Invited review: Functional genomics in the mouse: Powerful techniques for unraveling the basis of human development and disease

Journal of Applied Physiology

Volumn 94, Issue 6, 2003, Pages 2502-2509

  Bogue, Clifford W ^a  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Genome; Phenotype

Indexed keywords

DNA SEQUENCE; GENE FUNCTION; GENE IDENTIFICATION; GENE MAPPING; GENE MUTATION; GENETIC ENGINEERING; GENETIC MODEL; GENOMICS; HUMAN; MUTAGENESIS; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; REVIEW; ANIMAL; GENE; GENE EXPRESSION REGULATION; GENETIC DISORDER; GENETIC SCREENING; GENETICS; HUMAN DEVELOPMENT; MOUSE; PHYSIOLOGY;

ANIMALS; GENE EXPRESSION REGULATION; GENES; GENETIC DISEASES, INBORN; GENETIC SCREENING; GENOMICS; HUMAN DEVELOPMENT; HUMANS; MICE; MUTAGENESIS;

EID: 0037502792     PISSN: 87507587     EISSN: None     Source Type: Journal    
DOI: 10.1152/japplphysiol.00209.2003     Document Type: Review

References (55)

1. Angrand PO, Daigle N, van der Hoeven F, Scholer HR, and Stewart AF. Simplified generation of targeting constructs using ET recombination. Nucleic Acids Res 27: e16, 1999.
2. Baron U and Bujard H. Tet repressor-based system for regulated gene expression in eukaryotic cells: principles and advances. Methods Enzymol 327: 401-421, 2000.
3. Batzoglou S, Pachter L, Mesirov JP, Berger B, and Lander ES. Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Res 10: 950-958, 2000.
4. Baudin A, Ozier-Kalogeropoulos O, Denouel A, Lacroute F, and Cullin C. A simple and efficient method for direct gene deletion in Saccharomyces cerevisae. Nucleic Acids Res 21: 3329-3330, 1993.
5. Beck J, Lloyd S, Hafenparast M, Lennon-Pierce M, Eppig J, Festing M, and Fisher E. Genealogies of mouse inbred strains. Nat Genet 24: 23-25, 2000.
6. Botta A, Lindsay EA, Jurecic V, and Baldini A. Comparative mapping of the DiGeorge syndrome region in mouse shows inconsistent gene order and differential degree of gene conservation. Mamm Genome 8: 890-895, 1997.
7. Bradshaw MS, Bollekens JA, and Ruddle FH. A new vector for recombination-based cloning of large DNA fragments from yeast artificial chromosomes. Nucleic Acids Res 23: 4850-4856, 1995.
8. Bradshaw MS, Shashikant CS, Belting HG, Bollekens JA, and Ruddle FH. A long-range regulatory element of Hoxc8 identified by using the pClasper vector. Proc Natl Acad Sci USA 93: 2426-2430, 1996.
9. Brown SD and Peters J. Combining mutagenesis and genomics in the mouse - closing the phenotype gap. Trends Genet 12: 433-435, 1996.
10. Byrne GW and Ruddle FH. Multiplex gene regulation: a two-tiered approach to transgene regulation in transgenic mice. Proc Natl Acad Sci USA 86: 5473-5477, 1989.
11. Copeland NG, Jenkins NA, and Court DL. Recombineering: a powerful new tool for mouse functional genomics. Nat Rev Genet 2: 769-779, 2001.
12. Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, and Salzberg SL. Alignment of whole genomes. Nucleic Acids Res 27: 2369-2376, 1999.
13. Gossen M and Bujard H. Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. Proc Natl Acad Sci USA 89: 5547-5551, 1992.
14. Gossen M, Freundlieb S, Bender G, Muller G, Hillen W, and Bujard H. Transcriptional activation by tetracyclines in mammalian cells. Science 268: 1766-1769, 1995.
15. Gottgens B, Barton LM, Gilbert JG, Bench AJ, Sanchez MJ, Bahn S, Mistry S, Grafham D, McMurray A, Vaudin M, Amaya E, Bentley DR, Green AR, and Sinclair AM. Analysis of vertebrate SCL loci identifies conserved enhancers. Nat Biotechnol 18: 181-186, 2000.
16. Haldane JBS, Sprunt AD, and Haldan NM. Reduplication in mice. J Genet 5: 133-135, 1915.
17. Hoit BD, Kiatchoosakun S, Restivo J, Kirkpatrick D, Olszens K, Shao H, Pao YH, and Nadeau JH. Naturally occurring variation in cardiovascular traits among inbred mouse strains. Genomics 79: 679-685, 2002.
18. Hoit BD and Nadeau JH. Phenotype-driven genetic approaches in mice: high-throughput phenotyping for discovering new models of cardiovascular disease. Trends Cardiovasc Med 11: 82-89, 2001.
19. Hood L, Koop BF, Rowen L, and Wang K. Human and mouse T-cell-receptor loci: the importance of comparative large-scale DNA sequence analyses. Cold Spring Harb Symp Quant Biol 58: 339-348, 1993.
20. Jacob HJ and Kwitek AE. Rat genetics: attaching physiology and pharmacology to the genome. Nat Rev Genet 3: 33-42, 2002.
21. Justice MJ, Carpenter DA, Favor J, Neuhauser-Klaus A, Hrabe de Angelis M, Soewarto D, Moser A, Cordes S, Miller D, Chapman V, Weber JS, Rinchik EM, Hunsicker PR, Russell WL, and Bode VC. Effects of ENU dosage on mouse strains. Mamm Genome 11: 484-488, 2000.
22. Justice MJ, Zheng B, Woychik RP, and Bradley A. Using targeted large deletions and high-efficiency N-ethyl-N-nitrosourea mutagenesis for functional analyses of the mammalian genome. Methods 13: 423-436, 1997.
23. Keeler CE. The Laboratory Mouse: Its Origin, Heredity and Culture. Cambridge, MA: Harvard Univ. Press, 1931.
24. Klysik J. Mice and humans: chromosome engineering and its application to functional genomics. Acta Biochim Pol 49: 553-569, 2002.
25. Koop BF and Hood L. Striking sequence similarity over almost 100 kilobases of human and mouse T-cell receptor DNA. Nat Genet 7: 48-53, 1994.
26. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, et al. Initial sequencing and analysis of the human genome. Nature 409: 860-921, 2001.
27. Lee EC, Yu D, Martinez de Velasco J, Tessarollo L, Swing DA, Court DL, Jenkins NA, and Copeland NG. A highly efficient Escherichia coli-based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA. Genomics 73: 56-65, 2001.
28. Lewandoski M. Conditional control of gene expression in the mouse. Nat Rev Genet 2: 743-755, 2001.
29. Lindsay EA, Botta A, Jurecic V, Carattini-Rivera S, Cheah YC, Rosenblatt HM, Bradley A, and Baldini A. Congenital heart disease in mice deficient for the DiGeorge syndrome region. Nature 401: 379-383, 1999.
30. Lindsay EA, Vitelli F, Su H, Morishima M, Huynh T, Pramparo T, Jurecic V, Ogunrinu G, Sutherland HF, Scambler PJ, Bradley A, and Baldini A. Tbx1 haploinsufficieny in the DiGeorge syndrome region causes aortic arch defects in mice. Nature 410: 97-101, 2001.
31. Loots GG, Locksley RM, Blankespoor CM, Wang ZE, Miller W, Rubin EM, and Frazer KA. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 288: 136-140, 2000.
32. Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, Frazer KA, Pachter LS, and Dubchak I. VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16: 1046-1047, 2000.
33. Mills AA and Bradley A. From mouse to man: generating megabase chromosome rearrangements. Trends Genet 17: 331-339, 2001.
34. Morse H. The Mouse in Biomedical Research. New York: Academic, 1981.
35. Muyrers JP, Zhang Y, Benes V, Testa G, Ansorge W, and Stewart AF. Point mutation of bacterial artificial chromosomes by ET recombination. EMBO J 1: 239-243, 2000.
36. Muyrers JP, Zhang Y, and Stewart AF. Techniques: recombinogenic engineering - new options for cloning and manipulating DNA. Trends Biochem Sci 26: 325-331, 2001.
37. Nefedov M, Williamson R, and Ioannou PA. Insertion of disease-causing mutations in BACs by homologous recombination in Escherichia coli. Nucleic Acids Res 28: E79, 2000.
38. O'Gorman S, Fox DT, and Wahl GM. Recombinase-mediated gene activation and site-specific integration in mammalian cells. Science 251: 1351-1355, 1991.
39. Pennacchio LA and Rubin EM. Genomic strategies to identify mammalian regulatory sequences. Nat Rev Genet 2: 100-109, 2001.
40. Ramirez-Solis R, Liu P, and Bradley A. Chromosome engineering in mice. Nature 378: 720-724, 1995.
41. Roebroek AJ, Wu X, and Bram RJ. Knockin approaches. Methods Mol Biol 209: 187-200, 2003.
42. Sauer B and Henderson N. Cre-stimulated recombination at loxP-containing DNA sequences placed into the mammalian genome. Nucleic Acids Res 17: 147-161, 1989.
43. Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, and Miller W. PipMaker - a web server for aligning two genomic DNA sequences. Genome Res 10: 577-586, 2000.
44. Shastry BS. Gene disruption in mice: models of development and disease. Mol Cell Biochem 181: 163-179, 1998.
45. Silver L. Mouse Genetics. New York: Oxford Univ. Press, 1995.
46. Smith AJ, De Sousa MA, Kwabi-Addo B, Heppell-Parton A, Impey H, and Rabbitts P. A site-directed chromosomal translocation induced in embryonic stem cells by Cre-loxP recombination. Nat Genet 9: 376-385, 1995.
47. Stoll M, Cowley AW Jr, Tonellato PJ, Greene AS, Kaldunski ML, Roman RJ, Dumas P, Schork NJ, Wang Z, and Jacob HJ. A genomic-systems biology map for cardiovascular function. Science 294: 1723-1726, 2001.
48. Sumiyama K, Irvine SQ, Stock DW, Weiss KM, Kawasaki K, Shimizu N, Shashikant CS, Miller W, and Ruddle FH. Genomic structure and functional control of the Dlx3-7 bigene cluster. Proc Natl Acad Sci USA 99: 780-785, 2002.
49. Sumiyama K, Kim CB, and Ruddle FH. An efficient ciselement discovery method using multiple sequence comparisons based on evolutionary relationships. Genomics 71: 260-262, 2001.
50. Swaminathan S, Ellis HM, Waters LS, Yu D, Lee EC, Court DL, and Sharan SK. Rapid engineering of bacterial artificial chromosomes using oligonucleotides. Genesis 29: 14-21, 2001.
51. Szostak JW, Orr-Weaver TL, Rothstein RJ, and Stahl FW. The double-strand-break repair model for recombination. Cell 33: 25-35, 1983.
52. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, et al. The sequence of the human genome. Science 291: 1304-1351, 2001.
53. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigo R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562, 2002.
54. Yang XW, Model P, and Heintz N. Homologous recombination based modification in Escherichia coli and germline transmission in transgenic mice of a bacterial artificial chromosome. Nat Biotechnol 15: 859-865, 1997.
55. Zheng B, Mills AA, and Bradley A. A system for rapid generation of coat color-tagged knockouts and defined chromosomal rearrangements in mice. Nucleic Acids Res 27: 2354-2360, 1999.