A genome-wide landscape of retrocopies in primate genomes

Genome Biology and Evolution

Volumn 7, Issue 8, 2015, Pages 2265-2275

  Navarro, Fábio C P ^a,b   Galante, Pedro A F ^a  

^a HOSPITAL SÍRIO LIBANÊS   (Brazil)

^b UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Gene duplication; Primate genomes; Retrocopy; Retrogene

Indexed keywords

MESSENGER RNA; RETROPOSON; TRANSCRIPTOME;

ANIMAL; CATARRHINI; GENE DUPLICATION; GENETICS; GENOME; GENOMICS; HUMAN; LONG INTERSPERSED REPEAT; MOLECULAR EVOLUTION; MOUSE; PLATYRRHINI; RAT; RETROPOSON; SPECIES DIFFERENCE;

ANIMALS; CATARRHINI; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENOME; GENOMICS; HUMANS; LONG INTERSPERSED NUCLEOTIDE ELEMENTS; MICE; PLATYRRHINI; RATS; RETROELEMENTS; RNA, MESSENGER; SPECIES SPECIFICITY; TRANSCRIPTOME;

EID: 84954328457     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evv142     Document Type: Article

References (61)

1. Baertsch R, Diekhans M, Kent WJ, Haussler D, Brosius J. 2008. Retrocopy contributions to the evolution of the human genome. BMC Genomics 9:466.
2. Bai Y, Casola C, Feschotte C, Betrán E. 2007. Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila. Genome Biol. 8:R11.
3. Balasubramanian S, et al 2009. Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes. Genome Biol. 10:R2.
4. Brawand D, et al 2011. The evolution of gene expression levels in mammalian organs. Nature 478:343-348.
5. Carbone L, et al 2012. Centromere remodeling in Hoolock leuconedys (Hylobatidae) by a new transposable element unique to the gibbons. Genome Biol EVol. 4:648-658.
6. Carbone L, et al 2014. Gibbon genome and the fast karyotype evolution of small apes. Nature 513:195-201.
7. Charlesworth D, Charlesworth B, Morgan MT 1995. The pattern of neutral molecular variation under the background selection model. Genetics 141:1619-1632.
8. Chimpanzee Sequencing and Analysis Consortium. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437:69-87.
9. Conrad B, Antonarakis SE 2007. Gene duplication: a drive for phenotypic diversity and cause of human disease. Annu Rev Genomics Hum Genet. 8:17-35.
10. Emerson JJ, Kaessmann H, Betrán E, Long M. 2004. Extensive gene traffic on the mammalian X chromosome. Science 303:537-540.
11. Esnault C, Maestre J, Heidmann T. 2000. Human LINE retrotransposons generate processed pseudogenes. Nat Genet. 24:363-367.
12. Fairbanks DJ, Fairbanks AD, Ogden TH, Parker G.J., Maughan PJ. 2012. NANOGP8: evolution of a human-specific retro-oncogene. G3 2:1447-1457.
13. Feng Q, Moran JV, Kazazian HH, Boeke JD 1996. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87:905-916.
14. Flicek P, et al 2014. Ensembl 2014. Nucleic Acids Res. 42:D749-D755.
15. Galante PAF, Vidal DO, de Souza JE, Camargo AA, de Souza SJ. 2007. Sense-antisense pairs in mammals: functional and evolutionary considerations. Genome Biol. 8:R40.
16. Groves CP. 2001. Primate taxonomy. Washington (DC): Smithsonian Inst Press.
17. Hohjoh H, Singer MF 1997. Sequence-specific single-strand RNA binding protein encoded by the human LINE-1 retrotransposon. EMBO J. 16:6034-6043.
18. Hung M-S, et al. 2010. Functional polymorphism of the CK2alpha intronless gene plays oncogenic roles in lung cancer. PLoS One 5:e11418.
19. Jameson NM, Xu K, Yi SV, Wildman DE 2012. Development and annotation of shotgun sequence libraries from New World monkeys. Mol Ecol Resour. 12:950-955.
20. Jongeneel CV, et al 2005. An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Res. 15: 1007-1014.
21. Kaessmann H, Vinckenbosch N, Long M. 2009. RNA-based gene duplication: mechanistic and evolutionary insights. Nat Rev Genet. 10:19-31.
22. Kalyana-Sundaram S., et al 2012. Expressed pseudogenes in the transcriptional landscape of human cancers. Cell 149:1622-1634.
23. Karolchik D, et al 2014. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res. 42:D764-D770.
24. Lander ES, et al 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
25. Langmead B, Salzberg SL 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods. 9:357-359.
26. Larkin MA, et al 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948.
27. Letunic I, Bork P. 2011. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. 39:W475-W478.
28. Long M, Betrán E, Thornton K, Wang W. 2003. The origin of new genes: glimpses from the young and old. Nat Rev Genet. 4:865-875.
29. Lowe CB, Bejerano G, Haussler D. 2007. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci U S A. 104:8005-8010.
30. Mandal PK, Kazazian HH Jr. 2008. SnapShot: vertebrate transposons. Cell 135:192-192. e1.
31. Marques AC, Dupanloup I, Vinckenbosch N, Reymond A., Kaessmann H. 2005a. Emergence of young human genes after a burst of retroposition in primates. PLoS Biol. 3:e357.
32. Marques AC, Dupanloup I, Vinckenbosch N, Reymond A., Kaessmann H. 2005b. Emergence of young human genes after a burst of retroposition in primates. PLoS Biol. 3:e357.
33. Marques-Bonet T., Girirajan S, Eichler EE 2009. The origins and impact of primate segmental duplications. Trends Genet. 25:443-454.
34. Marques-Bonet T., Kidd JM, et al 2009. A burst of segmental duplications in the genome of the African great ape ancestor. Nature 457:877-881.
35. Mathias SL, Scott AF, Kazazian HH, Boeke J.D., Gabriel A. 1991. Reverse transcriptase encoded by a human transposable element. Science 254:1808-1810.
36. McCarrey JR, Thomas K. 1987. Human testis-specific PGK gene lacks introns and possesses characteristics of a processed gene. Nature 326:501-505.
37. McClintock B. 1953. Induction of instability at selected loci in maize. Genetics 38:579-599.
38. Navarro FCP, Galante PAF. 2013. RCPedia: a database of retrocopied genes. Bioinformatics 29:1235-1237.
39. Ohno S. 1970. Evolution by gene duplication. New York: Springer.
40. Ohshima K, et al 2003. Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. Genome Biol. 4:R74.
41. Pei B, et al 2012. The GENCODE pseudogene resource. Genome Biol. 13:R51.
42. Poliseno L, et al 2010. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465:1033-1038.
43. Prince VE, Pickett FB 2002. Splitting pairs: the diverging fates of duplicated genes. Nat Rev Genet. 3:827-837.
44. Pruitt KD, et al 2014. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 42:D756-D763.
45. Richler C, Soreq H, Wahrman J. 1992. X inactivation in mammalian testis is correlated with inactive X-specific transcription. Nat Genet. 2:192-195.
46. Sakai H, Koyanagi KO, Imanishi T, Itoh T, Gojobori T. 2007. Frequent emergence and functional resurrection of processed pseudogenes in the human and mouse genomes. Gene 389:196-203.
47. Scally A, et al 2012. Insights into hominid evolution from the gorilla genome sequence. Nature 483:169-175.
48. Schrider DR, et al 2013. Gene copy-number polymorphism caused by retrotransposition in humans. PLoS Genet. 9:e1003242.
49. Sharp AJ, et al 2005. Segmental duplications and copy-number variation in the human genome. Am J Hum Genet. 77:78-88.
50. Steiper ME, Young NM 2006. Primate molecular divergence dates. Mol Phylogenet EVol. 41:384-394.
51. Tam OH, et al 2008. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 453:534-538.
52. Trembley JH, et al 2005. Activation of pre-mRNA splicing by human RNPS1 is regulated by CK2 phosphorylation. Mol Cell Biol. 25:1446-1457.
53. Vanin EF. 1985. Processed pseudogenes: characteristics and evolution. Annu Rev Genet. 19:253-272.
54. Venter JC, et al 2001. The sequence of the human genome. Science 291:1304-1351.
55. 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.
56. Wirkner U, et al 1992. Human casein kinase II subunit alpha: sequence of a processed (pseudo) gene and its localization on chromosome 11. Biochim Biophys Acta. 1131:220-222.
57. Wu TD, Nacu S. 2010. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics. 26:873-881.
58. Yanai I, et al 2005. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21:650-659.
59. Zhang J. 2003. Evolution by gene duplication: an update. Trends Ecol EVol. 18:292-298.
60. Zhang Q. 2013. The role of mRNA-based duplication in the evolution of the primate genome. FEBS Lett. 587:3500-3507.
61. Zhang Z, Carriero N, Gerstein M. 2004. Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends Genet. 20:62-67.