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Volumn 11, Issue 10, 2015, Pages

Inter-population Differences in Retrogene Loss and Expression in Humans

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; ETHNIC DIFFERENCE; GENE DELETION; GENE EXPRESSION; GENE FREQUENCY; GENE IDENTIFICATION; GENE LOSS; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HUMAN; HUMAN TISSUE; LYMPHOBLASTOID CELL LINE; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; POLYMERASE CHAIN REACTION; POPULATION DIFFERENTIATION; POPULATION GENETICS; QUANTITATIVE ANALYSIS; RNA SEQUENCE; ANIMAL; GENE DUPLICATION; GENE EXPRESSION REGULATION; GENETIC POLYMORPHISM; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN GENOME; HUMAN GENOME PROJECT; MOLECULAR EVOLUTION; PRIMATE;

EID: 84946599922     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1005579     Document Type: Article
Times cited : (12)

References (41)
  • 1
    • 0029588403 scopus 로고
    • mRNA retroposition in human cells: processed pseudogene formation
    • 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
    • (1995) The EMBO journal , vol.14 , Issue.24 , pp. 6333-6338
    • Maestre, J.1    Tchénio, T.2    Dhellin, O.3    Heidmann, T.4
  • 2
    • 57749177443 scopus 로고    scopus 로고
    • RNA-based gene duplication: mechanistic and evolutionary insights
    • 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
    • (2009) Nature reviews Genetics , vol.10 , Issue.1 , pp. 19-31
    • Kaessmann, H.1    Vinckenbosch, N.2    Long, M.3
  • 4
    • 44349130233 scopus 로고    scopus 로고
    • Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes
    • 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
    • (2008) Nature , vol.453 , Issue.7194 , pp. 539-543
    • Watanabe, T.1    Totoki, Y.2    Toyoda, A.3    Kaneda, M.4    Kuramochi-Miyagawa, S.5    Obata, Y.6
  • 5
    • 77953957633 scopus 로고    scopus 로고
    • A coding-independent function of gene and pseudogene mRNAs regulates tumour biology
    • 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
    • (2010) Nature , vol.465 , Issue.7301 , pp. 1033-1038
    • Poliseno, L.1    Salmena, L.2    Zhang, J.3    Carver, B.4    Haveman, W.J.5    Pandolfi, P.P.6
  • 6
    • 0013161988 scopus 로고    scopus 로고
    • The contribution of RNAs and retroposition to evolutionary novelties
    • Brosius J, The contribution of RNAs and retroposition to evolutionary novelties. Genetica. 2003;118(2–3):99–116. 12868601.
    • (2003) Genetica , vol.118 , Issue.2-3 , pp. 99-116
    • Brosius, J.1
  • 9
    • 43249118306 scopus 로고    scopus 로고
    • Chromosomal gene movements reflect the recent origin and biology of therian sex chromosomes
    • 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
    • (2008) PLoS biology , vol.6 , Issue.4 , pp. 80
    • Potrzebowski, L.1    Vinckenbosch, N.2    Marques, A.C.3    Chalmel, F.4    Jégou, B.5    Kaessmann, H.6
  • 10
    • 0035523359 scopus 로고    scopus 로고
    • Actin′ up: RhoB in cancer and apoptosis
    • Prendergast GC, Actin′ up: RhoB in cancer and apoptosis. Nature Reviews Cancer. 2001;1(2):162–8. 11905808
    • (2001) Nature Reviews Cancer , vol.1 , Issue.2 , pp. 162-168
    • Prendergast, G.C.1
  • 11
    • 84930673290 scopus 로고    scopus 로고
    • A novel X-linked trichothiodystrophy associated with a nonsense mutation in RNF113A
    • 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
    • (2015) J Med Genet , vol.52 , Issue.4 , pp. 269-274
    • Corbett, M.A.1    Dudding-Byth, T.2    Crock, P.A.3    Botta, E.4    Christie, L.M.5    Nardo, T.6
  • 12
    • 3242876747 scopus 로고    scopus 로고
    • Cyclophilin A retrotransposition into TRIM5 explains owl monkey resistance to HIV–1
    • 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
    • (2004) Nature , vol.430 , Issue.6999 , pp. 569-573
    • Sayah, D.M.1    Sokolskaja, E.2    Berthoux, L.3    Luban, J.4
  • 13
    • 84975795680 scopus 로고    scopus 로고
    • An integrated map of genetic variation from 1,092 human genomes
    • 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
    • (2012) Nature , vol.491 , Issue.7422 , pp. 56-65
    • Consortium, G.P.1    Abecasis, G.R.2    Auton, A.3    Brooks, L.D.4    DePristo, M.A.5    Durbin, R.M.6
  • 14
    • 84879028815 scopus 로고    scopus 로고
    • Retrotransposition of gene transcripts leads to structural variation in mammalian genomes
    • 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
    • (2013) Genome biology , vol.14 , Issue.3 , pp. 22
    • Ewing, A.D.1    Ballinger, T.J.2    Earl, D.3    Platform, B.I.G.S.A.P.4    Harris, C.C.5    Ding, L.6
  • 15
    • 84890474385 scopus 로고    scopus 로고
    • Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division
    • 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
    • (2013) Genome research , vol.23 , Issue.12 , pp. 2042-2052
    • Abyzov, A.1    Iskow, R.2    Gokcumen, O.3    Radke, D.W.4    Balasubramanian, S.5    Pei, B.6
  • 18
    • 84885645853 scopus 로고    scopus 로고
    • Transcriptome and genome sequencing uncovers functional variation in humans
    • 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
    • (2013) Nature , vol.501 , Issue.7468 , pp. 506-511
    • Lappalainen, T.1    Sammeth, M.2    Friedländer, M.R.3    't Hoen, P.A.C.4    Monlong, J.5    Rivas, M.A.6
  • 19
    • 84903702769 scopus 로고    scopus 로고
    • RetrogeneDB–-a database of animal retrogenes
    • 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
    • (2014) Mol Biol Evol , vol.31 , Issue.7 , pp. 1646-1648
    • Kabza, M.1    Ciomborowska, J.2    Makalowska, I.3
  • 20
    • 63449122253 scopus 로고    scopus 로고
    • Burst of young retrogenes and independent retrogene formation in mammals
    • 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
    • (2009) PloS one , vol.4 , Issue.3 , pp. 5040
    • Pan, D.1    Zhang, L.2
  • 21
    • 70349845921 scopus 로고    scopus 로고
    • The Birth of New Genes by RNA- and DNA-Mediated Duplication during Mammalian Evolution
    • 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.
    • (2009) dxdoiorg , vol.16 , Issue.10 , pp. 1429-1444
    • Jun, J.1    Ryvkin, P.2    Hemphill, E.3    Mandoiu, I.4    Nelson, C.5
  • 22
    • 78650460773 scopus 로고    scopus 로고
    • Primate and rodent specific intron gains and the origin of retrogenes with splice variants
    • 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
    • (2011) Mol Biol Evol , vol.28 , Issue.1 , pp. 33-37
    • Szczesniak, M.W.1    Ciomborowska, J.2    Nowak, W.3    Rogozin, I.B.4    Makalowska, I.5
  • 23
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
    • 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
    • (2014) Genome Biol , vol.15 , Issue.12 , pp. 550
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 25
    • 56749119854 scopus 로고    scopus 로고
    • Sequencing the nuclear genome of the extinct woolly mammoth
    • 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
    • (2008) Nature , vol.456 , Issue.7220 , pp. 387-390
    • Miller, W.1    Drautz, D.I.2    Ratan, A.3    Pusey, B.4    Qi, J.5    Lesk, A.M.6
  • 27
    • 0034889978 scopus 로고    scopus 로고
    • A possible meiotic function of the peculiar patterns of gene expression in mammalian spermatogenic cells
    • 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
    • (2001) Mechanisms of development , vol.106 , Issue.1-2 , pp. 3-23
    • Kleene, K.C.1
  • 28
    • 37349093019 scopus 로고    scopus 로고
    • Genome organization and gene expression shape the transposable element distribution in the Drosophila melanogaster euchromatin
    • 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
    • (2007) PLoS genetics , vol.3 , Issue.11 , pp. 210
    • Fontanillas, P.1    Hartl, D.L.2    Reuter, M.3
  • 30
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: a flexible suite of utilities for comparing genomic features
    • Quinlan AR, Hall IM, BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (Oxford, England). 2010;26(6):841–2.
    • (2010) Bioinformatics (Oxford, England) , vol.26 , Issue.6 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 31
    • 59549102237 scopus 로고    scopus 로고
    • Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment
    • 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
    • (2009) Bioinformatics , vol.25 , Issue.3 , pp. 295-301
    • Paten, B.1    Herrero, J.2    Beal, K.3    Birney, E.4
  • 33
    • 84942887758 scopus 로고    scopus 로고
    • SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
    • 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
    • (2012) GigaScience , vol.1 , Issue.1 , pp. 18
    • Luo, R.1    Liu, B.2    Xie, Y.3    Li, Z.4    Huang, W.5    Yuan, J.6
  • 34
    • 84870431038 scopus 로고    scopus 로고
    • CD-HIT: accelerated for clustering the next-generation sequencing data
    • 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.
    • (2012) Bioinformatics (Oxford, England) , vol.28 , Issue.23 , pp. 3150-3152
    • Fu, L.1    Niu, B.2    Zhu, Z.3    Wu, S.4    Li, W.5
  • 35
    • 0032849859 scopus 로고    scopus 로고
    • CAP3: A DNA sequence assembly program
    • Huang X, Madan A, CAP3: A DNA sequence assembly program. Genome research. 1999;9(9):868–77. 10508846
    • (1999) Genome research , vol.9 , Issue.9 , pp. 868-877
    • Huang, X.1    Madan, A.2
  • 36
    • 79952256999 scopus 로고    scopus 로고
    • Adaptive seeds tame genomic sequence comparison
    • 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
    • (2011) Genome Res , vol.21 , Issue.3 , pp. 487-493
    • Kielbasa, S.M.1    Wan, R.2    Sato, K.3    Horton, P.4    Frith, M.C.5
  • 38
    • 0002051540 scopus 로고    scopus 로고
    • BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
    • 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.
    • (1999) Nucleic Acids Symposium Series , vol.41 , pp. 95-98
    • Hall, T.1
  • 39
    • 65549107425 scopus 로고    scopus 로고
    • RDML: structured language and reporting guidelines for real-time quantitative PCR data
    • 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
    • (2009) Nucleic Acids Res , vol.37 , Issue.7 , pp. 2065-2069
    • Lefever, S.1    Hellemans, J.2    Pattyn, F.3    Przybylski, D.R.4    Taylor, C.5    Geurts, R.6
  • 40
    • 0037435395 scopus 로고    scopus 로고
    • Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data
    • 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
    • (2003) Neurosci Lett , vol.339 , Issue.1 , pp. 62-66
    • Ramakers, C.1    Ruijter, J.M.2    Deprez, R.H.3    Moorman, A.F.4
  • 41
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • 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
    • (2013) Genome biology , vol.14 , Issue.4 , pp. 36
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5    Salzberg, S.L.6


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