(TG/CA)n repeats in human gene families: Abundance and selective patterns of distribution according to function and gene length

BMC Genomics

Volumn 6, Issue , 2005, Pages

  Sharma, Vineet K ^a   Brahmachari, Samir K ^a   Ramachandran, Srinivasan ^a  

^a CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; COLLAGEN; CYTOSINE; GLYCINE; THYMINE;

ARTICLE; CELL COMMUNICATION; CELL FUNCTION; CHIMPANZEE; CLASSIFICATION; CONTROLLED STUDY; DINUCLEOTIDE REPEAT; GENE EXPRESSION; GENE FUNCTION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC CONSERVATION; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; HUMAN; IMMUNE RESPONSE; MODULATION; MOLECULAR BIOLOGY; MULTIGENE FAMILY; NONHUMAN; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION;

PAN TROGLODYTES;

EID: 25444525458     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-6-83     Document Type: Article

References (49)

1. Meyer A and Schart M: Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Current Opinion in Cell Biology 1999, 11: 699-704.
2. Wagner A: Selection and gene duplication: a view from the genome. Genome Biology 2002, 3(5) reviews:1012.1-1012.
3. King RC and Stansfield WD: A Dictionary of Genetics. Oxford University Press 1990.
4. Wain HM, Bruford EA, Lovering RC, Lush MJ, Wright MW, Povey S: Guidelines for human gene nomenclature. Genomics 2002, 79(4): 464-470.
5. International Human Genome Sequencing Consortium: Initial sequencing and analysis of the human genome. Nature 2001, 409: 860-921.
6. Dib C, Faure S, Fizames C, Samson D, Drouot N, Vignal A, Millasseau P, Marc S, Hazan J, Seboun E, Lathrop M, Gyapay G, Morissette J, Weissenbach J: A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 1996, 380: 152-4.
7. Brahmachari SK, Meera G, Sarkar PS, Balagurumoorthy P, Tripathi J, Raghavan S, Shaligram U, Pataskar S: Simple repetitive sequences in the genome: structure and functional significance. Electrophoresis 1995, 16(9): 1705-14.
8. Nordheim A, Rich A: The sequence (dC-dA)n X (dG-dT)n forms left-handed Z-DNA in negatively supercoiled plasmids. Proc. Natl. Acad. Sci. 1983, 80: 1821-1825.
9. Meera G, Ramesh N, Brahmachari SK: Zintrons in rat α-lactalbuman gene. FEBS Lett. 1989, 251: 245-249.
10. Tripathi J, Brahmachari, SK: Distribution of simple repetitive (TG/CA)n and (CT/AG)n sequences in human and rodent genomes. J Biomol Struct Dyn. 1991, 9(2): 387-97.
11. Naylor LH, Clark EM: d(TG)n.d(CA)n sequences upstream of the rat prolactin gene form Z-DNA and inhibit gene transcription. Nucleic Acids Res. 1990, 18: 1595-1601.
12. Shimajiri S, Arima N, Tanimoto A, Murata Y, Hamada T, Wang KY, Sasaguri Y: Shortened microsatellite d(CA)21 sequence down-regulates promoter activity of matrix metalloproteinase 9 gene. FEBS Lett. 1999, 455: 70-4.
13. Pravica V, Asderakis A, Perrey C, Hajeer A, Sinnott PJ, Hutchinson IV: In vitro production of IFN-gamma correlates with CA repeat polymorphism in the human IFN-gamma gene. Eur. J. Immunogenet. 1999, 26: 1-3.
14. Gebhardt F, Zanker KS, Brandt B: Modulation of epidermal growth factor receptor gene transcription by a polymorphic dinucleotide repeat in intron 1. J. Biol. Chem. 1999, 274: 13176-13180.
15. Agarwal AK, Giacchetti G, Lavery G, Nikkila H, Palermo M, Ricketts M, McTernan C, Bianchi G, Manunta P, Strazzullo P, Mantero F, White PC, Stewart PM: CA-Repeat polymorphism in intron 1 of HSD11B2: effects on gene expression and salt sensitivity. Hypertension 2000, 36: 187-94.
16. Streelman JT, Kocher, TD: Microsatellite variation associated with prolactin expression and growth of salt-challenged tilapia. Physiol Genomics. 2002, 9: 1-4.
17. n repeats in human housekeeping genes. J. Biomol. Str. Dyn. 2003, 21(2): 303-10.
18. Tracy RB, Baumohl JK, Kowalczykowski SC: The preference for GT-rich DNA by the yeast Rad51 protein defines a set of universal pairing sequences. Genes Dev. 1997, 11(24): 3423-31.
19. Dutreix M: (GT)n repetitive tracts affect several stages of RecA-promoted recombination. J Mol Biol. 1997, 273(1): 105-13.
20. Majewski J, Ott J: GT Repeats are associated with recombination on human chromosome 22. Genome Research 2000, 10(8): 1108-14.
21. Gabellini N: A polymorphic GT repeat from the human cardiac Na+Ca2+ exchanger intron 2 activates splicing. Eur J Biochem. 2001, 268(4): 1076-83.
22. Hui J, Stangl K, Lane WS, Bindereif A: HnRNP L stimulates splicing of the eNOS gene by binding to variable-length CA repeats. Nat Struct Biol. 2003, 10(1): 33-7.
23. Hinegardner R: Evolution of cellular DNA content in teleost fishes. Am. Nat. 1968, 104: 517-523.
24. Fyodor A, Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV: Selection in the evolution of gene duplications. Genome Biology 2002, 3(2): research0008.1-0008.9.
25. Gelse K, Poschl E, Aigner T: Collagens - structure, function, and biosynthesis. Adv Drug Deliv Rev. 2003, 55(12): 1531-46.
26. Hardison RC: Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet. 2000, 16: 369-372.
27. Tagle DA, Koop BF, Goodman M, Slightom JL, Hess DL, and Jones RT: Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J. Mol. Biol. 1988, 203: 439-455.
28. Rivera MC, Jain R, Moore JE, Lake JA: Genomic evidence for two functionally distinct gene classes. Proc. Natl. Acad. Sci USA 1998, 95: 6239-6244.
29. Castillo-Davis CI, Mekhedov SL, Hartl DL, Koonin EV, Kondrashov FA: Selection for short introns in highly expressed genes. Nat. Genet. 2002, 31: 415-418.
30. Dotan I, Ziv E, Dafni N, Beckman JS, McCann RO, Glover CV, Canaani D: Functional Conservation between the Human, Nematode, and Yeast CK2 Cell Cycle Genes. Biochem. Biophys. Res. Commun. 2001, 288: 603-609.
31. Dover GA: Evolution of genetic redundancy for advanced players. Curr Opin Genet Dev. 1993, 3(6): 902-10.
32. Ramachandran GN, Sasisekharan V: Structure of collagen. Nature. 1961, 190: 1004-5.
33. Alt FW, Oltz EM, Young F, Gorman J, Taccioli G, Chen J: VDJ recombination. Immunol Today. 1992, 13(8): 306-14.
34. Fondon JW 3rd, Mele GM, Brezinschek RI, Cummings D, Pande A, Wren J, O'Brien KM, Kupfer KC, Wei MH, Lerman M, Minna JD, Garner HR: Computerized polymorphic marker identification: experimental validation and a predicted human polymorphism catalog. Proc. Natl. Acad. Sci. 1998, 95: 7514-7519.
35. Rockman MV, Wray GA: Abundant raw material for Cis- regulatory evolution in humans. Mol. Biol. Evol. 2002, 19: 1991-2004.
36. Epplen C, Santos EJ, Maueler W, van Helden P, Epplen JT: On simple repetitive DNA sequences and complex diseases. Electrophoresis 1997, 18(9): 1577-85.
37. Yagil G: Paranemic structures of DNA and their role in DNA unwinding. Critical Reviews in Biochemistry and Molecular Biology 1991, 26(5): 475-559.
38. Nelson DR, Koymans L, Kamataki T, Stegeman JJ, Feyereisen R, Waxman DJ, Waterman MR, Gotoh O, Coon MJ, Estabrook RW, Gunsalus IC, Nebert DW: P450 superfamily: update on new sequences, gene mapping, accession numbers and nomenclature. Pharmacogenetics 1996, 6: 1-42.
39. Mackenzie PI, Owens IS, Burchell B, Bock KW, Bairoch A, Belanger A, Fournel-Gigleux S, Green M, Hum DW, Iyanagi T, Lancet D, Louisot P, Magdalou J, Chowdhury JR, Ritter JK, Schachter H, Tephly TR, Tipton KF, Nebert DW: The UDP glycosyltransferase gene superfamily: recommended nomenclature update based on evolutionary divergence. Pharmacogenetics 1997, 7: 255-69.
40. Adams MD, Kerlavage AR, Fleischmann RD, Fuldner RA, Bult CJ, Lee NH, Kirkness EF, Weinstock KG, Gocayne JD, White O, Sutton G, Blake JA, Brandon RC, Chiu M, Clayton RA, Cline RT, Cotton MD, Earle-Hughes J, Fine LD, FitzGerald LM, FitzHugh WM, Fritchman JL, Geoghagen NSM, Glodek A, Gnehm CL, Hanna MC, Hedblom E, Hinkle PS, Jr, Kelley JM, Klimek KM, Kelley JC, Liu L, Marmaros SM, Merrick JM, Moreno-Palanques RF, McDonald LA, Nguyen DT, Pellegrino SM, Phillips CA, Ryder SE, Scott JL, Saudek DM, Shirley R, Small KV, Spriggs TA, Utterbach TR, Weidman JF, Li Y, Barthlow R, Bednarik DP, Cao L, Cepeda MA, Coleman TA, Collins E, Dimke D, Feng P, Ferrie A, Fischer C, Hastings GA, He W, Hu J, Huddleston KA, Greene JM, Gruber J, Hudson P, Kim A, Kozak DL, Kunsch C, Ji H, Li H, Meissner PS, Olsen H, Raymond L, Wei Y, Wing J, Xu C, Yu G, Ruben SM, Dillon PJ, Fannon MR, Rosen CA, Haseltine WA, Fields C, Fraser CM, Venter JC: Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature 1995, 377: 3-174.
41. Andrade MA, Ouzounis C, Sander C, Tamames J, Valencia A: Functional classes in the three domains of life. J. Mol. Evol. 1999, 49: 551-557.
42. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R; Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004, 32(Database issue): D258-61.
43. Wheeler DL, Church DM, Edgar R, Federhen S, Helmberg W, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, Suzek TO, Tatusova TA, Wagner L: Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res. 2004, 32(Database issue): D35-40.
44. Gu Z, Rifkin SA, White KP, Li Wen-Hsiung: Duplicate genes increase gene expression diversity within and between species. Nature Genetics 2004, 36: 577-579.
45. Thornton JW, DeSalle R: Gene family evolution and homology: Genomics Meets Phylogenetics. Annu. Rev. Genomics Hum. Genet. 2000, 01: 41-73.
46. Check E: Geneticists study chimp-human divergence. Nature. 2004, 428(6980):242.
47. Whittaker JC, Harbord RM, Boxall N, Mackay I, Dawson G, Sibly RM: Likelihood-based estimation of microsatellite mutation rates. Genetics. 2003, 164:781-787.
48. Sainudiin R, Durrett RT, Aquadro CF, Nielsen R: Microsatellite mutation models: insights from a comparison of humans and chimpanzees. Genetics. 2004, 168(1):383-95.
49. Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ; University of California Santa Cruz: The UCSC GC Genome Browser Database. Nucleic Acids Res. 2003, 31(1):51-4.