Most mammalian genes will soon be characterized as cDNA sequences with little information as to their function. To utilize this sequence information of large-scale functional studies, a process of tagged-sequence mutagenesis has been developed to disrupt genes expressed in mouse embryo-derived stem (ES) cells. Libraries of ES cell clones will be isolated in which expressed cellular genes have been disrupted by a gene trap retrovirus shuttle vector. Flanking regions adjacent to the integrated provirus in each clone will be isolated by plasmid rescue and sequenced. The flanking sequences, designated PSTs, will be compared with the nucleic acid databases to identify instances in which the provirus has disrupted known genes or previously characterized cDNAs. In practice, this requires only 300 nucleotides of flanking sequence, since gene entrapment selects for proviruses inserted in or near transcribed exons. Presently, approximately 15 percent of inserts (65 or 400) have disrupted previously characterized genes or cDNAs. Insertion mutations will be characterized at a rate of 300 per month, allowing a significant fraction of the estimated 10-20,000 genes expressed in ES cells to be disrupted and characterized in the next five years. ES cell clones containing specific mutations will be made available to interested investigators. Each clone will be stored in liquid nitrogen, providing an immediate source of mutated genes for transmission into the mouse germline. The appropriately annotated PST sequences will be submitted to GenBank, so that later, investigators worldwide can learn of the existence of mutations affecting specific genes and cDNA sequences by standard database searches. The appropriate ES cell clones will then be provided on request. The ability to induce, characterize and maintain mutations in ES cells circumvents many limitations associated with conventional mammalian genetics, and will greatly increase the number of mutant alleles (typically loss of function mutations) by which gene functions can be studied in mice and in cell lines derived from such mice. The process will facilitate a functional analysis of a mammalian genome and will provide animal models for human genetic diseases.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Research Project (R01)
Project #
5R01RR013166-05
Application #
6540614
Study Section
Genome Study Section (GNM)
Program Officer
Harding, John D
Project Start
1998-04-15
Project End
2004-04-14
Budget Start
2002-04-15
Budget End
2004-04-14
Support Year
5
Fiscal Year
2002
Total Cost
$500,265
Indirect Cost
Name
Vanderbilt University Medical Center
Department
Microbiology/Immun/Virology
Type
Schools of Medicine
DUNS #
004413456
City
Nashville
State
TN
Country
United States
Zip Code
37212
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Donahue, Sarah L; Lin, Qing; Cao, Shang et al. (2006) Carcinogens induce genome-wide loss of heterozygosity in normal stem cells without persistent chromosomal instability. Proc Natl Acad Sci U S A 103:11642-6
Scott, Robert E; White-Grindley, Erica; Ruley, H Earl et al. (2005) P2P-R expression is genetically coregulated with components of the translation machinery and with PUM2, a translational repressor that associates with the P2P-R mRNA. J Cell Physiol 204:99-105
Osipovich, Anna B; Singh, Aparna; Ruley, H Earl (2005) Post-entrapment genome engineering: first exon size does not affect the expression of fusion transcripts generated by gene entrapment. Genome Res 15:428-35
Osipovich, Anna B; White-Grindley, Erica K; Hicks, Geoffrey G et al. (2004) Activation of cryptic 3' splice sites within introns of cellular genes following gene entrapment. Nucleic Acids Res 32:2912-24
Lin, Qing; Jo, Daewoong; Gebre-Amlak, Kassatihun D et al. (2004) Enhanced cell-permeant Cre protein for site-specific recombination in cultured cells. BMC Biotechnol 4:25
Organ, Edward L; Sheng, Jinsong; Ruley, H Earl et al. (2004) Discovery of mammalian genes that participate in virus infection. BMC Cell Biol 5:41
Roshon, Michael; DeGregori, James V; Ruley, H Earl (2003) Gene trap mutagenesis of hnRNP A2/B1: a cryptic 3' splice site in the neomycin resistance gene allows continued expression of the disrupted cellular gene. BMC Genomics 4:2
Jo, Daewoong; Lin, Qing; Nashabi, Abudi et al. (2003) Cell cycle-dependent transduction of cell-permeant Cre recombinase proteins. J Cell Biochem 89:674-87
Pawlak, Maciej R; Banik-Maiti, Sarbani; Pietenpol, Jennifer A et al. (2002) Protein arginine methyltransferase I: substrate specificity and role in hnRNP assembly. J Cell Biochem 87:394-407

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