Inter-population Differences in Retrogene Loss and Expression in Humans

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Many retrogenes, long considered to be genomic “junk”, were recently revealed as vitally important. Retroposition plays an important role in shaping differences between species, populations and individuals. Variation may result either from new retroposition events and/or retrocopy loss, as well as from differences in retrocopy expression. Genome analysis of 1092 individuals from various populations and transcriptomes from 50 individuals, revealed differences between populations in the frequency of transcriptionally active ancient retrocopy loss, as well as differences in retrocopy expression levels. Overall, these results provide new insights into the genomic events of inter-population variation, which has not been evaluated much with respect to gene loss.

Vyšlo v časopise: Inter-population Differences in Retrogene Loss and Expression in Humans. PLoS Genet 11(10): e32767. doi:10.1371/journal.pgen.1005579
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005579

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Zdroje

1. Maestre J, Tchénio T, Dhellin O, Heidmann T. mRNA retroposition in human cells: processed pseudogene formation. The EMBO journal. 1995;14(24):6333–8. PubMed 8557053

2. Kaessmann H, Vinckenbosch N, Long M. RNA-based gene duplication: mechanistic and evolutionary insights. Nature reviews Genetics. 2009;10(1):19–31. doi: 10.1038/nrg2487 19030023

3. Dai H, Chen Y, Chen S, Mao Q, Kennedy D, Landback P, et al. The evolution of courtship behaviors through the origination of a new gene in Drosophila. Proceedings of the National Academy of Sciences of the United States of America. 2008;105(21):7478–83. doi: 10.1073/pnas.0800693105 18508971

4. Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi-Miyagawa S, Obata Y, et al. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature. 2008;453(7194):539–43. doi: 10.1038/nature06908 18404146

5. Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature. 2010;465(7301):1033–8. doi: 10.1038/nature09144 20577206

6. Brosius J. The contribution of RNAs and retroposition to evolutionary novelties. Genetica. 2003;118(2–3):99–116. 12868601.

7. 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. 16201836

8. Ciomborowska J, Rosikiewicz W, Szklarczyk D, Makalowski W, Makalowska I. "Orphan" retrogenes in the human genome. Mol Biol Evol. 2013;30(2):384–96. doi: 10.1093/molbev/mss235 23066043

9. Potrzebowski L, Vinckenbosch N, Marques AC, Chalmel F, Jégou B, Kaessmann H. Chromosomal gene movements reflect the recent origin and biology of therian sex chromosomes. PLoS biology. 2008;6(4):e80. doi: 10.1371/journal.pbio.0060080 18384235

10. Prendergast GC. Actin′ up: RhoB in cancer and apoptosis. Nature Reviews Cancer. 2001;1(2):162–8. 11905808

11. Corbett MA, Dudding-Byth T, Crock PA, Botta E, Christie LM, Nardo T, et al. A novel X-linked trichothiodystrophy associated with a nonsense mutation in RNF113A. J Med Genet. 2015;52(4):269–74. doi: 10.1136/jmedgenet-2014-102418 25612912

12. Sayah DM, Sokolskaja E, Berthoux L, Luban J. Cyclophilin A retrotransposition into TRIM5 explains owl monkey resistance to HIV–1. Nature. 2004;430(6999):569–73. 15243629

13. Consortium GP, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, et al. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491(7422):56–65. doi: 10.1038/nature11632 23128226

14. Ewing AD, Ballinger TJ, Earl D, Platform BIGSaAPa, Harris CC, Ding L, et al. Retrotransposition of gene transcripts leads to structural variation in mammalian genomes. Genome biology. 2013;14(3):R22. doi: 10.1186/gb-2013-14-3-r22 23497673

15. Abyzov A, Iskow R, Gokcumen O, Radke DW, Balasubramanian S, Pei B, et al. Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division. Genome research. 2013;23(12):2042–52. doi: 10.1101/gr.154625.113 24026178

16. Schrider DR, Navarro FCP, Galante PAF, Parmigiani RB, Camargo AA, Hahn MW, et al. Gene copy-number polymorphism caused by retrotransposition in humans. PLoS genetics. 2013;9(1):e1003242. doi: 10.1371/journal.pgen.1003242 23359205

17. Richardson SR, Salvador-Palomeque C, Faulkner GJ. Diversity through duplication: whole-genome sequencing reveals novel gene retrocopies in the human population. BioEssays: news and reviews in molecular, cellular and developmental biology. 2014;36(5):475–81.

18. Lappalainen T, Sammeth M, Friedländer MR, 't Hoen PAC, Monlong J, Rivas MA, et al. Transcriptome and genome sequencing uncovers functional variation in humans. Nature. 2013;501(7468):506–11. doi: 10.1038/nature12531 24037378

19. Kabza M, Ciomborowska J, Makalowska I. RetrogeneDB–-a database of animal retrogenes. Mol Biol Evol. 2014;31(7):1646–8. doi: 10.1093/molbev/msu139 24739306

20. Pan D, Zhang L. Burst of young retrogenes and independent retrogene formation in mammals. PloS one. 2009;4(3):e5040. doi: 10.1371/journal.pone.0005040 19325906

21. Jun J, Ryvkin P, Hemphill E, Mandoiu I, Nelson C. The Birth of New Genes by RNA- and DNA-Mediated Duplication during Mammalian Evolution. dxdoiorg. 2009;16(10):1429–44.

22. Szczesniak MW, Ciomborowska J, Nowak W, Rogozin IB, Makalowska I. Primate and rodent specific intron gains and the origin of retrogenes with splice variants. Mol Biol Evol. 2011;28(1):33–7. doi: 10.1093/molbev/msq260 20889727

23. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. 25516281

24. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, et al. A draft sequence of the Neandertal genome. Science (New York, NY). 2010;328(5979):710–22.

25. Miller W, Drautz DI, Ratan A, Pusey B, Qi J, Lesk AM, et al. Sequencing the nuclear genome of the extinct woolly mammoth. Nature. 2008;456(7220):387–90. doi: 10.1038/nature07446 19020620

26. 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):3220–5. 16492757

27. Kleene KC. A possible meiotic function of the peculiar patterns of gene expression in mammalian spermatogenic cells. Mechanisms of development. 2001;106(1–2):3–23. 11472831

28. Fontanillas P, Hartl DL, Reuter M. Genome organization and gene expression shape the transposable element distribution in the Drosophila melanogaster euchromatin. PLoS genetics. 2007;3(11):e210. 18081425

29. Emerson JJ, Kaessmann H, Betrán E, Long M. Extensive gene traffic on the mammalian X chromosome. Science (New York, NY). 2004;303(5657):537–40.

30. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (Oxford, England). 2010;26(6):841–2.

31. Paten B, Herrero J, Beal K, Birney E. Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. Bioinformatics. 2009;25(3):295–301. doi: 10.1093/bioinformatics/btn630 19056777

32. Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, et al. Ensembl 2014. Nucleic acids research. 2014;42(Database issue):D749–55. doi: 10.1093/nar/gkt1196 24316576

33. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience. 2012;1(1):18. doi: 10.1186/2047-217X-1-18 23587118

34. Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics (Oxford, England). 2012;28(23):3150–2.

35. Huang X, Madan A. CAP3: A DNA sequence assembly program. Genome research. 1999;9(9):868–77. 10508846

36. Kielbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011;21(3):487–93. doi: 10.1101/gr.113985.110 21209072

37. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. Journal of molecular biology. 1990;215(3):403–10. 2231712

38. Hall T. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series. 1999;41:95–8.

39. Lefever S, Hellemans J, Pattyn F, Przybylski DR, Taylor C, Geurts R, et al. RDML: structured language and reporting guidelines for real-time quantitative PCR data. Nucleic Acids Res. 2009;37(7):2065–9. doi: 10.1093/nar/gkp056 19223324

40. Ramakers C, Ruijter JM, Deprez RH, Moorman AF. Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci Lett. 2003;339(1):62–6. 12618301

41. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome biology. 2013;14(4):R36. doi: 10.1186/gb-2013-14-4-r36 23618408