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Genes on X and Y Chromosomes

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Evolution of the Human Genome I

Part of the book series: Evolutionary Studies ((EVOLUS))

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Abstract

It is widely accepted that therian (placental and marsupial mammal) X and Y chromosomes were differentiated from a pair of autosomes by means of either chromosomal inversions or accumulation of linked sex-determining genes or both. This evolutionary process has been dynamic and involved stepwise differentiation of proto-sex chromosomes with leaving footprints of ancient pseudo-autosomal boundaries on the X chromosome and deterioration of gametologous genes on the Y chromosome without recombination. Genes or gene families on the X and Y chromosomes have been originated in three different ways: allelic pairs on the proto-sex chromosomes, retropositions, or translocations of autosomal genes. Gene duplication and conversion have also played important roles in the evolution of these genes particularly when they form palindromic structures. Because of the rapid evolution and unique structure of the therian X and Y chromosomes, there exist quite a few genes that are specific to humans. In this chapter, we overview our current knowledge about the origin and evolution of the therian sex chromosomes and genes and discuss future perspectives.

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References

  • Bellott DW, Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Cho T-J, Koutseva N, Zaghlul S, Graves T, Rock S, Kremitzki C, Fulton RS, Dugan S, Ding Y, Morton D, Khan Z, Lewis L, Buhay C, Wang Q, Watt J, Holder M, Lee S, Nazareth L, Rozen S, Muzny DM, Warren WC, Gibbs RA, Wilson RK, Page DC (2014) Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature 508:494–499

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bhowmick BK, Satta Y, Takahata N (2007) The origin and evolution of human ampliconic gene families and ampliconic structure. Genome Res 17:441–450

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Charchar FJ, Svartman M, El-Mogharbel N, Ventura M, Kirby P, Matarazzo MR, Ciccodicola A, Rocchi M, D’Esposito M, Graves JAM (2003) Complex events in the evolution of the human pseudoautosomal region 2 (PAR2). Genome Res 13:281–286

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Charlesworth B, Charlesworth D (2000) The degeneration of Y chromosomes. Philos Trans R Soc Lond Ser B Biol Sci 355:1563–1572

    Article  CAS  Google Scholar 

  • Charlesworth D, Charlesworth B, Marais G (2005) Steps in the evolution of heteromorphic sex chromosomes. Heredity 95:118–128

    Article  CAS  PubMed  Google Scholar 

  • Cortez D, Martin R, Toledo-Flores D, Froidevaux L, Waters PD, Grützver F, Kaessmann H (2014) Origins and functional evolution of Y chromosomes across mammals. Nature 508:488–493

    Article  CAS  PubMed  Google Scholar 

  • Engelstädter J (2008) Muller’s ratchet and the degeneration of Y chromosomes: a simulation study. Genetics 180:957–967

    Article  PubMed  PubMed Central  Google Scholar 

  • Graves J (2006) Sex chromosome specialization and degeneration in mammals. Cell 124:901–914

    Article  PubMed  Google Scholar 

  • Grützner F, Rens W, Tsend-Ayush E, El-Mogharbel N, O’Brien PCM, Jones RC, Ferguson-Smith MA, Graves JAM (2004) In the platypus a meiotic chain of ten sex chromosomes shares genes with the bird Z and mammal X chromosomes. Nature 432:913–917

    Article  PubMed  Google Scholar 

  • Hughes JF, Skaletsky H, Pyntikova T, Graves TA, van Daalen SKM, Minx PJ, Fulton RS, McGrath SD, Locke DP, Friedman C, Trask BJ, Mardis ER, Warren WC, Repping S, Rozen S, Wilson RK, Page DC (2010) Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature 463:536–539

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Iwase M, Satta Y, Hirai Y, Hirai H, Imai H, Takahata N (2003) The amelogenin loci span an ancient pseudoautosomal boundary in diverse mammalian species. Proc Natl Acad Sci U S A 100:5258–5263

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Iwase M, Kaneko S, Kim HL, Satta Y, Takahata N (2007) Evolutionary history of sex-linked mammalian amelogenin genes. Cells Tissues Organs 186:49–59

    Article  PubMed  Google Scholar 

  • Iwase M, Satta Y, Hirai H, Hirai Y, Takahata N (2010) Frequent gene conversion events between the X and Y homologous chromosomal regions in primates. BMC Evol Biol 10:225. https://doi.org/10.1186/1471-2148-10-225

    Article  PubMed  PubMed Central  Google Scholar 

  • Katsura Y, Satta Y (2011) Evolutionary history of the cancer immunity antigen MAGE gene family. PLoS One 6.:Article ID:e20365

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Katsura Y, Satta Y (2012) No evidence for a second evolutionary stratum during the early evolution of mammalian sex chromosomes. PLoS One 7:e45488

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Katsura Y, Iwase M, Satta Y (2012) Evolution of genomic structures on mammalian sex chromosomes. Curr Genomics 13:115–123

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim HL, Iwase M, Igawa T, Nishioka T, Kaneko S, Katsura Y, Takahata N, Satta Y (2012) Genomic structure and evolution of multigene families: “Flowers” on the human genome. Int J Evol Biol 2012:Article ID 917678

    Google Scholar 

  • Kuroda-Kawaguchi T, Skaletsky H, Brown LG, Minx PJ, Cordum HS, Waterston RH, Wilson RK, Silber S, Oates R, Rozen R, Page DC (2001) The AZFc region of the Y chromosome features massive palindromes and uniform recurrent deletions in infertile men. Nat Genet 29:279–286

    Article  CAS  PubMed  Google Scholar 

  • Kuroiwa A, Ishiguchi Y, Yamada F, Abe S, Matsuda Y (2010) The process of Y-loss event in XO/XO mammal, Ryukyu spiny rat. Chromosoma 119:519–526

    Article  PubMed  Google Scholar 

  • Kuroki Y, Toyoda A, Noguchi H, Taylor TD, Itoh T, Kim DS, Kim DW, Choi SH, Kim IC, Choi HH, Kim YS, Satta Y, Saitou N, Yamada T, Morishita S, Hattori M, Sakaki Y, Park HS, Fujiyama A (2006) Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway. Nat Genet 38:158–167

    Article  CAS  PubMed  Google Scholar 

  • Lahn B, Page D (1999) Four evolutionary strata on the human X chromosome. Science 286:964–967

    Article  CAS  PubMed  Google Scholar 

  • Lemaitre C, Braga MDV, Gautier C, Sagot M-F, Tannier E, Marais GAB (2009) Footprints of inversion at present and past pseudoautosomal boundaries in human sex chromosomes. Genome Biol Evol 1:56–66

    Article  PubMed  PubMed Central  Google Scholar 

  • Matsuranaga S (2006) Sex chromosome-linked genes in plants. Genes Genet Syst 81:219–226

    Article  Google Scholar 

  • Mueller JL, Skaletsky H, Brown LG, Zaghlul S, Rock S, Graves T, Auger K, Warren WC, Wilson RK, Page DC (2013) Independent specialization of the human and mouse X chromosomes for the male germ line. Nat Genet 45:1083–1087

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Muller H (1914) A factor for the fourth chromosome of drosophila. Science 39:906

    Article  CAS  PubMed  Google Scholar 

  • Nei M (1969) Heterozygous effects and frequency changes of lethal genes in populations. Genetics 63:669–680

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ohno S (1967) Sex chromosome and sex linked genes. Springer, New York

    Book  Google Scholar 

  • Pandey RS, Sayres MAW, Azad RK (2013) Detecting evolutionary strata on the human X chromosome in the absence of gametologous Y-linked sequences. Genome Biol Evol (in press)

    Google Scholar 

  • Rens W, CM O’Brien PCM, Grützner F, Clarke O, Graphodatskaya D, Tsend-Ayush E, Trifonov VA, Skelton H, Wallis MC, Johnston S, Veyrunes F, Graves JAM, Ferguson-Smith MA (2007) The multiple sex chromosomes of platypus and echidna are not completely identical and several share homology with the avian Z. Genome Biol 8:R243

    Google Scholar 

  • Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K et al (2007) The DNA sequence of the human X chromosome. Nature 434:325–337

    Google Scholar 

  • Ross J, Peichel CL (2008) Molecular cytogenetic evidence of rearrangements on the Y chromosome of the three spine stickleback fish. Genetics 179:2173–2182

    Article  PubMed  PubMed Central  Google Scholar 

  • Shevchenko AI, Zakharova IS, Zaikan SM (2013) The evolutionary pathway of X chromosome inactivation in mammals. ACTA Nat 5:40–53

    CAS  Google Scholar 

  • Sinclair AH, Berta P, Palmer MS, Hawkins JR, Griffiths BL, Smith MJ, Foster JW, Frischauf A-M, Lovell-Badge R, Goodfellow PN (1990) A gene from the human sex-determining region encodes a protein with homology to a conserved DNA-binding motif. Nature 346:240–244

    Article  CAS  PubMed  Google Scholar 

  • Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier L, Brown LG, Repping S, Pyntikova T, Ali J, Bieri T, Chinwalla A, Delehaunty A, Delehaunty K, Du H, Fewell G, Fulton L, Fulton R, Graves T, Hou SF, Latrielle P, Leonard S, Mardis E, Maupin R, McPherson J, Miner T, Nash W, Nguyen C, Ozersky P, Pepin K, Rock S, Rohlfing T, Scott K, Schultz B, Strong C, Tin-Wollam A, Yang SP, Waterston RH, Wilson RK, Rozen S, Page DC (2003) The malespecific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423:825–837

    Article  CAS  PubMed  Google Scholar 

  • Toll-Riera M, Bosch N, Bellora N, Castelo R, Armengol L, Estivill X, Alba MM (2008) Origin of primate orphan genes: a comparative genomics approach. Mol Biol Evol 26:603–612

    Article  PubMed  Google Scholar 

  • Veyrunes F, Waters PD, Miethke P, Rens W, McMillan D, Alsop AE, Grützner F, Deakin JE, Whittington CM, Schatzkamer K, Kremitzki CL, Graves T, Ferguson-Smith MA, Warren W, Graves JAM (2008) Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes. Genome Res 18:965–973

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wilson MA, Makova KD (2009) Evolution and survival on eutherian sex chromosomes. PLoS Genet 5:e1000568

    Article  PubMed  PubMed Central  Google Scholar 

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Correspondence to Yoko Satta .

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Satta, Y., Katsura, Y., Iwase, M. (2017). Genes on X and Y Chromosomes. In: Saitou, N. (eds) Evolution of the Human Genome I. Evolutionary Studies. Springer, Tokyo. https://doi.org/10.1007/978-4-431-56603-8_8

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