 filed Aug. 8, 1997 (which further disclose screening
protocols that can be used to assay for specific gene trap events
either biochemically or phenotypically) the disclosures of which
are herein incorporated by reference.
[0101] Typically, the orientation of the gene trap cassettes
incorporated into retroviral vectors is opposite to that of normal
retroviral transcription; however, retroviral vectors are also
contemplated where one or more gene trap cassettes are incorporated
in the same orientation as normal retrovirus transcription.
Typically, the reason for placing a gene trap cassette in an
opposite orientation relative to the LTRs is that the presence of
engineered control elements such as polyadenylation signals, splice
sites and the promoters, can interfere with the proper
transcription of the retroviral genome in the packaging cell line,
and subsequently reduce retroviral titers.
[0102] Additionally, since a `cryptic` splice donor sequence is
found in the inverted LTRs, this splice donor can be removed by
site specific mutagenesis so that it does not adversely effect
trapping related splicing events. Optionally, the LTR promoter
and/or enhancer function can be inactivated by deleting all or a
portion of the promoter and/or enhancer sequences.
[0103] 5.5. Molecular Genetic Applications
[0104] 5.5.1. Gene Activation
[0105] Another embodiment of the present invention is the use of
the 3' gene trap cassette to screen for both gain or loss of
function in animals, e.g., mice, and cultured cells. When vectors
are used that incorporate a 3' gene trap having an exon that lacks
a translation start site, a given target gene can be either over
expressed or insertionally inactivated (mutated) depending on where
the vector has integrated within the gene. If the vector lands in
an intron preceding the start of translation, it can cause over
expression of the full open reading frame encoding the cellular
protein. Using these types of trapping events one can conduct
genetic screens based upon gene over expression. These screens
could be done in cell culture or in mice, for example, in order to
discover genes that play significant roles in disease processes.
For example, these screens could be used to identify oncogenes by
introducing the 3' gene trap cassette into primary embryo
fibroblasts and selecting for an ability to grow in soft agar.
Alternatively, assaying for cells able to escape cellular
senescence would also allow the identification of potential
oncogenes.
[0106] In order to demonstrate that the present vectors can be used
to select for trapping events that result in gene expression (or
over expression), an experiment was conducted to determine whether
genes could be trapped that allow expression of factors that
promote ES cell differentiation. Large numbers of genes were
trapped in cell culture on tissue culture plates. Multiple plates
were infected in parallel and the resulting plates were observed
for ES cell differentiation. Some plates showed almost no
differentiation whereas some plates-would have 100% differentiated
ES cells. This differentiation is likely the result of the
expression of a gene that is either a differentiation factor or
causes the ES cells to produce a differentiation factor and pump it
into the media resulting in differentiation of all the cells on the
dish. Importantly, this also demonstrates that the 3' gene trap
system can be used to activate and screen for secreted molecules
that produce specific biological responses by testing supernatants
of the gene trap pools. Screening for ES cell differentiation
factors is one example but this technique can be used to identify
secreted molecules involved in any cellular response of interest.
One could for example screen for secreted molecules that induce
apoptosis or hematopoietic cell differentiation.
[0107] Given the increased expression afforded by the presently
described 3' gene trap cassette, an additional application of the
presently described 3' gene trap cassettes is gene activation. For
example, after suitable animal cells are treated or infected with
vectors that incorporate the described 3' gene trap cassette, if
the vector integrates into the 5' intron of an otherwise quiescent
gene, the gene can be "activated" and over expressed by the
regulatory elements, e.g., enhancer/promoter elements incorporated
into the 3' gene trap cassette. Using such nontargeted,
nonspecific, or biased nonspecific (see U.S. Applic. Ser. No.
08/907,598) gene activation, modified animal cells, including human
cells, can be produced that over express any of a wide variety of
natural cellular products.
[0108] Products that are particularly deemed useful for such
application include normally secreted molecules or hormones such
as, but are not limited to, erythropoietin (epo), tPA, cytokines,
interleukins, tumor suppressors, chemokines, secreted molecules,
G-CSF, GM-CSF, nerve growth factor (NGF), ciliary neurotropic
factor (CNTF), brain-derived neurotropic factor (BDNF),
interleukins 1-2 and 4-14, tumor necrosis factor-.alpha.
(TNF-.alpha.), .alpha. or .gamma. interferons and the like, leptin,
and factors VIII and IX.
[0109] The activation of quiescent genes, over expression, or
abnormal expression of genes by the 3' gene trap cassette can also
be used to study gene function within an organism. Gene over
expression may be used to study gene function, and by trapping
genes with the 3' cassette, genes can be over expressed within an
organism. The over expression may cause a phenotype in the organism
that sheds light on the function of the gene. For example, the
specifically described retroviral vector contains the PGK promoter
which is ubiquitously expressed. When a gene is trapped in ES cells
and the ES cells are subsequently used to make mice, the mice will
over express the trapped gene ubiquitously. Further modifications
could be made for instance to use a promoter that is
tissue-specific rather than the PGK promoter in order to over
express the trapped gene in a tissue-specific manner. The albumin
promoter could be used for liver-specific over expression.
Additionally, a signal sequence could be added to the 3' trapping
cassette to cause secretion of the trapped gene's protein product
from the cell into the extracellular space, into the bloodstream,
or mammary excretions. This could facilitate the understanding of
gene function.
[0110] Since over expression is one possible outcome of a gene trap
event using the 3' gene trap cassette, it could prove useful to be
able to remove the 3' trap/over expression component. This can be
accomplished by flanking any essential component of the 3' trap
cassette (essential components may include the promoter, the exon,
the splice donor, the intronic sequence or the entire cassette)
with recombinase sites such as those recognized by the flp or cre
recombinases. In this way, the addition of the corresponding
recombinase in cells or in the organism allows one to conditionally
reverse or remove over expression as desired.
[0111] For gene activation, a generic 3' gene trap cassette can be
employed that incorporates an exon that is native to, or compatible
with the biology of, the target cell, or a specific 3' gene trap
cassette can be constructed that utilizes a specific exon and
splice donor site from a known gene. Optionally, given that gene
activation using 3' gene traps typically requires that the vector
integrate or insert upstream (5') from the translation start site
of the activated gene, the gene activation exon will preferably not
incorporate a functional translation start site (IRES or Kozak
sequence), or will only incorporate a nominally functional (or
cryptic) translation start site capable of mediating only
incidental levels of translational activity. Alternatively, the
incorporation of an internal ribosome entry site into the exon can
result in the over expression of the 3' gene trapped, or activated,
gene.
[0112] Where a fusion product between the 3' gene trap exon and a
downstream cellularly encoded exon (e.g., that only encodes a
particular domain of the protein product of the "activated" gene)
is desired, the gene trap vector will typically incorporate a
functional translation start site or internal ribosome entry site
and translation start site.
[0113] Alternatively, in those instances where the described
vectors integrate downstream from the translation start site, the
gene will be mutated, and screens to detect such loss of function
can be employed. An example of this approach would be to mutate
fibroblasts, for example, with the present vectors and screen for
hits that allow growth in soft agar. In this way genes encoding
tumor suppressors could be identified. Although only 1 of 2 alleles
will typically be trapped, the genome of cells in culture is often
unstable and, through selection, events can be found in which the
second allele is lost. This makes it possible to also screen for
recessive phenotypes.
[0114] 5.5.2. Function-Based Gene Discovery
[0115] The gene activation capabilities of the presently described
vectors have further application for selective gene discovery. For
example, proliferation deficient cells (e.g., tumor suppressor or
DNA repair knockout cells, etc.) can be infected with the presently
described gene activation vectors. The infected cells can
subsequently be screened for cells/colonies that display a
partially or fully corrected proliferation phenotype. When cells
displaying the corrected phenotype are identified, the "activated"
genes responsible for correcting the proliferation deficient
phenotype can be rapidly identified by DNA sequencing using, for
example, 3' RACE. Typically, genes that partially or fully correct
a DNA repair mutation (mutations often associated with cancer in
animals and humans), are more likely to encode a tumor suppressor,
or possibly oncogene, activity (see generally, Selten et al., 1985,
EMBO J., 4(7):1793-17988).
[0116] Conversely, cancerous or transformed cells (or cell lines)
can be infected with the described gene activation vectors and
subsequently subject to various cytotoxic agents that are toxic to
growing, or rapidly growing, cells (see generally Wilson et al.,
1986, Cell, 44:477-487; Stephenson et al., 1973, J. Virol.,
11:218-222; Sacks et al., 1979, Virology, 97:231-240; Inoue et al.,
1983, Virology 125:242-245; Norton et al., 1984, J. Virol.,
50:439-444; Cho et al., 1976, Science, 194:951-953; Steinberg et
al., 1978, Cell 13:19-32; Maruyama et al., 1981, J. Virol.,
37:1028-1043; Varmus et al., 1981, Cell, 25:23-26; Varmus et al.
1-981, Virology, 108:28-46; Mathey-Prevot et al., 1984, J. Virol.,
50:325-334; and Ryan et al., 1985, Mol. Cell. Biol., 5:3477-3582).
Preferably, the infected cells are exposed to the cytotoxic or
chemotherapeutic agents under conditions where cells that have
reverted to a non-transformed phenotype are contact inhibited, and
are less susceptible to cytotoxic agents present in the culture
medium. This further contributes to the preferential elimination of
rapidly growing or transformed cells and, after several cycles, the
eventual isolation of cells that have partially or fully reverted
to the noncancerous or nontransformed phenotype. The "activated"
genes responsible for correcting the transformed phenotype, or
suppressing the tumorigenic phenotype, can subsequently be rapidly
identified by DNA sequencing using the described 3' RACE
protocols.
[0117] The presently described-methods are also useful for
identifying the genetic basis of cancer. Cancers that may be
studied, and potentially corrected, using the presently described
methods include, but are not limited to: Cardiac: sarcoma
(angiosarcoma, fibrosarcoma, rhabdomyosarcoma, liposarcoma),
myxoma, rhabdomyoma, fibroma, liporfa and teratoma; Lung:
bronchogenic carcinoma (squiamous cell, undifferentiated small
cell, undifferentiated large cell, adenocarcinoma), alveolar
(bronchiolar) carcinoma, bronchial adenoma, sarcoma, lymphoma,
chondromatous hamartoma, mesothelioma; Gastrointestinal: esophagus
(squamous cell carcinoma, adenocarcinoma, leiomyosarcoma,
lymphoma), stomach (carcinoma, lymphoma, leiomyosarcoma), pancreas
(ductal adenocarcinoma, insulinoma, glucagonoma, gastrinoma,
carcinoid tumors, vipoma), small bowel (adenocarcinoma, lymphoma,
carcinoid tumors, Karposi's sarcoma, leiomyoma, hemangioma, lipoma,
neurofibroma, fibroma), large bowel (adenocarcinoma, tubular
adenoma, villous adenoma, hamartoma, leiomyoma); Genitourinary
tract: kidney (adenocarcinoma, Wilm's tumor [nephroblastoma],
lymphoma, leukemia), bladder and urethra (squamous cell carcinoma,
transitional cell carcinoma, adenocarcinoma), prostate
(adenocarcinoma, sarcoma), testis (seminoma, teratoma, embryonal
carcinoma, teratocarcinoma, choriocarcinoma, sarcoma, interstitial
cell carcinoma, fibroma, fibroadenoma, adenomatoid tumors, lipoma);
Liver: hepatoma (hepatocellular carcinoma), cholangiocarcinoma,
hepatoblastoma, angiosarcoma, hepatocellular adenoma, hemangioma;
Bone: osteogenic sarcoma (osteosarcoma), fibrosarcoma, malignant
fibrous histiocytoma, chondrosarcoma, Ewing's sarcoma, malignant
lymphoma (reticulum cell sarcoma), multiple myeloma, malignant
giant cell tumor, chordoma, osteochronfroma (osteocartilaginous
exostoses), benign chondroma, chondroblastoma, chondromyxofibroma,
osteoid osteoma and giant cell tumors, Nervous system: skull
(osteoma, hemangioma, granuloma, xanthoma, osteitis deformans),
meninges (meningioma, meningiosarcoma, gliomatosis), brain
(astrocytoma, medulloblastoma, glioma, ependymoma, germinoma
(pinealoma) glioblastoma multiforme, oligodendroglioma, schwannoma,
retinoblastoma, congenital tumors), spinal cord (neurofibroma,
meningioma, glioma, sarcoma); Gynecological: uterus (endometrial
carcinoma), cervix (cervical carcinoma, pre-tumor cervical
dysplasia), ovaries (ovarian carcinoma [serous cystadenocarcinoma,
mucinous cystadenocarcinoma, endometrioid tumors, celioblastoma,
clear cell carcinoma, unclassified carcinoma], granulosa-thecal
cell tumors, Sertoli-Leydig cell tumors, dysgerminoma, malignant
teratoma), vulva (squamous cell carcinoma, intraepithelial
carcinoma, adenocarcinoma, fibrosarcoma, melanoma), vagina (clear
cell carcinoma, squamous cell carcinoma, botryoid sarcoma
[embryonal rhabdomyosarcoma], fallopian tubes (carcinoma);
Hematologic: blood (myeloid leukemia [acute and chronic], acute
lymphoblastic leukemia, chronic lymphocytic leukemia,
myeloproliferative diseases, multiple myeloma, myelodysplastic
syndrome), Hodgkin's disease, non-Hodgkin's lymphoma [malignant
lymphoma]; Skin: malignant melanoma, basal cell carcinoma, squamous
cell carcinoma, Karposi's sarcoma, moles, dysplastic nevi, lipoma,
angioma, dermatofibroma, keloids, psoriasis; Breast: carcinoma and
sarcoma, and Adrenal glands: neuroblastoma.
[0118] Modifications to the above studies include the use of
retroviral gene trapping vectors in conjunction with a chimeric
integrase that targets, or biases, retroviral integration to genes
regulated by specific control sequences or transcription factors.
For example, the presently described retroviral gene activation
vectors can be packaged into a virus incorporating a p53-chimeric
integrase (as described in U.S. Applic. Ser. No. 08/907,598) that
preferentially targets vector-mediated gene activation to genes
regulated by this known tumor suppressor activity.
[0119] Appropriately modified, the presently described vectors
additionally provide a vehicle for placing virtually any DNA
sequence throughout the target cell genome and rapidly identifying
where the vectors have integrated. A growing number of DNA
sequences have been identified that one might wish to place
throughout the genome. Examples of such sequences include
recombination sites such as frt sites or lox P sites respectively
identified by flp and cre recombinases. Although these sites can be
placed throughout the genome by homologous recombination or other
transformation methods, the present invention allows for the rapid
identification and cataloging of the integration sites using
automated processes. These recombination sites can be used for
specific DNA insertion or, along with insertions in other
positions, and they can be used to create chromosomal
rearrangements such as inversions, deletions and translocations.
Thus the presently described vectors are particularly useful for
studying gene function through chromosomal rearrangements. Other
sequences one might wish to place throughout the genome include,
but are not limited to, tet, ecdysone, or estrogen receptor DNA
binding sites or response elements. These sites are commonly used
for inducing or repressing gene expression and by placing these
sites throughout the genome, preferably in tens of thousands of
different genes, will provide an opportunity to create conditional
or tissue-specific regulation of gene expression.
[0120] An additional feature of the described mutagenesis strategy
is that vector encoded sequences and structural features can be
exploited to allow the rapid identification of genomic DNA directly
flanking the integrated gene trap constructs. This approach
exploits the fact that exon sequence identifying the gene into
which the construct has integrated is accessible via the sequence
acquisition capabilities of the 3' gene trap cassette.
Oligonucleotides that hybridize to suitably identified (by
bioinformatics) cellular exons can be used in conjunction with
oligonucleotides that hybridize to vector encoded sequence in PCR
reactions that produce templates that can be cloned, or directly
sequenced to identify the integration site. Where PCR might not
prove wholly suitable, PCR reactions can be augmented by using
vectors that have been-engineered to incorporate a relatively rare
cutter restriction site, e.g., Sfi I, etc. Such restriction sites
can be exploited to subclone the PCR products, or even genomic
sequence flanking the vector, into suitable cloning vectors, or
libraries thereof, that can subsequently be used to, for example,
identify vector integration sites using established methods, e.g.,
PCR, long-range PCR, cycle sequencing, etc.
[0121] Another aspect of the present invention places a gene
encoding a recombinase activity (e.g., flp or cre, etc., see U.S.
Pat. Nos. 5,654,182 and 4,959,317 herein incorporated by reference)
into the vector containing the described 3' gene trap cassette. The
recombinase gene can be expressed in a manner similar to that
described for the marker genes, supra. In brief, the recombinase
can be expressed from an independent expression cassette, can be
incorporated into a 5' gene trap, or can be expressed from a vector
promoter. Depending on the strategy employed to express the
recombinase, it can be present on a separate construct, or in the
vector either 5' or 3' from the 3' gene trap cassette. By
incorporating the recombinase gene into the described gene trap
vectors, a collection, or library, of mutated cells can be obtained
that express the recombinase in essentially the same pattern as the
various trapped genes. The above discussion describes just a few
examples of how the presently described vectors can be used to
place any DNA sequence throughout the genome in a manner that
allows for the rapid identification of where the vectors have
integrated into the target cell genome. Those skilled in the art
will appreciate that the described vectors constitute technology of
broad applicability to the field of eukaryotic molecular genetics.
As such any of a wide variety of vectors and genetic applications
are contemplated as within the scope of the present disclosure. For
example, retroviral vectors can be designed that contain a 3' gene
trap cassette without the other described features, or downstream
from a mutagenic mini-exon and/or a transcription terminator and/or
a self-cleaving RNA sequence. Additionally, 3' gene traps can be
designed with tandem promoters where the one of the promoters is
inducible. Alternatively, hybrid gene traps are also contemplated
where, for example, the SAneo from the described 5' gene trap had
been fused, preferably in-frame, to the exon of the described 3'
gene trap-cassette (i.e., deleting the pA and promoter sequences).
Such a construct takes-advantage both the enhanced SA and SD
functions of the described gene trap cassettes, and allows for the
automated identification of the genes expressed in a given target
cell. Optionally, such a construct is used in conjunction with an
upstream mutagenic mini-exon.
[0122] 5.5.3. Conditional Mutagenesis
[0123] Another aspect of the present invention is the ability to
produce mutations that can be switched on and off temporally and
spatially in cells or in an organism or animal. The ability to
mutate a gene only in a specific place or at a specific time has
important implications for understanding gene function. For
example, the orientation of SA.beta.geo within an intron regulates
its ability to trap, and thus mutate, the normal transcript
produced by the trapped gene. Suitably oriented frt recombinase
sites can be used in conjunction with flp recombinase to effect the
above genome rearrangements (i.e., "flip", or even remove, the gene
trap cassette and thus turn the mutation "on" or "off").
Alternatively, the cre/lox system, for example, can also be
employed to produce conditional mutations where a given mutagenic
construct can be selectively modified (replaced, flipped, deleted,
etc.) only in tissues or cells expressing the cre recombinase.
[0124] To validate the above concept, a vector was constructed that
placed the SA.beta.geo cassette within two inverted lox sites.
These sites are recognized by the cre recombinase which can
effectively flip DNA sequences located in between the lox sites. A
retroviral vector containing SA.beta.geo flanked by inverted lox
sites was integrated into'an intron of the HPRT gene by homologous
recombination. When SA.beta.geo was present in the forward
orientation, HPRT function was abolished as demonstrated by
survival of cells in the presence of 6-thioguanine. However, when
cre recombinase was expressed in these cells, the orientation of
SA.beta.geo was flipped to the reverse orientation and HPRT
function was regained as demonstrated by growth of cells in HAT
containing medium. Thus, the HPRT gene was effectively switched off
or on by flipping the orientation of SA.beta.geo. Accordingly, an
additional embodiment of the present invention is drawn to vectors
that enable the selective and reversible modulation of gene
expression. Using a similar methodology, gene trap mutations can
also be made conditional or tissue-specific by linking recombinase
expression, and hence the flipping of SA.beta.geo, for example, to
various stimuli/control elements. It is also possible to engineer
an allelic series using a recombinase-mediated strategy to "swap."
in or out, i.e., or, engineer, any of a variety of more or less
mutagenic constructs (appropriately flanked by lox or
frt-sites).
[0125] An alternative strategy for using the presently described
vectors for tissue-specific or regulatable expression is to place
specific DNA binding sites such as frt or lox sites within the
LTRs. With lox sites in the LTRs, once an insertion is made and
identified, the cre recombinase, for example, can be added and used
to remove the entire insert except for one LTR containing a single
frt or lox site. Additionally, a DNA response element that allows
regulatable gene expression can be incorporated, wholly or in part,
in conjunction with the recombinase sites. When the vector or gene
trap insert is removed by the recombinase activity, the same
recombination event that results in the production of the single
LTR will also produce a functional DNA response element. This
single LTR does not interfere with gene function, but the DNA
element can be used to modulate gene expression. Typical DNA
elements or operators used for modulating eukaryotic gene
expression include the tet, ecdysone or estrogen DNA binding sites.
The presence of the tet operator in combination with the tet
repressor protein would allow the expression of the gene to be
modulated up and down. This can be carried out in mice by breeding
the line of mice carrying the LTR insertion with lines of mice
expressing the tet repressor either ubiquitously or only in
specific tissues.
[0126] Another embodiment of the present invention is based on the
fact that the flp recombinase, for example, can mediate the
replacement of frt flanked integrated vector sequences with
exogenously added frt flanked sequences. Accordingly, once a
suitably constructed vector (incorporating flanking recombinase
sites) is incorporated into a given region of the target cell
genome, virtually any of a wide variety of DNA sequences (i.e.,
promoters, enhancers, IRES, response elements, etc.) that also
incorporate the same flanking recombinase sites can be exchanged
into or out of the vector by employing the proper recombinase
protein.
[0127] 5.5.4. Biological Assays
[0128] As is evident, vectors, particularly retroviral vectors,
incorporating the presently described 3' gene trap cassette can be
used to mutagenize, activate, or control the expression of
endogenous genes in a wide variety of eukaryotic target cells.
Accordingly, the presently described vectors are particularly
useful to practice molecular genetic techniques in plants as well
as higher eukaryotes such as birds, fish, and mammals. Examples of
such molecular genetic techniques include both in vitro and in vivo
screens for gene activation, mutation, and regulation.
[0129] For example, CD4 positive human T cells can be infected with
the presently described vectors in vitro, and subsequently infected
with a cytopathic strain of human immunodeficiency virus (HIV).
Cells that are capable of surviving HIV infection, can be isolated
and rapidly screened for genetic mutations that are associated with
HIV resistance.
[0130] Another screening strategy that can be employed in vitro is
mutating transformed cells with the described gene trap vectors and
selecting for mutations that prevent rapid proliferation of the
transformed cells. This strategy can be used to identify oncogenes
or tumor suppressor genes. After mutation of the cells, various
chemicals can be used to kill cells that divide rapidly in order to
select for insertions in genes that play a role in cell
proliferation and the transformed phenotype. One example of a
chemical that kills rapidly proliferating cells is
bromodeoxyuridine (BrdU), Pestov and Lau, 1994, Proc. Natl. Acad.
Sci., USA, 91(26):12549-12553. BrdU preferentially intercalates
into the DNA of rapidly dividing cells and, after the addition of
Hoechst 33258, treatment with fluorescent light negatively selects
against rapidly dividing cells while simultaneously selecting for
slow growing cells.
[0131] Another application of cells transduced with the described
vectors is cell based in vitro phenotypic screens that can be
conducted using heterozygous cells, or using cells that have been
cultured or manipulated to homozygosity (using, for example, high
concentrations of antibiotics to select for homozygous
representation of the corresponding selectable marker gene
incorporated into an applicable gene trap vector) prior to such
screening assays.
[0132] An in vivo assay contemplated by the present invention
includes the application of vectors employing the 3' gene trap
cassette to mutagenize and screen animals in vivo. In these assays,
the present vectors are used in place of, or in addition to
classical chemical mutagens such as, for example, ENU (see
generally, Vitaterna et al., 1994, Science, 264:719-725). For
example, test animals can be infected in various locations, and
with varying concentrations of the presently described viral
vectors. Preferable modes of administration include oral,
intranasal, rectal, topical, intraperitoneal, intravenous,
intramuscular, subcutaneous, subdermal, intracranial, intrathecal,
and the like. The aberrant cellular phenotypes resulting from such
mutagenic stimuli can then be identified, isolated, and screened.
Where tumor cells are observed and isolated, 3' RACE can be used to
rapidly identify the mutation associated with the tumorigenic
phenotype, and thus identify a candidate tumor suppressor gene or
potential oncogene.
[0133] An additional in vivo application of the presently described
vectors involves the generation of mutant transgenic, and somatic
transgenic, cells., animals, and plants that are abnormally
resistant or susceptible to infection by pathogens associated with
infectious diseases.
[0134] Another powerful application of the present invention is the
large scale production of mutant nonhuman transgenic animals. Such
nonhuman transgenic animals may include, for example, transgenic
pigs, transgenic rats, transgenic rabbits, transgenic cattle,
transgenic goats, and other transgenic animal species such as birds
and fish, particularly mammalian species, known in the art.
Additionally, bovine, ovine, and porcine species, other members of
the rodent family, e.g., rat, as well as rabbit and guinea pig and
non-human primates, such as chimpanzee, may be used to practice the
present invention. Particularly preferred animals are rats,
rabbits, guinea pigs, and most preferably mice. Both somatic cell
transgenic animals (see above), and germ line transgenic animals
are specifically contemplated. Additionally, such animals are a
source of tissues and cells for further gene trapping studies using
cultured cells.
[0135] The production of mutations in mouse embryonic stem cells by
homologous recombination is well established and has proven useful
for studying gene function in a mammalian system. However,
homologous gene targeting suffers from a number of limitations. One
such limitation is the need for a gene to be both known and mapped
in order to determine exon/intron structure of the genomic
sequence. Even when a gene and its structure are known, a targeting
vector must be made for each individual gene one wishes to mutate.
This limits the speed at which large numbers of genes can be
mutated by homologous recombination. The presently described
methods of non-homologous, or nonspecific, 3' gene trapping and
mutation do not suffer from the above limitations. Generally,
nonspecifically inserted, or nontargeted, vectors can be
distinguished from vectors designed for homologous recombination by
the fact that such vectors lack the (often extensive) flanking
regions of homologous targeting sequence typical of DNA vectors
designed to insert sequence by homologous recombination (see, for
example, U.S. Pat. No. 5,733,761 herein incorporated by
reference).
[0136] Other methods can be used to create mutations in mice. These
include chemical or radiation induced mutations which can be used
to mutate genes without any prior knowledge of the gene. These
mutations can be made on a large scale but often require lengthy
and involved processes to identify the mutated genes by, for
example, positional cloning. Additionally, these mutations are
identified only after large numbers of mice are screened for
phenotypes. This necessitates a large mouse colony, the great
expense of maintaining this colony, and time for breeding animals.
Methods are required that allow the rapid mutation of genes
regardless of prior knowledge of the gene and allow the gene to be
easily identified. Gene trapping as described in the present
invention confers the ability to mutate large numbers of genes and
to allow the (almost) simultaneous identification of the mutations
while still in the embryonic stem cell stage. This allows for
substantial analysis before without incurring the costs of large
scale mouse production, and, as discussed supra, provides a
powerful gene discovery component. Mice can subsequently be
produced from ES cells containing gene trap mutations in the genes
selected, and the resulting phenotypes can-be rapidly identified
and characterized. The resulting knockout mice can subsequently be
bred with other mouse strains, and, back crossed to produce
congenic or recombinant congenic animals that allow for the
evaluation of the gene trap mutation in different genetic
backgrounds. A representative listing of various strains and
genetic manipulations that can be used to practice the above
aspects of the present invention (including the ES cell libraries)
is provided in "Genetic Variants and Strains of the Laboratory
Mouse" 3rd Ed., Vols. 1 and 2, 1996, Lyon et al., eds., Oxford
University Press, NY, N.Y., herein incorporated by reference in its
entirety.
[0137] Given that altered cellular phenotypes can be associated
with the presently described methods of gene trapping and
activation, additional aspects of the invention are the use of
screening assays to detect altered cellular and animal phenotypes.
Altered phenotypes can also be detected upon exposing the mutated
cells and animals to exogenous materials and compounds.
Additionally, the genes/proteins associated with the mutant
phenotypes can be isolated and subject to further biochemical
analysis to identify drug candidates that can alter, replace,
interact with, inhibit, or augment the normal function of the
protein.
[0138] The present invention is further illustrated by the
following examples, which are not intended to be limiting in any
way whatsoever.
6.0. EXAMPLES
[0139] When vectors containing both SA.beta.geo (as a 5' exon trap)
and PGKpuroSD (as a 3' exon trap) were tested, it was found that 13
times as many G418 resistant-colonies were obtained as compared to
puro resistant colonies. This indicated that, in many cases, when
SA.beta.geo trapped a gene, the puro SD portion of the gene trap
vector was unable to effectively trap the 3' portions of the same
gene (as evidenced by the failure to confer puromycin resistance to
the target cell) In addition, when the G418 resistant colonies were
isolated and subjected to 3' RACE to determine whether puro was
splicing into downstream exons but not at sufficiently high levels
to provide puro selection, it was found that only about 10% of the
colonies yielded a 3' RACE product. Moreover, the sequence data
indicated that splicing was not occurring in the majority of cases.
These data-indicated that the PGKpuroSD 3' gene trap cassette could
only splice into and trap downstream exons of genes with limited
efficiency. Similar inefficiencies have also been observed using a
variety of other selectable markers in addition to puro. This could
be-due to the fact that most selectable markers are derived from
microorganisms. For example, the puro gene was derived from
Streptomyces alboniger and therefore incorporates a codon usage
that is distinct from that typically used by mammalian cells.
[0140] In order to test whether codon usage was responsible for the
observed inefficiency in splicing, a puro gene was synthesized that
incorporated an optimal mammalian codon usage. However, 3' gene
trap cassettes that incorporated the modified puro exon were not
efficiently spliced. Another possible reason for inadequate
splicing is that the puromycin marker is 700 bp long whereas the
average length of a first exon is only about 100 bp. Thus, it
further remained possible that placing a selectable marker gene
next to a promoter hindered the optimal recognition of the puro
exon and splice donor sequence by the splicing machinery.
[0141] Given the important discovery that the cellular RNA splicing
machinery could only process the puro gene exon with limited
efficiency, it was reasoned that 3' gene trap cassettes
incorporating naturally occurring mammalian exons might exhibit
markedly enhanced splicing, and hence trapping, efficiencies. To
test this hypothesis, a 3' gene trap cassette was engineered that
replaced the puro exon and splice donor site with a naturally
occurring mouse exon with a native splice donor sequence as well as
a portion of the naturally occurring intronic sequence following
the splice donor site (the first exon of the mouse btk gene,
nucleotides 40,043 to 40,250 of GenBank accession number MMUSB105).
This cassette was subsequently inserted 3' to the SA.beta.geo gene
in a viral gene trap vector. The first exon of the mouse btk gene
was selected because it is about the size of an average mammalian
first exon and, importantly, it had previously been determined
that, although it naturally occurs in the murine genome, the btk
gene is not expressed in murine ES cells. This feature is important
because if it were expressed in ES cells, the 3' RACE product would
always be contaminated with btk sequence from the endogenous gene
and might hinder the ability to identify the trapped genes.
Consequently, a preferred feature of the 3' gene trap cassette exon
is that it is derived from a naturally occurring gene that is not
normally expressed by the target cell, or not expressed absent
external stimulus or manipulation.
[0142] Exons that can be incorporated into the presently described
3' gene trap cassette can be taken or derived from sequences that
naturally occur in any of a wide variety of eukaryotic cells (e.g.,
yeast, insect, fungi, plants, birds, reptiles, fish, etc.),
although animal cells, specifically mammalian cells, are typically
preferred. Alternatively, exons can be designed and synthesized
(e.g., "consensus" exons) such that they can be efficiently and
functionally processed by the mRNA processing machinery of the
eukaryotic target cell (e.g., splicing, capping, polyadenylation,
transport, and degradation).
[0143] Although the first exon of btk has been specifically
exemplified herein, the present invention is not limited to this
exon. Virtually any naturally occurring exon of an eukaryotic gene,
series of exons from one or more eukaryotic genes, consensus exon,
or synthetic exon or exons that are readily recognized and
efficiently processed by the target cell RNA processing and
expression machinery can be incorporated into the presently
described 3' gene trap cassette. Typically, the first exons are
less than about 1,000 bp in length, more preferably less than about
700 bp, and more preferably less than about 500 bp, and most
preferably less than about 300 bp in length. Examples of such first
exons can be found in, for example, GenBank, and include, but are
not limited to, the first exons from human growth hormone,
erythropoietin, hprt, metallothionein I and II, maize, wheat, or
soybean ribulose 1,5-bisphosphate carboxylate, rat preproinsulin,
male sterility 2 (MS2) gene, prolifera (PRL) gene, etc.
[0144] Given that typical antibiotic resistance markers are not
native to animal or mammalian cells, markers that confer antibiotic
resistance or sensitivity (Herpes thymidine kinase) to mammalian
target cells are generally not preferred for incorporation into the
presently described 3' gene trap cassettes. Similarly, given that
typically available enzymatic markers that might be used in
chromogenic assays for the detection and selection of gene trap
events (such as .beta.-galactosidase, horse radish peroxidase,
bacterial alkaline phosphatase, etc.) are also not native to the
mammalian genome, such genes are not preferred for the practice of
the present invention. However, if suitable genetic manipulations
were found that increase the efficiency with which transcripts
encoding the above selectable and enzymatic markers are processed
and expressed by mammalian cells, such markers could be used to
practice the claimed invention. Although the above selectable
markers and enzymatic reporters are preferably not part of the
presently described 3' gene trap cassette, they can be used as part
of the 5' gene trap component in combination with the described 3'
gene trap cassette.
[0145] 6.1. Vector Construction
[0146] The promoter from the mouse phosphoglycerate kinase (PGK)
gene was placed upstream from the first exon of the naturally
occurring murine btk gene (nucleotides 40,043 to 40,250 of the
murine btk gene). The first exon of the btk gene does not contain a
translational start site and initiation codon marking the 5' region
of the coding sequence; however, these features could be engineered
into the exon if desired. The 3' end of the coding region of the
first exon is marked by a splice donor sequence. Given that splice
donor recognition sequences can extend into intronic sequence, 103
bases of intron DNA was retained after the end of the btk first
exon. The PGKbtkSD cassette lacks a 3' polyadenylation signal.
Accordingly, any transcript produced by the cassette cannot be
properly processed, and therefore identified by 3' RACE, unless the
transcript is spliced to a 3' exon that can be polyadenylated.
[0147] The above 3' gene trap cassette was placed into a retroviral
vector (in reverse orientation relative to the flanking LTR
regions) that incorporated a polyadenylation site 5' to the PGK
promoter of the 3' gene trap cassette, the neo gene was placed 5'
to the polyadenylation site, and a splice acceptor (SA) site was
placed 51' to the neo coding region to produce a functional
SAneopA, or optionally a SAIRESneopA 5' gene trap cassette. This
vector also incorporates, in operable combination, a pair of
recombinase recognition sites that flank the PGKbtkSD cassette (See
FIG. 2). This vector typically requires that the target cell
naturally express the trapped gene; however, this requirement can
be overcome by adding a promoter that independently controls the
expression of the selectable marker. FIG. 2 additionally indicates
the preferred locations of optional features such as the mutagenic
mini-exon and one or more mutagenesis enhancer regions.
[0148] 6.2. 3' Gene Trapping
[0149] The btk vector was introduced into the embryonic stem cells
using standard techniques. In brief, supernatant from GP+E
packaging cells was added to approximately 2.times.10.sup.6
embryonic stem cells (at an input ratio of approximately 0.1
virus/target dell) for 16 hours and the cells were subsequently
selected with G418 for 10 days. G418 resistant cells were
subsequently isolated, grown up on 96-well plates and subjected to
automated RNA isolation, reverse transcription, PCR and sequencing
protocols to obtain the gene trapped sequences.
[0150] RNA Isolation was carried out on DNA bind plates
(Corning/Costar) treated with 5'-amino-(dT).sub.42 (GenoSys
Biotechnologies) in a 50 mM Sodium Phosphate buffer, pH 8.6, and
allowed to sit at room temperature overnight. Immediately prior to
use the plates were rinsed three times with PBS and twice with TE.
Cells were rinsed with PBS, lysed with a solution containing 100 mM
Tris-HCl, 500 mM LiCl, 10 mM EDTA, 1% LiDS, and 5 mM DTT in DEPC
water, and transferred to the DNA binding plate where the mRNA was
captured. After a 15 minute incubation the RNA was washed twice
with a solution containing 10 mM Tris-HCl, 150 mM-LiCl, 1 mM EDTA,
and 0.1% LiDS in DEPC water. The RNA was then rinsed three times
with the same solution minus LiDS. Elution buffer containing 2 mM
EDTA in DEPC water was added and the plate was heated at 70.degree.
C. for five minutes. An RT premix containing 2.times. First Strand
buffer, 100 mM-Tris-HCl, pH 8.3, 150 mM KCl, 6 mM MgCl.sub.2, 2 mM
dNTPs, RNAGuard (1.5 units/reaction, Pharmacia), 20 mM DTT, QT
primer (3 pmol/rxn, GenoSys Biotechnologies, sequence: 5'
CCAGTGAGCAGAGTGACGAGG ACTCGAGCTCAAGCTTTTTTTTTTTTTTTTT 3', SEQ ID
NO:______) and Superscript II enzyme (200 units/rxn, Life
Technologies) was added. The plate was transferred to a thermal
cycler for the RT reaction (37.degree. C. for 5 min. 42.degree. C.
for 30 min. and 55.degree. C. for 10 min).
[0151] 6.2.1. PCR Product Generation
[0152] The cDNA was amplified using two rounds of PCR. The PCR
premix contains: 1.1.times. MGBII buffer (74 mM Tris pH 8.8, 18.3
mM Ammonium Sulfate, 7.4 mM MgCl.sub.2, 5.5 mM 2ME, 0.011%
Gelatin), 11.1% DMSO (Sigma), 1.67 mM dNTPS, Taq (5 units/rxn),
water and primers. The sequences of the first round primers are:
P.sub.o 5'AAGCCCGGTGCCTGACTAGCT- AG3', SEQ ID NO:______; BTK
5'GAATATGTCTCCAGGTCCAGAG3', SEQ ID NO:______; and Q.sub.o
5'CCAGTGAGCAGAGTGACGAGGAC3', SEQ ID NO: (pmol/rxn). The sequences
of the second round primers are P.sub.i 5'CTAGCTAGGGAGCTCGTC3', SEQ
ID NO:______; BTK.sub.i 5'CCAGAGTCTTCAGAGATCAAGTC3', SEQ ID
NO:______; and Q.sub.i 5'GAGGACTCGAGCTCAAGC3', SEQ ID NO:______ (50
pmol/rxn). The outer premix was added to an aliquot of cDNA and run
for 17 cycles (95.degree. C. for 1 min. 94.degree. C. for 30 sec.,
58.degree. C. for 30 sec 65.degree. C. for 3.5 min). An aliquot of
this product was added to the inner premix and cycled at the same
temperatures 40 times.
[0153] The nested 3' RACE products were purified in a 96-well
microtiter plate format using a two-step protocol as follows.
Twenty-five microliters of each PCR product was applied to a 0.25
ml bed of Sephacryl.RTM. S-300 (Pharmacia Biotech AB, Uppsala,
Sweden) that was previously equilibrated with STE buffer (150 mM
NaCl, 10 MM Tris-HCL, 1 mM EDTA, pH 8.0) The products were
recovered by centrifugation at 1200.times.g for 5 minutes. This
step removes unincorporated nucleotides, oligonucleotides, and
primer-dimers. Next, the products were applied to a 0.25 ml bed of
Sephadex.TM. G-50 (DNA Grade, Pharmacia Biotech AB) that was
equilibrated in MilliQ H.sub.2O, and recovered by centrifugation as
described earlier. Purified PCR products were quantified by
fluorescence using PicoGreen (Molecular Probes, Inc., Eugene Oreg.)
as per the manufacturer's instructions.
[0154] Dye terminator cycle sequencing reaction with AmpliTaq.RTM.
FS DNA polymerase (Perkin Elmer Applied Biosystems, Foster City,
Calif.) were carried out using 7 pmoles of primer (Oligonucleotide
OBS; 5'CTGTAAAACGACGGCCAGTC3', SEQ ID NO:______) and approximately
30-120 ng of 3' RACE product. The cycling profile was 35 cycles of
95.degree. C. for 0.10 sec, 55.degree. C. for 30 sec, and
60.degree. C. for 2 min. Unincorporated dye terminators were
removed from the completed sequencing reactions using G-50 columns
as described earlier. The reactions were dried under vacuum,
resuspending in loading buffer, and electrophoresed through a 6%
Long Ranger acrylamide gel (FMC BioProducts, Rockland, Me.) on an
ABI Prism.RTM. 377 with XL upgrade as per the manufacturer's
instructions.
[0155] The automated 96-well format was used to obtain sequence,
and data was obtained from 70% of the colonies. Upon examination,
the sequence from the first exon of btk was identified followed by
the btk splice junction. The splice junction was followed by unique
sequences from each separate gene trap event. These sequences
averaged 500 bp in length and were of high quality often containing
long open reading frames. In addition 80% of these sequences can be
matched using blast searches to sequences found in the GenBank
database indicating that transcribed exonic sequences were
identified. These gene trap sequence tags are of significantly
better length and quality than those produced by previous gene trap
designs. The new tags are improved in both length and quality and
the fact that 80% of the tags match GenBank sequences suggests that
they efficiently trap genes.
[0156] These data indicate that the splicing machinery is better
able to recognize an exon type sequence present adjacent to or
relatively close to a promoter when splicing into downstream exons.
These data also indicate that the majority of G418 resistant
colonies can be identified using gene trap sequence tags. DNA
sequence data had already been obtained that represents
approximately 7,000 different genes trapped by a vector
incorporating a PGKpuroSD 3' gene trap cassette in conjunction with
puro selection. Given that it has already been established that
such vectors typically produce 13 fold more G418 resistant colonies
than puro colonies, vectors incorporating the presently described
3' gene trap cassette have a very large target size, probably well
over 70,000 genes. This target can be further increased by using
SAneopA rather than the SA.beta.geo fusion to increase the
sensitivity of antibiotic selection, and any other selectable, or
otherwise identifiable, marker could be used in the 5' gene trap
cassette instead of neo. The use of IRESneo increased the number of
G418 resistant colonies to over 15.times. the number of puro
resistant colonies demonstrating its increased sensitivity. Other
potential 5' trapping markers include, but are not limited to,
antibiotic resistance genes (e.g., .beta.-lactamase), colorimetric
marker genes, genes encoding recombinase activity (e.g., flp or
cre, etc.), enzymes, fluorescent marker genes (e.g., genes encoding
activities that directly or indirectly mediate cellular
fluorescence) such as the gene encoding green fluorescent protein,
and assays for detecting the same, which are described, inter alia,
in U.S. Pat. No. 5,625,048, herein incorporated by reference.
[0157] Typically, the more sensitive the selectable marker, the
greater the number of target genes that can be trapped. The ability
to use the btk first exon to obtain gene trap sequence tags from
the 3' exons of the G418 resistant colonies produced approximately
13 fold more mutated cells than could be mutated and rapidly
sequenced using previous vectors, and thus represents a significant
improvement in gene trapping technology.
[0158] Given the above results, it is clear that the surprising and
unexpected properties that resulted in an order of magnitude
improvement over any previously reported 3' gene trap cassettes
were only realized by departing from our established selectable
marker paradigm for gene trapping.
[0159] 6.3. Pharmacogenomics
[0160] As discussed above, an additional method of augmenting the
target size of the described vectors and constructs is to dispense
with selection all together, and use other, i.e., molecular
genetic, means to isolate trapped exons. Using such an approach
allows for the rapid generation and analysis of gene sequence
information. In addition to providing a clear advantage with
respect to the speed of sequence acquisition, the sequencing of
gene trapped libraries allows for substantial cost-savings because
of the reduced rate of repeat sequences relative to conventional
cDNA libraries. The economies inherent in the presently described
system of sequence acquisition make it practical to rapidly obtain
a broad based survey of an individual's genome, or a collection of
individuals' genomes, to identify, inter alia, genetic
polymorphisms, particularly SNPs and cSNPs, that can be associated
with the disease (where a portion of the individuals surveyed are
known to manifest common disease traits or symptoms). Additionally,
similar methods can be employed in broad-based genomic assays that
identify the genetic basis for behavioral traits, drug
susceptibility, drug sensitivity, drug allergy, etc. in both humans
and non-human animals.
[0161] In such methods, high-to-saturating concentrations of
constructs comprising the described 3' gene trap cassette can be
introduced into suitable target cells, including primary human or
non-human cells (for example, primary nucleated blood cells such as
leukocytes and lymphocytes, etc.), using established methods. After
the 3' sequence acquisition cassette has integrated into the target
cell genome, RNA is isolated from the target cells, cDNA is
produced (and optionally PCR amplified as described above), and a
cDNA library is constructed. The library is subsequently sequenced
and catalogued/compared relative to a control library as well as
other "experimental" libraries. As SNPs, cSNPs, or other more gross
polymorphisms are identified that correlate with the "experimental"
or "disease" groups, a catalog of genetic polymorphisms will be
developed that provides both a multi-loci analysis as well as
highlights the regions of the genome that correlate with specific
diseases, or may other wise warrant further study and analysis.
Such information can also prove valuable for the identification of
genetic polymorphisms associated with drug effectiveness (or
adverse drug reactions), as well as the design of diagnostic
assays.
[0162] 7.0. Reference to Microorganism Deposits
[0163] The following plasmid has been deposited at the American
Type Culture Collection (ATCC), Manassas, Va., USA, under the terms
of the Budapest Treaty on the International Recognition of the
Deposit of Microorganisms for the Purposes of Patent Procedure and
Regulations thereunder (Budapest Treaty) and is thus maintained and
made available according to the terms of the Budapest Treaty.
Availability of such plasmid is not to be construed as a license to
practice the invention in contravention of the rights granted under
the authority of any government in accordance with its patent
laws.
[0164] The deposited plasmid has been assigned the indicated ATCC
deposit number:
2 Plasmid ATCC No. pbtK 209712
[0165] All publications and patents mentioned in the above
specification are herein incorporated by reference. Various
modifications and variations of the described invention will be
apparent to those skilled in the art without departing from the
scope and spirit of the invention. Although the invention has been
described in connection with specific preferred embodiments, it
should be understood that the invention as claimed should not be
unduly limited to such specific embodiments. Indeed, various
modifications of the above-described modes for carrying out the
invention which are obvious to those skilled in the field of animal
genetics and molecular biology or related fields are intended to be
within the scope of the following claims.
Sequence CWU 1
1
24 1 68 DNA Artificial Sequence Synthetic sequence 1 cacgtctgca
gatcatgagg atgctaatcc ttgatggcat gcactatgcg cgatgatctg 60 cagacgtg
68 2 68 RNA Artificial Sequence Synthetic sequence 2 cacgucugca
gaucaugagg augcuaaucc uugauggcau gcacuaugcg cgaugaucug 60 cagacgug
68 3 70 DNA Artificial Sequence Synthetic sequence 3 cacgtctgca
gtccggagga gtgtgtttct cctccgctga tgagtccgtg aggacgaaac 60
tgcagacgtg 70 4 70 RNA Artificial Sequence Synthetic sequence 4
cacgucugca guccggagga guguguuucu ccuccgcuga ugaguccgug aggacgaaac
60 ugcagacgug 70 5 279 DNA Artificial Sequence Synthetic sequence 5
ggatccgaat tctcgaggct aagccagttt tcgtaccctt gactgcgttt catcgattcg
60 ctactaacat tgccttttcc tccttccctc ccacaggtgg aagagctcgg
gtaccaggag 120 aggagaggag aggagaggag aggagaggag aggagaggag
aggagaggag aggagatctc 180 aggtgagttc gcatgtgctt cgaacttgtg
tgcatgcgtt ctaaaagggc ttctcttggt 240 gttcgatctg gggctaagct
taattaagaa ttcggatcc 279 6 43 DNA Mus musculus 6 gcaaccagta
acctctgccc tttctcctcc atgacaacca ggt 43 7 41 DNA Adenovirus 7
gatgatgtca tacttatcct gtcccttttt tttccacagc t 41 8 35 DNA Mus
musculus 8 ggcggtcagg ctgccctctg ttcccattgc aggaa 35 9 42 DNA Mus
musculus 9 tgtcagtctg tcatccttgc cccttcagcc gcccggatgg cg 42 10 39
DNA Mus musculus 10 tgctgacacc ccactgttcc ctgcaggacc gccttcaac 39
11 34 DNA Mus musculus 11 taattgtgta attattgttt ttcctccttt agat 34
12 40 DNA Mus musculus 12 cagaatcttc tttttaattc ctgattttat
ttctatagga 40 13 37 DNA Artificial Sequence Synthetic sequence 13
tactaacatt gccttttcct ccttccctcc cacaggt 37 14 37 DNA Mus musculus
14 tgctccactt tgaaacagct gtctttcttt tgcagat 37 15 36 DNA Mus
musculus 15 ctctctgcct attggtctat tttcccaccc ttaggc 36 16 35 DNA
Mus musculus 16 attaattact ctgcccattc ctctctttca gagtt 35 17 52 DNA
Artificial Sequence Primer 17 ccagtgagca gagtgacgag gactcgagct
caagcttttt tttttttttt tt 52 18 23 DNA Artificial Sequence Primer 18
aagcccggtg cctgactagc tag 23 19 22 DNA Artificial Sequence Primer
19 gaatatgtct ccaggtccag ag 22 20 23 DNA Artificial Sequence Primer
20 ccagtgagca gagtgacgag gac 23 21 18 DNA Artificial Sequence
Primer 21 ctagctaggg agctcgtc 18 22 23 DNA Artificial Sequence
Primer 22 ccagagtctt cagagatcaa gtc 23 23 18 DNA Artificial
Sequence Primer 23 gaggactcga gctcaagc 18 24 20 DNA Artificial
Sequence Primer 24 ctgtaaaacg acggccagtc 20
* * * * *