Sự tiến hóa của gia đình gen RPS4Y ở động vật linh trưởng

Nygard , Nika : Identification by RNA-protein cross-linking of ribosomal proteins located at the interface between the small and the large subunits of mammalian ribosomes. EMBO J. 1982, 1: 357-362. Bergen AW, Pratt M, Mehlman PT, Goldman D: Evolution of RPS4Y. Mol Biol Evol. 1998, 15: 1412-1419. Fisher EM, Beer-Romero P, Brown LG, Ridley A, McNeil JA, Lawrence JB, Willard HF, Bieber FR, Page DC: Homologous ribosomal protein genes on the human X and Y chromosomes: escape from X inactivation and possible implications for Turner syndrome. Cell. 1990, 63: 1205-1218. 10.1016/0092-8674(90)90416-C. Omoe K, Endo A: Relationship between the monosomy X phenotype and Y linked ribosomal protein S4 (Rps4) in several species of mammals: a molecular evolutionary analysis of Rps4 homologs. Genomics. 1996, 31: 44-50. 10.1006/geno.1996.0007. Jegalian K, Page DC: A proposed path by which genes common to mammalian X and Y chromosomes evolve to become X inactivated. Nature. 1998, 394: 776-780. 10.1038/29522. Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, (40 co-authors): The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature. 2003, 423: 825-837. 10.1038/nature01722. Hubbard TJP, Aken BL, Beal K, (58 co-authors): Ensembl 2007. Nucleic Acids Res. 2007, D610-7. 10.1093/nar/gkl996. 35 Database Meyuhas O, Avni D, Shama S: Translational control of ribosomal protein mRNAs in eukaryotes. Translational Control. Edited by: Hershey JWB, Mathews MB, Sonenberg N. 1996, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 363-388. Watanabe M, Zinn AR, Page DC, Nishimoto T: Functional equivalence of human X and Y-encoded isoforms of ribosomal protein S4 consistent with a role in Turner syndrome. Nat Genet. 1993, 4: 268-271. 10.1038/ng0793-268. Zinn AR, Alagappan RK, Brown LG, Wool I, Page DC: Structure and function of ribosomal protein S4 genes on the human and mouse sex chromosomes. Mol Cell Biol. 1994, 14: 2485-2492. Lambertsson A: The Minute genes in Drosophila and their molecular functions. Adv Genet. 1998, 38: 69-134. Wool IG: Extraribosomal functions of ribosomal proteins. TIBS. 1996, 21: 164-165. Yoshihama M, Uechi T, Asakawa S, Kawasaki K, Kato S, Higa S, Maeda N, Minoshima S, Tanaka T, Shimizu N, Kenmochi N: The human ribosomal protein genes: sequencing and comparative analysis of 73 genes. Genome Res. 2002, 12: 379-390. 10.1101/gr.214202. Castillo-Davis CI, Mekhedov SL, Hartl DL, Koonin EV, Kondrashov FA: Selection for short introns in highly expressed genes. Nature. 2002, 31: 415-418. Parsch J: Selective constraints on intron evolution in Drosophila. Genetics. 2003, 165: 1843-1851. Goodman M, Porter CA, Czelusniak J, Page SL, Schneider H, Shoshani J, Gunnell G, Groves CP: Toward a phylogenetic classification of Primates based on DNA evidence complemented by fossil evidence. Mol Phylogenet Evol. 1998, 9: 585-598. 10.1006/mpev.1998.0495. Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 1997, 13: 555-556. Benjamini Y, Hochberg Y: Controlling the false discovery rate: A practical and powerful approach to multiple testing. J Royal Stat Soc B. 1995, 57: 289-300. Nielsen R, Yang Z: Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics. 1998, 148: 929-936. Yang Z, Nielsen R, Goldman N, Pedersen AM: Codon substitution models for heterogeneous selection pressure at amino acid sites. Genetics. 2000, 155: 431-449. Yang Z, Nielsen R: Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol. 2002, 19: 908-917. Graves JAM: Sex chromosome specialization and degeneration in mammals. Cell. 2006, 124: 901-914. 10.1016/j.cell.2006.02.024. Graves JAM, Koina E, Sankovic N: How the gene content of human sex chromosomes evolved. Curr Opinion Genet Develop. 2006, 16: 219-224. 10.1016/j.gde.2006.04.007. Uechi T, Maeda N, Tanaka T, Kenmochi N: Functional second genes generated by retrotransposition of the X-linked ribosomal protein genes. Nucleic Acids Res. 2002, 30: 5369-5375. 10.1093/nar/gkf696. Lynch M, Conery JS: The evolutionary demography of duplicate genes. J Struct Funct Genomics. 2003, 3: 35-44. 10.1023/A:1022696612931. Ohno S: Evolution by gene duplication. 1970, Berlin: Springer Ferris SD, Whitt GS: Evolution of the differential regulation of duplicate genes after polyploidization. J Mol Evol. 1979, 12: 267-317. 10.1007/BF01732026. Shiu SH, Byrnes JK, Pan R, Zhang P, Li WH: Role of positive selection in the retention of duplicate genes in mammalian genomes. Proc Natl Acad Sci USA. 2006, 103: 2232-2236. 10.1073/pnas.0510388103. Wilda M, Bächner D, Zechner U, Kehrer-Sawatzki H, Vogel W, Hameister H: Do the constraints of human speciation cause expression of the same set of genes in brain, testis, and placenta?. Cytogenet Cell Genet. 2000, 91: 300-302. 10.1159/000056861. Kyrpides NC, Woese CR, Ouzounis CA: KOW: a novel motif linking a bacterial transcription factor with ribosomal proteins. Trends Biochem Sci. 1998, 21: 425-426. 10.1016/S0968-0004(96)30036-4. Hopps CV, Mielnik A, Goldstein M, Palermo GD, Rosenwaks Z, Schlegel PN: Detection of sperm in men with Y chromosome microdeletions of the AZFa, AZFb and AZFc regions. Hum Reprod. 2003, 18: 1660-1665. 10.1093/humrep/deg348. Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, Hubisz MJ, Fledel-Alon A, Tanenbaum DM, Civello D, White TJ, J Sninsky J, Adams MD, Cargill M: A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol. 2005, 3: e170-10.1371/journal.pbio.0030170. Arbiza L, Dopazo J, Dopazo H: Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome. PLoS Comput Biol. 2006, 2: e38-10.1371/journal.pcbi.0020038. Repeatmasker. [http://www.repeatmasker.org] Hall TA: BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser. 1999, 41: 95-98. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22: 4673-4680. 10.1093/nar/22.22.4673. Morgenstern B: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics. 1999, 15: 211-218. 10.1093/bioinformatics/15.3.211. Castresana J: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000, 17: 540-552. Rozas J, Sánchez-Delbarrio JC, Messeguer X, Rozas R: DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics. 2003, 19: 2496-2497. 10.1093/bioinformatics/btg359. Posada D, Crandall KA: Modeltest: testing the model of DNA substitution. Bioinformatics. 1998, 14: 817-818. 10.1093/bioinformatics/14.9.817. Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987, 4: 406-425. Swofford DL: PAUP*: phylogenetic analysis using parsimony (* and other methods). Version 4.0b10. Sunderland (MA): Sinauer Associates. 2002 Felsenstein J: Confidence limits on phylogenies: An approach using the bootstrap. Evolution. 1985, 39: 783-791. 10.2307/2408678. Robinson-Rechavi M, Huchon D: RRTree: Relative-rate tests between groups of sequences on a phylogenetic tree. Bioinformatics. 2000, 16: 296-297. 10.1093/bioinformatics/16.3.296. Page RDM: TREEVIEW: An application to display phylogenetic trees on personal computers. Comput Appl Biosci. 1996, 12: 357-358.