Sexy gene conversions: Locating gene conversions on the X-chromosome

Nucleic Acids Research

Volumn 37, Issue 14, 2009, Pages 4570-4579

  Lawson, Mark J ^a   Zhang, Liqing ^a,b  

^a State University   (United States)

^b Bioinformatics   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FERRITIN; GENE PRODUCT; PHOSPHATIDATE PHOSPHATASE; PROTEIN LDOC1; PROTEIN WD; RAS PROTEIN; REGULATOR PROTEIN; TRANSCRIPTION ELONGATION FACTOR; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN;

ARTICLE; GENE CONVERSION; GENE IDENTIFICATION; HUMAN; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; SYNTENY; X CHROMOSOME;

ANIMALS; CHROMOSOMES, HUMAN, X; GENE CONVERSION; GENES, X-LINKED; HUMANS; MACACA MULATTA; MICE; MULTIGENE FAMILY; PAN TROGLODYTES; PHYLOGENY; RATS; SOFTWARE; SYNTENY; X CHROMOSOME;

HOMO SAPIENS; MUS MUSCULUS; PAN; PAN TROGLODYTES; PRIMATES; RATTUS NORVEGICUS; RODENTIA;

EID: 69049098188     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp421     Document Type: Article

References (40)

1. Ross,M., Grafham,D., Coffey,A., Scherer,S., McLay,K., Muzny,D., Platzer,M., Howell,G., Burrows,C., Bird,C. et al. (2005) The DNA sequence of the human X chromosome. Nature, 434, 325-337.
2. Skuse,D. (2005) X-linked genes and mental functioning. Hum. Mol. Genet., 14, R27-R32.
3. Zechner,U., Wilda,M., Kehrer-Sawatzki,H., Vogel,W., Fundele,R. and Hameister,H. (2001) A high density of X-linked genes for general cognitive ability: A run-away process shaping human evolution? Trends Genet., 17, 697-701.
4. Graves,J., Koina,E. and Sankovi,C.N. (2006) How the gene content of human sex chromosomes evolved. Curr. Opin. Genet. Dev.
5. Wheeler,D.L., Barrett,T., Benson,D.A., Bryant,S.H., Canese,K., Chetvernin,V., Church,D.M., DiCuccio,M., Edgar,R., Federhen,S. et al. (2008) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 36, D13-D21.
6. Reyniers,E., Vanthienes,M., Meire,F., Boulle,K., Devries,K., Kestelijn,P. and Willems,P. (1995) Gene conversion between red and defective green opsin gene in blue cone monochromacy. Genomics, 29, 323-328.
7. Hayashi,T., Motulsky,A.G. and Deeb,S.S. (1999) Position of a 'green-red' hybrid gene in the visual pigment array determines colour-vision phenotype. Nat. Genet., 22, 90-93.
8. Verrelli,B. and Tishkoff,S. (2004) Signatures of selection and gene conversion associated with human color vision variation. Am. J. Hum. Genet., 75, 363-375.
9. Fitzgerald,J., Dahl,H., Jakobsen,I. and Easteal,S. (1996) Evolution of mammalian X-linked and autosomal Pgk and Pdh E1 alpha subunit genes. Mol. Biol. Evol., 13, 1023-1031.
10. Bagnall,R., Ayres,K., Green,P. and Giannelli,F. (2005) Gene conversion and evolution of Xq28 duplicons involved in recurring inversions causing severe hemophilia a. Genome Res., 15, 214-223.
11. Kouprina,N., Mullokandov,M., Rogozin,I., Collins,N., Solomon,G., Otstot,J., Risinger,J., Koonin,E., Barrett,J. and Larionov,V. (2004) The spanx gene family of cancer/testis-specific antigens: Rapid evolution and amplification in African great apes and hominids. Proc. Natl Acad. Sci. USA, 101, 3077-3082.
12. Kouprina,N., Pavlicek,A., Noskov,V., Solomon,G., Otstot,J., Isaacs,W., Carpten,J., Trent,J., Schleutker,J., Barrett,J. et al. (2005) Dynamic structure of the SPANX gene cluster mapped to the prostate cancer susceptibility locus HPCX at Xq27. Genome Res., 15, 1477-1486.
13. Mi,H., Lazareva-Ulitsky,B., Loo,R., Kejariwal,A., Vandergriff,J., Rabkin,S., Guo,N., Muruganujan,A., Doremieux,O., Campbell,M. et al. (2005) The panther database of protein families, subfamilies, functions and pathways. Nucleic Acids Res., 33, D284-D288.
14. Matsuya,A., Sakate,R., Kawahara,Y., Koyanagi,K.O., Sato,Y., Fujii,Y., Yamasaki,C., Habara,T., Nakaoka,H., Todokoro,F. et al. (2008) Evola: Ortholog database of all human genes in H-INvDB with manual curation of phylogenetic trees. Nucleic Acids Res., 36, D787-D792.
15. Flicek,P., Aken,B.L., Beal,K., Ballester,B., Caccamo,M., Chen,Y., Clarke,L., Coates,G., Cunningham,F., Cutts,T. et al. (2008) Ensembl 2008. Nucleic Acids Res., 36, D707-D714.
16. Hasegawa,M., Kishino,H. and Yano,T. (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22, 160-174.
17. Felsenstein,J. (2005) Phylip (phylogeny inference package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
18. Sawyer,S. (1989) Statistical tests for detecting gene conversion. Mol. Biol. Evol., 6, 526-538.
19. Jakobsen,I.B., Wilson,S.R. and Easteal,S. (1997) The partition matrix: exploring variable phylogenetic signals along nucleotide sequence alignments. Mol. Biol. Evol., 14, 474-484.
20. Hidaka,K., Caffrey,J.J., Hua,L., Zhang,T., Falck,J.R., Nickel,G.C., Carrel,L., Barnes,L.D. and Shears,S.B. (2002) An adjacent pair of human NUDT genes on chromosome X are preferentially expressed in testis and encode two new isoforms of diphosphoinositol polyphosphate phosphohydrolase. J. Biol. Chem., 277, 32730-32738.
21. Leslie,N.R., McLennan,A.G. and Safrany,S.T. (2002) Cloning and characterisation of hAps1 and hAps2, human diadenosine polyphosphate-metabolising nudix hydrolases. BMC Biochem., 3 20.
22. Nagasaki,K., Manabe,T., Hanzawa,H., Maass,N., Tsukada,T. and Yamaguchi,K. (1999) Identification of a novel gene, LDOC1, down-regulated in cancer cell lines. Cancer Lett., 140, 227-234.
23. Greig,G.M., Sharp,C.B., Carrel,L. and Willard,H.F. (1993) Duplicated zinc finger protein genes on the proximal short arm of the human X chromosome: Isolation, characterization and X-inactivation studies. Hum. Mol. Genet., 2, 1611-1618.
24. Marais,G. (2003) Biased gene conversion: Implications for genome and sex evolution. Trends Genet., 19, 330-338.
25. Birdsell,J.A. (2002) Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution. Mol. Biol. Evol., 19, 1181-1197.
26. Galtier,N. and Duret,L. (2007) Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution. Trends Genet. 23, 273-277.
27. Ardlie,K., Liu-Cordero,S.N., Eberle,M.A., Daly,M., Barrett,J., Winchester,E., Lander,E.S. and Kruglyak,L. (2001) Lower-than-expected linkage disequilibrium between tightly linked markers in humans suggests a role for gene conversion. Am. J. Hum. Genet., 69, 582-589.
28. Frisse,L., Hudson,R.R., Bartoszewicz,A., Wall,J.D., Donfack,J. and Di Rienzo,A. (2001) Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am. J. Hum. Genet., 69, 831-843.
29. Lazzaro,B.P. and Clark,A.G. (2001) Evidence for recurrent paralogous gene conversion and exceptional allelic divergence in the Attacin genes of Drosophila melanogaster. Genetics, 159, 659-671.
30. Bailey,J.A., Gu,Z., Clark,R.A., Reinert,K., Samonte,R.V., Schwartz,S., Adams,M.D., Myers,E.W., Li,P.W. and Eichler,E.E. (2002) Recent segmental duplications in the human genome. Science, 297, 1003-1007.
31. Zhang,L.Q., Lu,H.H.S., Chung,W.Y., Yang,J. and Li,W.H. (2005) Patterns of segmental duplication in the human genome. Mol. Biol. Evol., 22, 135-141.
32. Zhang,L. (2008) Adaptive evolution and frequent gene conversion in the brain expressed X-linked gene family in mammals. Biochem. Genet., 46, 293-311.
33. Alvarez,E., Zhou,W., Witta,S.E. and Freed,C.R. (2005) Characterization of the BEX gene family in humans, mice, and rats. Gene, 357, 18-28.
34. Saito-Ohara,F., Fukuda,Y., Ito,M., Agarwala,K.L., Hayashi,M., Matsuo,M., Imoto,I., Yamakawa,K., Nakamura,Y. and Inazawa,J. (2002) The Xq22 inversion breakpoint interrupted a novel Ras-like GTpase gene in a patient with duchenne muscular dystrophy and profound mental retardation. Am. J. Hum. Genet., 71, 637-645.
35. Maizels,N. (2005) Immunoglobulin gene diversification. Ann. Rev. Genet., 39, 23-46.
36. Chen,J.M., Cooper,D.N., Chuzhanova,N., Ferec,C. and Patrinos,G.P. (2007) Gene conversion: Mechanisms, evolution and human disease. Nat. Rev. Genet., 8, 762-775.
37. Pan,D. and Zhang,L. (2007) Quantifying the major mechanisms of recent gene duplications in the human and mouse genomes: A novel strategy to estimate gene duplication rates. Genome Biol., 8, R158.
38. Lawson,M.J., Heath,L.S., Ramakrishnan,N. and Zhang,L. (2008) Using cost-sensitive learning to determine gene conversions. In Huang,D.-S., II,D.C.W., Levine,D.S. and Jo,K.-H. (eds), ICIC (2), Vol. 5227 of Lecture Notes in Computer Science, pp. 1030-1038.
39. Winter,E. and Ponting,C. (2005) Mammalian BEX, WEX and GASP genes: coding and non-coding chimaerism sustained by gene conversion events. BMC Evol. Biol., 5.
40. Schienman,J.E., Holt,R.A., Auerbach,M.R. and Stewart,C.B. (2006) Duplication and divergence of 2 distinct pancreatic ribonuclease genes in leaf-eating African and Asian colobine monkeys. Mol. Biol. Evol. 23, 1465-1479.