Hominoid-Specific De Novo Protein-Coding Genes Originating from Long Non-Coding RNAs

PLoS Genetics

Volumn 8, Issue 9, 2012, Pages

  Xie, Chen ^a   Zhang, Yong E ^b   Chen, Jia Yu ^a   Liu, Chu Jun ^a   Zhou, Wei Zhen ^a   Li, Ying ^a   Zhang, Mao ^a   Zhang, Rongli ^a   Wei, Liping ^a   Li, Chuan Yun ^a  

^a PEKING UNIVERSITY   (China)

^b INSTITUTE OF ZOOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

UNTRANSLATED RNA;

ADIPOSE TISSUE; APE; ARTICLE; CHIMPANZEE; DNA MICROARRAY; EXON; GENE DUPLICATION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC ASSOCIATION; LIVER; MICROARRAY ANALYSIS; NONHUMAN; OPEN READING FRAME; PHYLOGENY; POLYADENYLATION; PREFRONTAL CORTEX; RHESUS MONKEY; RNA SEQUENCE; SEQUENCE ANALYSIS; SKELETAL MUSCLE; TESTIS;

ANIMALS; EVOLUTION, MOLECULAR; HOMINIDAE; HUMANS; MACACA MULATTA; OPEN READING FRAMES; PAN TROGLODYTES; PHYLOGENY; RNA, LONG UNTRANSLATED; SPECIES SPECIFICITY; TISSUE DISTRIBUTION; TRANSCRIPTOME;

HOMINOIDEA; MACACA MULATTA; PAN; VERTEBRATA;

EID: 84866952741     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1002942     Document Type: Article

References (44)

1. Susumu O (1970) Evolution by gene duplication. Springer-Verlag ISBN 0-04-575015-7.
2. Jacob F, (1977) Evolution and tinkering. Science 196: 1161-1166.
3. Long M, Betran E, Thornton K, Wang W, (2003) The origin of new genes: glimpses from the young and old. Nat Rev Genet 4: 865-875.
4. Siepel A, (2009) Darwinian alchemy: Human genes from noncoding DNA. Genome Res 19: 1693-1695.
5. Wu D-D, Irwin DM, Zhang Y-P, (2011) De Novo Origin of Human Protein-Coding Genes. PLoS Genet 7: e1002379 doi:10.1371/journal.pgen.1002379.
6. Toll-Riera M, Bosch N, Bellora N, Castelo R, Armengol L, et al. (2008) Origin of primate orphan genes: a comparative genomics approach. Mol Biol Evol.
7. Knowles DG, McLysaght A, (2009) Recent de novo origin of human protein-coding genes. Genome Res 19: 1752-1759.
8. Li CY, Zhang Y, Wang Z, Zhang Y, Cao C, et al. (2010) A human-specific de novo protein-coding gene associated with human brain functions. PLoS Comput Biol 6: e1000734 doi:10.1371/journal.pcbi.1000734.
9. Begun DJ, Lindfors HA, Kern AD, Jones CD, (2007) Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade. Genetics 176: 1131-1137.
10. Cai J, Zhao R, Jiang H, Wang W, (2008) De novo origination of a new protein-coding gene in Saccharomyces cerevisiae. Genetics 179: 487-496.
11. Chen ST, Cheng HC, Barbash DA, Yang HP, (2007) Evolution of hydra, a recently evolved testis-expressed gene with nine alternative first exons in Drosophila melanogaster. PLoS Genet 3: e107 doi:10.1371/journal.pgen.0030107.
12. Levine MT, Jones CD, Kern AD, Lindfors HA, Begun DJ, (2006) Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression. Proc Natl Acad Sci U S A 103: 9935-9939.
13. Kaessmann H, (2010) Origins, evolution, and phenotypic impact of new genes. Genome Res 20: 1313-1326.
14. Tautz D, Domazet-Loso T, (2011) The evolutionary origin of orphan genes. Nat Rev Genet 12: 692-702.
15. Khalturin K, Hemmrich G, Fraune S, Augustin R, Bosch TC, (2009) More than just orphans: are taxonomically-restricted genes important in evolution? Trends Genet 25: 404-413.
16. Begun DJ, Lindfors HA, Thompson ME, Holloway AK, (2006) Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland expressed sequence tags. Genetics 172: 1675-1681.
17. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
18. Bornberg-Bauer E, Huylmans AK, Sikosek T, (2010) How do new proteins arise? Curr Opin Struct Biol 20: 390-396.
19. Schuster SC, (2008) Next-generation sequencing transforms today's biology. Nat Methods 5: 16-18.
20. Brawand D, Soumillon M, Necsulea A, Julien P, Csardi G, et al. (2011) The evolution of gene expression levels in mammalian organs. Nature 478: 343-348.
21. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470-476.
22. Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y, (2010) Sex-specific and lineage-specific alternative splicing in primates. Genome Res 20: 180-189.
23. Zhang YE, Landback P, Vibranovski MD, Long M, (2011) Accelerated recruitment of new brain development genes into the human genome. PLoS Biol 9: e1001179 doi:10.1371/journal.pbio.1001179.
24. Guerzoni D, McLysaght A, (2011) De Novo Origins of Human Genes. PLoS Genet 7: e1002381 doi:10.1371/journal.pgen.1002381.
25. Kimura M, (1977) Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 267: 275-276.
26. Librado P, Rozas J, (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
27. Zhou Q, Wang W, (2008) On the origin and evolution of new genes-a genomic and experimental perspective. J Genet Genomics 35: 639-648.
28. Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, et al. (2009) EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Research 19: 327-335.
29. Vinckenbosch N, Dupanloup I, Kaessmann H, (2006) Evolutionary fate of retroposed gene copies in the human genome. Proc Natl Acad Sci U S A 103: 3220-3225.
30. Mercer TR, Dinger ME, Mattick JS, (2009) Long non-coding RNAs: insights into functions. Nat Rev Genet 10: 155-159.
31. Zhou Q, Zhang G, Zhang Y, Xu S, Zhao R, et al. (2008) On the origin of new genes in Drosophila. Genome Res 18: 1446-1455.
32. Zhang YE, Vibranovski MD, Landback P, Marais GA, Long M, (2010) Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene gain on the X chromosome. PLoS Biol 8doi:10.1371/journal.pbio.1000494.
33. Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, et al. (2011) The UCSC Genome Browser database: update 2011. Nucleic Acids Res 39: D876-882.
34. Slater GS, Birney E, (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6: 31.
35. Flicek P, Amode MR, Barrell D, Beal K, Brent S, et al. (2011) Ensembl 2011. Nucleic Acids Res 39: D800-806.
36. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, et al. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12: 1611-1618.
37. Stabenau A, McVicker G, Melsopp C, Proctor G, Clamp M, et al. (2004) The Ensembl core software libraries. Genome Res 14: 929-933.
38. Vizcaino JA, Cote R, Reisinger F, Barsnes H, Foster JM, et al. (2010) The Proteomics Identifications database: 2010 update. Nucleic Acids Res 38: D736-742.
39. Deutsch EW, (2010) The PeptideAtlas Project. Methods Mol Biol 604: 285-296.
40. The-UniProt-Consortium (2011) Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res 39: D214-219.
41. Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, et al. (2009) Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 37: e123.
42. Trapnell C, Pachter L, Salzberg SL, (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
43. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B, (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628.
44. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.