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Volumn 17, Issue 1, 2016, Pages

Genome-wide characterization of human L1 antisense promoter-driven transcripts

Author keywords

Antisense promoter; Chimeric transcript; EST; L1; LINE 1; PacBio; Retrotransposon; Transposon; YY1

Indexed keywords

MESSENGER RNA; TRANSCRIPTION FACTOR YY1; COMPLEMENTARY RNA; RETROPOSON;

EID: 84974795127     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-016-2800-5     Document Type: Article
Times cited : (59)

References (66)
  • 1
    • 84860879005 scopus 로고    scopus 로고
    • Human transposon tectonics
    • Burns KH, Boeke JD. Human transposon tectonics. Cell. 2012;149:740-52.
    • (2012) Cell , vol.149 , pp. 740-752
    • Burns, K.H.1    Boeke, J.D.2
  • 3
    • 23744454779 scopus 로고    scopus 로고
    • Gene-breaking: a new paradigm for human retrotransposon-mediated gene evolution
    • Wheelan SJ, Aizawa Y, Han JS, Boeke JD. Gene-breaking: a new paradigm for human retrotransposon-mediated gene evolution. Genome Res. 2005;15:1073-8.
    • (2005) Genome Res , vol.15 , pp. 1073-1078
    • Wheelan, S.J.1    Aizawa, Y.2    Han, J.S.3    Boeke, J.D.4
  • 4
    • 30044433182 scopus 로고    scopus 로고
    • Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates
    • Khan H, Smit A, Boissinot S. Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res. 2006;16:78-87.
    • (2006) Genome Res , vol.16 , pp. 78-87
    • Khan, H.1    Smit, A.2    Boissinot, S.3
  • 7
    • 0034999474 scopus 로고    scopus 로고
    • Antisense promoter of human L1 retrotransposon drives transcription of adjacent cellular genes
    • Speek M. Antisense promoter of human L1 retrotransposon drives transcription of adjacent cellular genes. Mol Cell Biol. 2001;21:1973-85.
    • (2001) Mol Cell Biol , vol.21 , pp. 1973-1985
    • Speek, M.1
  • 8
    • 33746658129 scopus 로고    scopus 로고
    • L1 antisense promoter drives tissue-specific transcription of human genes
    • Matlik K, Redik K, Speek M. L1 antisense promoter drives tissue-specific transcription of human genes. J Biomed Biotechnol. 2006;2006:71753.
    • (2006) J Biomed Biotechnol , vol.2006 , pp. 71753
    • Matlik, K.1    Redik, K.2    Speek, M.3
  • 9
    • 0036251775 scopus 로고    scopus 로고
    • Many human genes are transcribed from the antisense promoter of L1 retrotransposon
    • Nigumann P, Redik K, Matlik K, Speek M. Many human genes are transcribed from the antisense promoter of L1 retrotransposon. Genomics. 2002;79:628-34.
    • (2002) Genomics , vol.79 , pp. 628-634
    • Nigumann, P.1    Redik, K.2    Matlik, K.3    Speek, M.4
  • 11
    • 78049349212 scopus 로고    scopus 로고
    • Demethylation of a LINE-1 antisense promoter in the cMet locus impairs Met signalling through induction of illegitimate transcription
    • Weber B, Kimhi S, Howard G, Eden A, Lyko F. Demethylation of a LINE-1 antisense promoter in the cMet locus impairs Met signalling through induction of illegitimate transcription. Oncogene. 2010;29:5775-84.
    • (2010) Oncogene , vol.29 , pp. 5775-5784
    • Weber, B.1    Kimhi, S.2    Howard, G.3    Eden, A.4    Lyko, F.5
  • 13
    • 70449107061 scopus 로고    scopus 로고
    • Isolation of cancer-specific chimeric transcripts induced by hypomethylation of the LINE-1 antisense promoter
    • Cruickshanks HA, Tufarelli C. Isolation of cancer-specific chimeric transcripts induced by hypomethylation of the LINE-1 antisense promoter. Genomics. 2009;94:397-406.
    • (2009) Genomics , vol.94 , pp. 397-406
    • Cruickshanks, H.A.1    Tufarelli, C.2
  • 17
    • 80054080269 scopus 로고    scopus 로고
    • Intronic L1 retrotransposons and nested genes cause transcriptional interference by inducing intron retention, exonization and cryptic polyadenylation
    • Kaer K, Branovets J, Hallikma A, Nigumann P, Speek M. Intronic L1 retrotransposons and nested genes cause transcriptional interference by inducing intron retention, exonization and cryptic polyadenylation. PLoS One. 2011;6:e26099.
    • (2011) PLoS One , vol.6 , pp. e26099
    • Kaer, K.1    Branovets, J.2    Hallikma, A.3    Nigumann, P.4    Speek, M.5
  • 19
    • 84866030009 scopus 로고    scopus 로고
    • C-GATE - catalogue of genes affected by transposable elements
    • Rebollo R, Farivar S, Mager DL. C-GATE - catalogue of genes affected by transposable elements. Mob DNA. 2012;3:9.
    • (2012) Mob DNA , vol.3 , pp. 9
    • Rebollo, R.1    Farivar, S.2    Mager, D.L.3
  • 22
    • 33846912203 scopus 로고    scopus 로고
    • Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons
    • Lee J, Cordaux R, Han K, Wang J, Hedges DJ, Liang P, Batzer MA. Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons. Gene. 2007;390:18-27.
    • (2007) Gene , vol.390 , pp. 18-27
    • Lee, J.1    Cordaux, R.2    Han, K.3    Wang, J.4    Hedges, D.J.5    Liang, P.6    Batzer, M.A.7
  • 23
    • 3242706180 scopus 로고    scopus 로고
    • A YY1-binding site is required for accurate human LINE-1 transcription initiation
    • Athanikar JN, Badge RM, Moran JV. A YY1-binding site is required for accurate human LINE-1 transcription initiation. Nucleic Acids Res. 2004;32:3846-55.
    • (2004) Nucleic Acids Res , vol.32 , pp. 3846-3855
    • Athanikar, J.N.1    Badge, R.M.2    Moran, J.V.3
  • 24
    • 0027500890 scopus 로고
    • Binding of the ubiquitous nuclear transcription factor YY1 to a cis regulatory sequence in the human LINE-1 transposable element
    • Becker KG, Swergold G, Ozato K, Thayer RE. Binding of the ubiquitous nuclear transcription factor YY1 to a cis regulatory sequence in the human LINE-1 transposable element. Human Molecul Genet. 1993;2:1697-702.
    • (1993) Human Molecul Genet , vol.2 , pp. 1697-1702
    • Becker, K.G.1    Swergold, G.2    Ozato, K.3    Thayer, R.E.4
  • 25
    • 0026724644 scopus 로고
    • Identification of an internal cis-element essential for the human L1 transcription and a nuclear factor(s) binding to the element
    • Minakami R, Kurose K, Etoh K, Furuhata Y, Hattori M, Sakaki Y. Identification of an internal cis-element essential for the human L1 transcription and a nuclear factor(s) binding to the element. Nucleic Acids Res. 1992;20:3139-45.
    • (1992) Nucleic Acids Res , vol.20 , pp. 3139-3145
    • Minakami, R.1    Kurose, K.2    Etoh, K.3    Furuhata, Y.4    Hattori, M.5    Sakaki, Y.6
  • 26
    • 0029134032 scopus 로고
    • RNA polymerase III dependence of the human L1 promoter and possible participation of the RNA polymerase II factor YY1 in the RNA polymerase III transcription system
    • Kurose K, Hata K, Hattori M, Sakaki Y. RNA polymerase III dependence of the human L1 promoter and possible participation of the RNA polymerase II factor YY1 in the RNA polymerase III transcription system. Nucleic Acids Res. 1995;23:3704-9.
    • (1995) Nucleic Acids Res , vol.23 , pp. 3704-3709
    • Kurose, K.1    Hata, K.2    Hattori, M.3    Sakaki, Y.4
  • 27
    • 0028263414 scopus 로고
    • YY1 is involved in the regulation of the bi-directional promoter of the Surf-1 and Surf-2 genes
    • Gaston K, Fried M. YY1 is involved in the regulation of the bi-directional promoter of the Surf-1 and Surf-2 genes. FEBS Lett. 1994;347:289-94.
    • (1994) FEBS Lett , vol.347 , pp. 289-294
    • Gaston, K.1    Fried, M.2
  • 28
    • 0030764856 scopus 로고    scopus 로고
    • A functional YY1 binding site is necessary and sufficient to activate Surf-1 promoter activity in response to serum growth factors
    • Cole EG, Gaston K. A functional YY1 binding site is necessary and sufficient to activate Surf-1 promoter activity in response to serum growth factors. Nucleic Acids Res. 1997;25:3705-11.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3705-3711
    • Cole, E.G.1    Gaston, K.2
  • 31
    • 0344022572 scopus 로고    scopus 로고
    • Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity
    • Ng HH, Robert F, Young RA, Struhl K. Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol Cell. 2003;11:709-19.
    • (2003) Mol Cell , vol.11 , pp. 709-719
    • Ng, H.H.1    Robert, F.2    Young, R.A.3    Struhl, K.4
  • 37
    • 84876842759 scopus 로고    scopus 로고
    • Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells
    • Danko CG, Hah N, Luo X, Martins AL, Core L, Lis JT, Siepel A, Kraus WL. Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol Cell. 2013;50:212-22.
    • (2013) Mol Cell , vol.50 , pp. 212-222
    • Danko, C.G.1    Hah, N.2    Luo, X.3    Martins, A.L.4    Core, L.5    Lis, J.T.6    Siepel, A.7    Kraus, W.L.8
  • 40
    • 84899020502 scopus 로고    scopus 로고
    • An antisense promoter in mouse L1 retrotransposon open reading frame-1 initiates expression of diverse fusion transcripts and limits retrotransposition
    • Li J, Kannan M, Trivett AL, Liao H, Wu X, Akagi K, Symer DE. An antisense promoter in mouse L1 retrotransposon open reading frame-1 initiates expression of diverse fusion transcripts and limits retrotransposition. Nucleic Acids Res. 2014;42:4546-62.
    • (2014) Nucleic Acids Res , vol.42 , pp. 4546-4562
    • Li, J.1    Kannan, M.2    Trivett, A.L.3    Liao, H.4    Wu, X.5    Akagi, K.6    Symer, D.E.7
  • 41
    • 84904086862 scopus 로고    scopus 로고
    • Transcriptional landscape of repetitive elements in normal and cancer human cells
    • Criscione SW, Zhang Y, Thompson W, Sedivy JM, Neretti N. Transcriptional landscape of repetitive elements in normal and cancer human cells. BMC Genomics. 2014;15:583.
    • (2014) BMC Genomics , vol.15 , pp. 583
    • Criscione, S.W.1    Zhang, Y.2    Thompson, W.3    Sedivy, J.M.4    Neretti, N.5
  • 44
    • 84904247696 scopus 로고    scopus 로고
    • Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing
    • Helman E, Lawrence MS, Stewart C, Sougnez C, Getz G, Meyerson M. Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing. Genome Res. 2014;24:1053-63.
    • (2014) Genome Res , vol.24 , pp. 1053-1063
    • Helman, E.1    Lawrence, M.S.2    Stewart, C.3    Sougnez, C.4    Getz, G.5    Meyerson, M.6
  • 52
    • 57149107578 scopus 로고    scopus 로고
    • Differentiating protein-coding and noncoding RNA: challenges and ambiguities
    • Dinger ME, Pang KC, Mercer TR, Mattick JS. Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PLoS Comput Biol. 2008;4:e1000176.
    • (2008) PLoS Comput Biol , vol.4 , pp. e1000176
    • Dinger, M.E.1    Pang, K.C.2    Mercer, T.R.3    Mattick, J.S.4
  • 54
    • 84887995915 scopus 로고    scopus 로고
    • Gene regulation by antisense transcription
    • Pelechano V, Steinmetz LM. Gene regulation by antisense transcription. Nat Rev Genet. 2013;14:880-93.
    • (2013) Nat Rev Genet , vol.14 , pp. 880-893
    • Pelechano, V.1    Steinmetz, L.M.2
  • 55
    • 33748363713 scopus 로고    scopus 로고
    • L1 retrotransposition is suppressed by endogenously encoded small interfering RNAs in human cultured cells
    • Yang N, Kazazian Jr HH. L1 retrotransposition is suppressed by endogenously encoded small interfering RNAs in human cultured cells. Nat Struct Mol Biol. 2006;13:763-71.
    • (2006) Nat Struct Mol Biol , vol.13 , pp. 763-771
    • Yang, N.1    Kazazian, H.H.2
  • 56
    • 52949095077 scopus 로고    scopus 로고
    • Retrotransposons revisited: the restraint and rehabilitation of parasites
    • Goodier JL, Kazazian Jr HH. Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell. 2008;135:23-35.
    • (2008) Cell , vol.135 , pp. 23-35
    • Goodier, J.L.1    Kazazian, H.H.2
  • 57
    • 84964995809 scopus 로고    scopus 로고
    • RepeatMasker Open-4.0
    • Smit A, Hubley, R & Green, P.: RepeatMasker Open-4.0. http://www.repeatmasker.org
    • Smit, A.1    Hubley, R.2    Green, P.3
  • 58
    • 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. 2010;26:841-2.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 59
    • 84892511644 scopus 로고    scopus 로고
    • Large-scale gene function analysis with the PANTHER classification system
    • Mi H, Muruganujan A, Casagrande JT, Thomas PD. Large-scale gene function analysis with the PANTHER classification system. Nat Protocols. 2013;8:1551-66.
    • (2013) Nat Protocols , vol.8 , pp. 1551-1566
    • Mi, H.1    Muruganujan, A.2    Casagrande, J.T.3    Thomas, P.D.4
  • 62
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.
    • (2009) Genome Biol , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 63
    • 84906246053 scopus 로고    scopus 로고
    • metaseq: a Python package for integrative genome-wide analysis reveals relationships between chromatin insulators and associated nuclear mRNA
    • Dale RK, Matzat LH, Lei EP. metaseq: a Python package for integrative genome-wide analysis reveals relationships between chromatin insulators and associated nuclear mRNA. Nucleic Acids Res. 2014;42:9158-70.
    • (2014) Nucleic Acids Res , vol.42 , pp. 9158-9170
    • Dale, R.K.1    Matzat, L.H.2    Lei, E.P.3
  • 64
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589-95.
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 66
    • 2142826519 scopus 로고    scopus 로고
    • Proteinase K added to the extraction procedure markedly increases RNA yield from primary breast tumors for use in microarray studies
    • Egyhazi S, Bjohle J, Skoog L, Huang F, Borg AL, Frostvik Stolt M, Hagerstrom T, Ringborg U, Bergh J. Proteinase K added to the extraction procedure markedly increases RNA yield from primary breast tumors for use in microarray studies. Clin Chem. 2004;50:975-6.
    • (2004) Clin Chem , vol.50 , pp. 975-976
    • Egyhazi, S.1    Bjohle, J.2    Skoog, L.3    Huang, F.4    Borg, A.L.5    Frostvik Stolt, M.6    Hagerstrom, T.7    Ringborg, U.8    Bergh, J.9


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.