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Volumn 20, Issue 9, 2010, Pages 1262-1270

High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

EID: 77955160719     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.106419.110     Document Type: Article
Times cited : (245)

References (63)
  • 1
    • 44849120649 scopus 로고    scopus 로고
    • Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition
    • DOI 10.1101/gr.075770.107
    • Akagi K, Li J, Stephens RM, Volfovsky N, Symer DE. 2008. Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition. Genome Res 18: 869-880. (Pubitemid 351793059)
    • (2008) Genome Research , vol.18 , Issue.6 , pp. 869-880
    • Akagi, K.1    Li, J.2    Stephens, R.M.3    Volfovsky, N.4    Symer, D.E.5
  • 3
    • 0037383453 scopus 로고    scopus 로고
    • ATLAS: A system to selectively identify human-specific L1 insertions
    • Badge RM, Alisch RS, Moran JV. 2003. ATLAS: A system to selectively identify human-specific L1 insertions. Am J Hum Genet 72: 823-838.
    • (2003) Am J Hum Genet , vol.72 , pp. 823-838
    • Badge, R.M.1    Alisch, R.S.2    Moran, J.V.3
  • 6
    • 8544229065 scopus 로고    scopus 로고
    • Natural genetic variation caused by transposable elements in humans
    • DOI 10.1534/genetics.104.031757
    • Bennett EA, Coleman LE, Tsui C, Pittard WS, Devine SE. 2004. Natural genetic variation caused by transposable elements in humans. Genetics 168: 933-951. (Pubitemid 39491469)
    • (2004) Genetics , vol.168 , Issue.2 , pp. 933-951
    • Bennett, E.A.1    Coleman, L.E.2    Tsui, C.3    Pittard, W.S.4    Devine, S.E.5
  • 7
    • 0035207819 scopus 로고    scopus 로고
    • Adaptive evolution in LINE-1 retrotransposons
    • Boissinot S, Furano AV. 2001. Adaptive evolution in LINE-1 retrotransposons. Mol Biol Evol 18: 2186-2194.
    • (2001) Mol Biol Evol , vol.18 , pp. 2186-2194
    • Boissinot, S.1    Furano, A.V.2
  • 8
    • 0034086210 scopus 로고    scopus 로고
    • L1 (LINE-1) retrotransposon evolution and amplification in recent human history
    • Boissinot S, Chevret P, Furano AV. 2000. L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Mol Biol Evol 17: 915-928. (Pubitemid 30346551)
    • (2000) Molecular Biology and Evolution , vol.17 , Issue.6 , pp. 915-928
    • Boissinot, S.1    Chevret, P.2    Furano, A.V.3
  • 9
    • 0034983677 scopus 로고    scopus 로고
    • Selection against deleterious LINE-1-containing loci in the human lineage
    • Boissinot S, Entezam A, Furano AV. 2001. Selection against deleterious LINE-1-containing loci in the human lineage. Mol Biol Evol 18: 926-935. (Pubitemid 32520464)
    • (2001) Molecular Biology and Evolution , vol.18 , Issue.6 , pp. 926-935
    • Boissinot, S.1    Entezam, A.2    Furano, A.V.3
  • 10
    • 3543151399 scopus 로고    scopus 로고
    • The insertional history of an active family of L1 retrotransposons in humans
    • DOI 10.1101/gr.2326704
    • Boissinot S, Entezam A, Young L, Munson PJ, Furano AV. 2004. The insertional history of an active family of L1 retrotransposons in humans. Genome Res 14: 1221-1231. (Pubitemid 39029219)
    • (2004) Genome Research , vol.14 , Issue.7 , pp. 1221-1231
    • Boissinot, S.1    Entezam, A.2    Young, L.3    Munson, P.J.4    Furano, A.V.5
  • 12
    • 0038620233 scopus 로고    scopus 로고
    • Genome-wide targeted search for human specific and polymorphic L1 integrations
    • Buzdin A, Ustyugova S, Gogvadze E, Lebedev Y, Hunsmann G, Sverdlov E. 2003. Genome-wide targeted search for human specific and polymorphic L1 integrations. Hum Genet 112: 527-533. (Pubitemid 36869046)
    • (2003) Human Genetics , vol.112 , Issue.5-6 , pp. 527-533
    • Buzdin, A.1    Ustyugova, S.2    Gogvadze, E.3    Lebedev, Y.4    Hunsmann, G.5    Sverdlov, E.6
  • 14
    • 0041353551 scopus 로고    scopus 로고
    • LINE-mediated retrotransposition of marked Alu sequences
    • DOI 10.1038/ng1223
    • Dewannieux M, Esnault C, Heidmann T. 2003. LINE-mediated retrotransposition of marked Alu sequences. Nat Genet 35: 41-48. (Pubitemid 37048594)
    • (2003) Nature Genetics , vol.35 , Issue.1 , pp. 41-48
    • Dewannieux, M.1    Esnault, C.2    Heidmann, T.3
  • 16
    • 0034079713 scopus 로고    scopus 로고
    • Human LINE retrotransposons generate processed pseudogenes
    • DOI 10.1038/74184
    • Esnault C, Maestre J, Heidmann T. 2000. Human LINE retrotransposons generate processed pseudogenes. Nat Genet 24: 363-367. (Pubitemid 30187433)
    • (2000) Nature Genetics , vol.24 , Issue.4 , pp. 363-367
    • Esnault, C.1    Maestre, J.2    Heidmann, T.3
  • 17
    • 0000122573 scopus 로고
    • PHYLIP - Phylogeny Inference Package
    • version 3.2
    • Felsenstein J. 1989. PHYLIP - Phylogeny Inference Package (version 3.2). Cladistics 5: 164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 18
    • 0026682501 scopus 로고
    • Estimating effective population size from samples of sequences: Inefficiency of pairwise and segregating sites as compared to phylogenetic estimates
    • Felsenstein J. 1992. Estimating effective population size from samples of sequences: Inefficiency of pairwise and segregating sites as compared to phylogenetic estimates. Genet Res 59: 139-147.
    • (1992) Genet Res , vol.59 , pp. 139-147
    • Felsenstein, J.1
  • 19
    • 0027220656 scopus 로고
    • Maximum likelihood estimation of population parameters
    • Fu YX, Li WH. 1993. Maximum likelihood estimation of population parameters. Genetics 134: 1261-1270. (Pubitemid 23220047)
    • (1993) Genetics , vol.134 , Issue.4 , pp. 1261-1270
    • Fu, Y.-X.1    Li, W.-H.2
  • 20
    • 0029670588 scopus 로고    scopus 로고
    • Analysis of the 5′ junctions of R2 insertions with the 28S gene: Implications for non-LTR retrotransposition
    • George JA, Burke WD, Eickbush TH. 2006. Analysis of the 5′ junctions of R2 insertions with the 28S gene: Implications for non-LTR retrotransposition. Genetics 142: 853-863.
    • (2006) Genetics , vol.142 , pp. 853-863
    • George, J.A.1    Burke, W.D.2    Eickbush, T.H.3
  • 22
    • 0021474109 scopus 로고
    • Defining the beginning and end of KpnI family segments
    • Grimaldi G, Skowronski J, SingerMF. 1984. Defining the beginning and end of KpnI family segments. EMBO J 3: 1753-1759.
    • (1984) EMBO J , vol.3 , pp. 1753-1759
    • Grimaldi, G.1    Skowronski, J.2    Singer, M.F.3
  • 23
    • 2442667886 scopus 로고    scopus 로고
    • Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes
    • Han JS, Szak ST, Boeke JD. 2004. Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature 429: 268-274.
    • (2004) Nature , vol.429 , pp. 268-274
    • Han, J.S.1    Szak, S.T.2    Boeke, J.D.3
  • 25
    • 12844258915 scopus 로고    scopus 로고
    • Straightening out the LINEs: LINE-1 orthologous loci
    • Ho HJ, Ray DA, Salem AH, Myers JS, Batzer MA. 2005. Straightening out the LINEs: LINE-1 orthologous loci. Genomics 85: 201-207.
    • (2005) Genomics , vol.85 , pp. 201-207
    • Ho, H.J.1    Ray, D.A.2    Salem, A.H.3    Myers, J.S.4    Ma, B.5
  • 26
    • 38649092410 scopus 로고    scopus 로고
    • Dendroscope: An interactive viewer for large phylogenetic trees
    • DOI 10.1186/1471-2105-8-460
    • Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R. 2007. Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinformatics 8: 460. doi: 10.1186/1471-2105-8-460. (Pubitemid 351168201)
    • (2007) BMC Bioinformatics , vol.8 , pp. 460
    • Huson, D.H.1    Richter, D.C.2    Rausch, C.3    Dezulian, T.4    Franz, M.5    Rupp, R.6
  • 27
    • 0033912515 scopus 로고    scopus 로고
    • The distribution of human genetic diversity: A comparison of mitochondrial, autosomal, and Y-chromosome data
    • Jorde LB, Watkins WS, Bamshad MJ, Dixon ME, Ricker CE, Seielstad MT, Batzer MA. 2000. The distribution of human genetic diversity: A comparison of mitochondrial, autosomal, and Y-chromosome data. Am J Hum Genet 66: 979-988.
    • (2000) Am J Hum Genet , vol.66 , pp. 979-988
    • Jorde, L.B.1    Watkins, W.S.2    Bamshad, M.J.3    Dixon, M.E.4    Ricker, C.E.5    Seielstad, M.T.6    Ma, B.7
  • 29
    • 0023867459 scopus 로고
    • Haemophilia a resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man
    • DOI 10.1038/332164a0
    • Kazazian HH Jr, Wong C, Youssoufian H, Scott AF, Phillips DG, Antonarakis SE. 1988. Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Nature 332: 164-166. (Pubitemid 18083562)
    • (1988) Nature , vol.332 , Issue.6160 , pp. 164-166
    • Kazazia Jr., H.H.1    Wong, C.2    Youssoufian, H.3    Scott, A.F.4    Phillips, D.G.5    Antonarakis, S.E.6
  • 30
    • 30044433182 scopus 로고    scopus 로고
    • Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates
    • DOI 10.1101/gr.4001406
    • Khan H, Smit A, Boissinot S. 2006. Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res 16: 78-87. (Pubitemid 43048936)
    • (2006) Genome Research , vol.16 , Issue.1 , pp. 78-87
    • Khan, H.1    Smit, A.2    Boissinot, S.3
  • 31
    • 33846897374 scopus 로고    scopus 로고
    • Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies
    • DOI 10.1016/j.gene.2006.07.040, PII S0378111906005087
    • Konkel MK, Wang J, Liang P, Batzer MA. 2007. Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies. Gene 390: 28-38. (Pubitemid 46241738)
    • (2007) Gene , vol.390 , Issue.1-2 , pp. 28-38
    • Konkel, M.K.1    Wang, J.2    Liang, P.3    Batzer, M.A.4
  • 33
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • doi: 10.1186/gb-2009-10-3-r25
    • Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25. doi: 10.1186/gb-2009-10-3-r25.
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 34
    • 0000244010 scopus 로고
    • The apportionment of human diversity
    • Lewontin RC. 1972. The apportionment of human diversity. Evol Biol 6: 381-398.
    • (1972) Evol Biol , vol.6 , pp. 381-398
    • Lewontin, R.C.1
  • 37
    • 0027450385 scopus 로고
    • Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: A mechanism for non-LTR retrotransposition
    • Luan DD, Korman MH, Jakubczak JL, Eickbush TH. 1993. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: A mechanism for non-LTR retrotransposition. Cell 72: 595-605.
    • (1993) Cell , vol.72 , pp. 595-605
    • Luan, D.D.1    Korman, M.H.2    Jakubczak, J.L.3    Eickbush, T.H.4
  • 39
  • 40
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • Mouse Genome Sequencing Consortium
    • Mouse Genome Sequencing Consortium. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
    • (2002) Nature , vol.420 , pp. 520-562
  • 41
    • 20544466648 scopus 로고    scopus 로고
    • Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition
    • DOI 10.1038/nature03663
    • Muotri AR, Chu VT, Marchetto MC, Deng W, Moran JV, Gage FH. 2005. Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature 435: 903-910. (Pubitemid 40896309)
    • (2005) Nature , vol.435 , Issue.7044 , pp. 903-910
    • Muotri, A.R.1    Chu, V.T.2    Marchetto, M.C.N.3    Deng, W.4    Moran, J.V.5    Gage, F.H.6
  • 44
    • 0035215372 scopus 로고    scopus 로고
    • Genomic characterization of recent human LINE-1 insertions: Evidence supporting random insertion
    • DOI 10.1101/gr.194701
    • Ovchinnikov I, Troxel AB, Swergold GD. 2001. Genomic characterization of recent human LINE-1 insertions: Evidence supporting random insertion. Genome Res 11: 2050-2058. (Pubitemid 33138802)
    • (2001) Genome Research , vol.11 , Issue.12 , pp. 2050-2058
    • Ovchinnikov, I.1    Troxel, A.B.2    Swergold, G.D.3
  • 46
    • 0037202376 scopus 로고    scopus 로고
    • Length distribution of long interspersed nuclear elements (LINEs) and processed pseudogenes of human endogenous retroviruses: Implications for retrotransposition and pseudogene detection
    • DOI 10.1016/S0378-1119(02)01047-8, PII S0378111902010478
    • Pavlicek A, Paces J, Zika R, Hejnar J. 2002. Length distribution of long interspersed nucleotide elements (LINEs) and processed pseudogenes of human endogenous retroviruses: Implications for retrotransposition and pseudogene detection. Gene 300: 189-194. (Pubitemid 35441174)
    • (2002) Gene , vol.300 , Issue.1-2 , pp. 189-194
    • Pavlicek, A.1    Paces, J.2    Zika, R.3    Hejnar, J.4
  • 53
    • 0023948714 scopus 로고
    • Unit-length line-1 transcripts in human teratocarcinoma cells
    • Skowronski J, Fanning TG, SingerMF. 1988. Unit-length line-1 transcripts in human teratocarcinoma cells. Mol Cell Biol 8: 1385-1397.
    • (1988) Mol Cell Biol , vol.8 , pp. 1385-1397
    • Skowronski, J.1    Fanning, T.G.2    Singer, M.F.3
  • 54
    • 0024313579 scopus 로고
    • Statistical method for testing the neutral mutation hypothesis by DNA polymorphism
    • Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595. (Pubitemid 19274682)
    • (1989) Genetics , vol.123 , Issue.3 , pp. 585-595
    • Tajima, F.1
  • 55
    • 33749627376 scopus 로고    scopus 로고
    • Long L1 insertions in human gene introns specifically reduce the content of corresponding primary transcripts
    • Ustyugova SV, Lebedev YB, Sverdlov ED. 2006. Long L1 insertions in human gene introns specifically reduce the content of corresponding primary transcripts. Genetica 128: 261-272.
    • (2006) Genetica , vol.128 , pp. 261-272
    • Ustyugova, S.V.1    Lebedev, Y.B.2    Sverdlov, E.D.3
  • 58
    • 33645786590 scopus 로고    scopus 로고
    • DbRIP: A highly integrated database of retrotransposon insertion polymorphisms in humans
    • Wang J, Song L, Grover D, Azrak S, Batzer MA, Liang P. 2006. dbRIP: A highly integrated database of retrotransposon insertion polymorphisms in humans. Hum Mutat 27: 323-329.
    • (2006) Hum Mutat , vol.27 , pp. 323-329
    • Wang, J.1    Song, L.2    Grover, D.3    Azrak, S.4    Batzer, M.A.5    Liang, P.6
  • 59
    • 0016491430 scopus 로고
    • On the number of segregating sites in genetical models without recombination
    • Watterson GA. 1975. On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7: 256-276.
    • (1975) Theor Popul Biol , vol.7 , pp. 256-276
    • Watterson, G.A.1


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