The rapid generation of chimerical genes expanding protein diversity in zebrafish

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Fu, Beide ^a,b   Chen, Ming ^a,b   Zou, Ming ^a,b   Long, Manyuan ^c   He, Shunping ^a  

^a INSTITUTE OF HYDROBIOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; CARP; CHIMERA; CONTROLLED STUDY; DROSOPHILA; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC TRANSCRIPTION; GENOME ANALYSIS; INTRON; MOLECULAR EVOLUTION; NONHUMAN; ORTHOLOGY; PSEUDOGENE; RICE; RNA SPLICING; ZEBRA FISH; ANIMAL; DUPLICATE GENE; EXPRESSED SEQUENCE TAG; GENE DUPLICATION; GENE EXPRESSION REGULATION; GENETIC VARIABILITY; GENETICS; GENOME; NUCLEOTIDE SEQUENCE;

CYPRINUS CARPIO; DANIO RERIO; MAMMALIA; PRIMATES; TELEOSTEI;

FISH PROTEIN;

ANIMALS; BASE SEQUENCE; EXPRESSED SEQUENCE TAGS; FISH PROTEINS; GENE DUPLICATION; GENE EXPRESSION REGULATION; GENES, DUPLICATE; GENETIC VARIATION; GENOME; TRANSCRIPTION, GENETIC; ZEBRAFISH;

EID: 78549247150     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-657     Document Type: Article

References (58)

1. Li W-H. Molecular Evolution. 1997, Sunderland, MA.: Sinauer Associates.
2. Brosius J. Retroposons--seeds of evolution. Science (New York, NY) 1991, 251(4995):753.
3. Long M, Wang W, Zhang J. Origin of new genes and source for N-terminal domain of the chimerical gene, jingwei, in Drosophila. Gene 1999, 238(1):135-141. 10.1016/S0378-1119(99)00229-2, 10570991.
4. Long M, Langley CH. Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science (New York, NY) 1993, 260(5104):91-95.
5. Wang W, Brunet FG, Nevo E, Long M. Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America 2002, 99(7):4448-4453. 10.1073/pnas.072066399, 123668, 11904380.
6. Damert A, Raiz J, Horn AV, Lower J, Wang H, Xing J, Batzer MA, Lower R, Schumann GG. 5'-Transducing SVA retrotransposon groups spread efficiently throughout the human genome. Genome Res 2009, 19(11):1992-2008. 10.1101/gr.093435.109, 2775593, 19652014.
7. Buzdin A, Gogvadze E, Kovalskaya E, Volchkov P, Ustyugova S, Illarionova A, Fushan A, Vinogradova T, Sverdlov E. The human genome contains many types of chimeric retrogenes generated through in vivo RNA recombination. Nucleic acids research 2003, 31(15):4385-4390. 10.1093/nar/gkg496, 169886, 12888497.
8. Buzdin A, Ustyugova S, Gogvadze E, Vinogradova T, Lebedev Y, Sverdlov E. A new family of chimeric retrotranscripts formed by a full copy of U6 small nuclear RNA fused to the 3' terminus of l1. Genomics 2002, 80(4):402-406. 10.1006/geno.2002.6843, 12376094.
9. Bantysh OB, Buzdin AA. Novel family of human transposable elements formed due to fusion of the first exon of gene MAST2 with retrotransposon SVA. Biochemistry 2009, 74(12):1393-1399.
10. Hancks DC, Ewing AD, Chen JE, Tokunaga K, Kazazian HH. Exon-trapping mediated by the human retrotransposon SVA. Genome Res 2009, 19(11):1983-1991. 10.1101/gr.093153.109, 2775590, 19635844.
11. Betran E, Thornton K, Long M. Retroposed new genes out of the × in Drosophila. Genome Res 2002, 12(12):1854-1859. 10.1101/gr.6049, 187566, 12466289.
12. Nisole S, Lynch C, Stoye JP, Yap MW. A Trim5-cyclophilin A fusion protein found in owl monkey kidney cells can restrict HIV-1. Proceedings of the National Academy of Sciences of the United States of America 2004, 101(36):13324-13328. 10.1073/pnas.0404640101, 516566, 15326303.
13. Zhang J, Dean AM, Brunet F, Long M. Evolving protein functional diversity in new genes of Drosophila. Proceedings of the National Academy of Sciences of the United States of America 2004, 101(46):16246-16250. 10.1073/pnas.0407066101, 528974, 15534206.
14. Long M, Betran E, Thornton K, Wang W. The origin of new genes: glimpses from the young and old. Nature reviews 2003, 4(11):865-875.
15. Emerson JJ, Kaessmann H, Betran E, Long M. Extensive gene traffic on the mammalian × chromosome. Science (New York, NY) 2004, 303(5657):537-540.
16. Krasnov AN, Kurshakova MM, Ramensky VE, Mardanov PV, Nabirochkina EN, Georgieva SG. A retrocopy of a gene can functionally displace the source gene in evolution. Nucleic acids research 2005, 33(20):6654-6661. 10.1093/nar/gki969, 1298928, 16314324.
17. Bai Y, Casola C, Feschotte C, Betran E. Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila. Genome biology 2007, 8(1):R11. 10.1186/gb-2007-8-1-r11, 1839131, 17233920.
18. Zhang Y, Wu Y, Liu Y, Han B. Computational identification of 69 retroposons in Arabidopsis. Plant physiology 2005, 138(2):935-948. 10.1104/pp.105.060244, 1150409, 15923328.
19. Yu Z, Morais D, Ivanga M, Harrison PM. Analysis of the role of retrotransposition in gene evolution in vertebrates. BMC bioinformatics 2007, 8:308. 10.1186/1471-2105-8-308, 2048973, 17718914.
20. Wang W, Zheng H, Fan C, Li J, Shi J, Cai Z, Zhang G, Liu D, Zhang J, Vang S, et al. High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell 2006, 18(8):1791-1802. 10.1105/tpc.106.041905, 1533979, 16829590.
21. Bellingham J, Tarttelin EE, Foster RG, Wells DJ. Structure and evolution of the teleost extraretinal rod-like opsin (errlo) and ocular rod opsin (rho) genes: is teleost rho a retrogene?. Journal of experimental zoology Part B 2003, 297(1):1-10.
22. Esnault C, Maestre J, Heidmann T. Human LINE retrotransposons generate processed pseudogenes. Nature genetics 2000, 24(4):363-367. 10.1038/74184, 10742098.
23. Furano AV. The biological properties and evolutionary dynamics of mammalian LINE-1 retrotransposons. Progress in nucleic acid research and molecular biology 2000, 64:255-294. full_text, 10697412.
24. Furano AV, Duvernell DD, Boissinot S. L1 (LINE-1) retrotransposon diversity differs dramatically between mammals and fish. Trends Genet 2004, 20(1):9-14. 10.1016/j.tig.2003.11.006, 14698614.
25. Volff JN, Bouneau L, Ozouf-Costaz C, Fischer C. Diversity of retrotransposable elements in compact pufferfish genomes. Trends Genet 2003, 19(12):674-678. 10.1016/j.tig.2003.10.006, 14642744.
26. Betran E, Long M. Dntf-2r, a young Drosophila retroposed gene with specific male expression under positive Darwinian selection. Genetics 2003, 164(3):977-988. 1462638, 12871908.
27. Betran E, Wang W, Jin L, Long M. Evolution of the phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene. Molecular biology and evolution 2002, 19(5):654-663.
28. Burki F, Kaessmann H. Birth and adaptive evolution of a hominoid gene that supports high neurotransmitter flux. Nature genetics 2004, 36(10):1061-1063. 10.1038/ng1431, 15378063.
29. Marques AC, Dupanloup I, Vinckenbosch N, Reymond A, Kaessmann H. Emergence of young human genes after a burst of retroposition in primates. PLoS biology 2005, 3(11):e357. 10.1371/journal.pbio.0030357, 1251493, 16201836.
30. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
31. Birney E, Clamp M, Durbin R. GeneWise and Genomewise. Genome research 2004, 14(5):988-995. 10.1101/gr.1865504, 479130, 15123596.
32. Pearson WR. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods in enzymology 1990, 183:63-98. full_text, 2156132.
33. Yeo G, Hoon S, Venkatesh B, Burge CB. Variation in sequence and organization of splicing regulatory elements in vertebrate genes. Proceedings of the National Academy of Sciences of the United States of America 2004, 101(44):15700-15705. 10.1073/pnas.0404901101, 524216, 15505203.
34. Kruiswijk CP, Hermsen TT, Westphal AH, Savelkoul HF, Stet RJ. A novel functional class I lineage in zebrafish (Danio rerio), carp (Cyprinus carpio), and large barbus (Barbus intermedius) showing an unusual conservation of the peptide binding domains. J Immunol 2002, 169(4):1936-1947.
35. Pan D, Zhang L. Burst of young retrogenes and independent retrogene formation in mammals. PloS one 2009, 4(3):e5040. 10.1371/journal.pone.0005040, 2657826, 19325906.
36. Reinartz J, Bruyns E, Lin JZ, Burcham T, Brenner S, Bowen B, Kramer M, Woychik R. Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms. Briefings in functional genomics & proteomics 2002, 1(1):95-104.
37. Harbers M, Carninci P. Tag-based approaches for transcriptome research and genome annotation. Nature methods 2005, 2(7):495-502. 10.1038/nmeth768, 15973418.
38. Vinckenbosch N, Dupanloup I, Kaessmann H. Evolutionary fate of retroposed gene copies in the human genome. Proceedings of the National Academy of Sciences of the United States of America 2006, 103(9):3220-3225. 10.1073/pnas.0511307103, 1413932, 16492757.
39. Harrison PM, Zheng D, Zhang Z, Carriero N, Gerstein M. Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic acids research 2005, 33(8):2374-2383. 10.1093/nar/gki531, 1087782, 15860774.
40. Wang W, Yu H, Long M. Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species. Nature genetics 2004, 36(5):523-527. 10.1038/ng1338, 15064762.
41. Zhu Z, Zhang Y, Long M. Extensive structural renovation of retrogenes in the evolution of the Populus genome. Plant physiology 2009, 151(4):1943-1951. 10.1104/pp.109.142984, 2785971, 19789289.
42. Torrents D, Suyama M, Zdobnov E, Bork P. A genome-wide survey of human pseudogenes. Genome Res 2003, 13(12):2559-2567. 10.1101/gr.1455503, 403797, 14656963.
43. Nekrutenko A, Makova KD, Li WH. The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study. Genome Res 2002, 12(1):198-202. 10.1101/gr.200901, 155263, 11779845.
44. Moore RC, Purugganan MD. The early stages of duplicate gene evolution. Proceedings of the National Academy of Sciences of the United States of America 2003, 100(26):15682-15687. 10.1073/pnas.2535513100, 307628, 14671323.
45. Kazazian HH. Mobile elements: drivers of genome evolution. Science (New York, NY) 2004, 303(5664):1626-1632.
46. Sayah DM, Sokolskaja E, Berthoux L, Luban J. Cyclophilin A retrotransposition into TRIM5 explains owl monkey resistance to HIV-1. Nature 2004, 430(6999):569-573. 10.1038/nature02777, 15243629.
47. Brosius J, Gould SJ. On "genomenclature": a comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA". Proceedings of the National Academy of Sciences of the United States of America 1992, 89(22):10706-10710. 10.1073/pnas.89.22.10706, 50410, 1279691.
48. Brosius J. Many G-protein-coupled receptors are encoded by retrogenes. Trends Genet 1999, 15(8):304-305. 10.1016/S0168-9525(99)01783-7, 10431191.
49. Robinson R. Retrocopied Genes May Enhance Male Fitness. PLoS biology 2005, 1283399, 16277560.
50. Baertsch R, Diekhans M, Kent WJ, Haussler D, Brosius J. Retrocopy contributions to the evolution of the human genome. BMC genomics 2008, 9:466. 10.1186/1471-2164-9-466, 2584115, 18842134.
51. Ravi V, Venkatesh B. Rapidly evolving fish genomes and teleost diversity. Current opinion in genetics & development 2008, 18(6):544-550.
52. Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, et al. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 2004, 431(7011):946-957. 10.1038/nature03025, 15496914.
53. Patthy L. Genome evolution and the evolution of exon-shuffling--a review. Gene 1999, 238(1):103-114. 10.1016/S0378-1119(99)00228-0, 10570989.
54. Long M, Deutsch M, Wang W, Betran E, Brunet FG, Zhang J. Origin of new genes: evidence from experimental and computational analyses. Genetica 2003, 118(2-3):171-182. 10.1023/A:1024153609285, 12868607.
55. Podlaha O, Zhang J. Nonneutral evolution of the transcribed pseudogene Makorin1-p1 in mice. Molecular biology and evolution 2004, 21(12):2202-2209. 10.1093/molbev/msh230, 15306660.
56. Hirotsune S, Yoshida N, Chen A, Garrett L, Sugiyama F, Takahashi S, Yagami K, Wynshaw-Boris A, Yoshiki A. An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature 2003, 423(6935):91-96. 10.1038/nature01535, 12721631.
57. Li WH. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. Journal of molecular evolution 1993, 36(1):96-99. 10.1007/BF02407308, 8433381.
58. Kent WJ. BLAT--the BLAST-like alignment tool. Genome research 2002, 12(4):656-664. 187518, 11932250.