메뉴 건너뛰기




Volumn 14, Issue 1, 2013, Pages

Divergent transcription is associated with promoters of transcriptional regulators

Author keywords

Bidirectional promoter; Developmental transcription factor; Divergent transcription; GC skew; lncRNA

Indexed keywords

HISTONE H3; HISTONE H3K79ME; LONG UNTRANSLATED RNA; MESSENGER RNA; RNA POLYMERASE II; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

EID: 84890772287     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-914     Document Type: Article
Times cited : (92)

References (78)
  • 1
    • 34249088350 scopus 로고    scopus 로고
    • Genome-wide transcription and the implications for genomic organization
    • 10.1038/nrg2083, 17486121
    • Kapranov P, Willingham AT, Gingeras TR. Genome-wide transcription and the implications for genomic organization. Nat Rev Genet 2007, 8:413-423. 10.1038/nrg2083, 17486121.
    • (2007) Nat Rev Genet , vol.8 , pp. 413-423
    • Kapranov, P.1    Willingham, A.T.2    Gingeras, T.R.3
  • 2
    • 81355142141 scopus 로고    scopus 로고
    • Non-coding RNAs in human disease
    • 10.1038/nrg3074, 22094949
    • Esteller M. Non-coding RNAs in human disease. Nat Rev Genet 2011, 12:861-874. 10.1038/nrg3074, 22094949.
    • (2011) Nat Rev Genet , vol.12 , pp. 861-874
    • Esteller, M.1
  • 3
    • 84857066786 scopus 로고    scopus 로고
    • Modular regulatory principles of large non-coding RNAs
    • 10.1038/nature10887, 22337053
    • Guttman M, Rinn JL. Modular regulatory principles of large non-coding RNAs. Nature 2012, 482:339-346. 10.1038/nature10887, 22337053.
    • (2012) Nature , vol.482 , pp. 339-346
    • Guttman, M.1    Rinn, J.L.2
  • 4
    • 84865727393 scopus 로고    scopus 로고
    • The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression
    • 10.1101/gr.132159.111, 3431493, 22955988
    • Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 2012, 22:1775-1789. 10.1101/gr.132159.111, 3431493, 22955988.
    • (2012) Genome Res , vol.22 , pp. 1775-1789
    • Derrien, T.1    Johnson, R.2    Bussotti, G.3    Tanzer, A.4    Djebali, S.5    Tilgner, H.6    Guernec, G.7    Martin, D.8    Merkel, A.9    Knowles, D.G.10
  • 6
    • 80053569699 scopus 로고    scopus 로고
    • Pervasive transcription - Lessons from yeast
    • 10.1016/j.biochi.2011.07.001, 21771634
    • Tisseur M, Kwapisz M, Morillon A. Pervasive transcription - Lessons from yeast. Biochimie 2011, 93:1889-1896. 10.1016/j.biochi.2011.07.001, 21771634.
    • (2011) Biochimie , vol.93 , pp. 1889-1896
    • Tisseur, M.1    Kwapisz, M.2    Morillon, A.3
  • 8
    • 84863861287 scopus 로고    scopus 로고
    • Regulation of chromatin structure by long noncoding RNAs: focus on natural antisense transcripts
    • 10.1016/j.tig.2012.03.013, 3768148, 22541732
    • Magistri M, Faghihi MA, St Laurent G, Wahlestedt C. Regulation of chromatin structure by long noncoding RNAs: focus on natural antisense transcripts. Trends Genet 2012, 28:389-396. 10.1016/j.tig.2012.03.013, 3768148, 22541732.
    • (2012) Trends Genet , vol.28 , pp. 389-396
    • Magistri, M.1    Faghihi, M.A.2    St Laurent, G.3    Wahlestedt, C.4
  • 11
    • 79959346319 scopus 로고    scopus 로고
    • Functional consequences of bidirectional promoters
    • 10.1016/j.tig.2011.04.002, 3123404, 21601935
    • Wei W, Pelechano V, Jarvelin AI, Steinmetz LM. Functional consequences of bidirectional promoters. Trends Genet 2011, 27:267-276. 10.1016/j.tig.2011.04.002, 3123404, 21601935.
    • (2011) Trends Genet , vol.27 , pp. 267-276
    • Wei, W.1    Pelechano, V.2    Jarvelin, A.I.3    Steinmetz, L.M.4
  • 12
    • 57849109058 scopus 로고    scopus 로고
    • Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
    • 10.1126/science.1162228, 2833333, 19056941
    • Core LJ, Waterfall JJ, Lis JT. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 2008, 322:1845-1848. 10.1126/science.1162228, 2833333, 19056941.
    • (2008) Science , vol.322 , pp. 1845-1848
    • Core, L.J.1    Waterfall, J.J.2    Lis, J.T.3
  • 15
    • 20444368036 scopus 로고    scopus 로고
    • Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase
    • 10.1016/j.cell.2005.04.030, 15935759
    • Wyers F, Rougemaille M, Badis G, Rousselle JC, Dufour ME, Boulay J, Regnault B, Devaux F, Namane A, Seraphin B, et al. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 2005, 121:725-737. 10.1016/j.cell.2005.04.030, 15935759.
    • (2005) Cell , vol.121 , pp. 725-737
    • Wyers, F.1    Rougemaille, M.2    Badis, G.3    Rousselle, J.C.4    Dufour, M.E.5    Boulay, J.6    Regnault, B.7    Devaux, F.8    Namane, A.9    Seraphin, B.10
  • 16
    • 80051764912 scopus 로고    scopus 로고
    • PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters
    • 10.1093/nar/gkr370, 3167610, 21596787
    • Preker P, Almvig K, Christensen MS, Valen E, Mapendano CK, Sandelin A, Jensen TH. PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters. Nucleic Acids Res 2011, 39:7179-7193. 10.1093/nar/gkr370, 3167610, 21596787.
    • (2011) Nucleic Acids Res , vol.39 , pp. 7179-7193
    • Preker, P.1    Almvig, K.2    Christensen, M.S.3    Valen, E.4    Mapendano, C.K.5    Sandelin, A.6    Jensen, T.H.7
  • 18
    • 60549114880 scopus 로고    scopus 로고
    • Widespread bidirectional promoters are the major source of cryptic transcripts in yeast
    • 10.1038/nature07747, 19169244
    • Neil H, Malabat C, Aubenton-Carafa D,Y, Xu Z, Steinmetz LM, Jacquier A. Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 2009, 457:1038-1042. 10.1038/nature07747, 19169244.
    • (2009) Nature , vol.457 , pp. 1038-1042
    • Neil, H.1    Malabat, C.2    Aubenton-Carafa, D.Y.3    Xu, Z.4    Steinmetz, L.M.5    Jacquier, A.6
  • 19
    • 77952148742 scopus 로고    scopus 로고
    • Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
    • 10.1038/nbt.1633, 2868100, 20436462
    • Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 2010, 28:503-510. 10.1038/nbt.1633, 2868100, 20436462.
    • (2010) Nat Biotechnol , vol.28 , pp. 503-510
    • Guttman, M.1    Garber, M.2    Levin, J.Z.3    Donaghey, J.4    Robinson, J.5    Adiconis, X.6    Fan, L.7    Koziol, M.J.8    Gnirke, A.9    Nusbaum, C.10
  • 20
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • 10.1101/gad.17446611, 3185964, 21890647
    • Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 2011, 25:1915-1927. 10.1101/gad.17446611, 3185964, 21890647.
    • (2011) Genes Dev , vol.25 , pp. 1915-1927
    • Cabili, M.N.1    Trapnell, C.2    Goff, L.3    Koziol, M.4    Tazon-Vega, B.5    Regev, A.6    Rinn, J.L.7
  • 23
    • 80052335127 scopus 로고    scopus 로고
    • Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling
    • 10.1186/1471-2164-12-441, 3180702, 21888672
    • Thiagarajan RD, Cloonan N, Gardiner BB, Mercer TR, Kolle G, Nourbakhsh E, Wani S, Tang D, Krishnan K, Georgas KM, et al. Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling. BMC Genomics 2011, 12:441. 10.1186/1471-2164-12-441, 3180702, 21888672.
    • (2011) BMC Genomics , vol.12 , pp. 441
    • Thiagarajan, R.D.1    Cloonan, N.2    Gardiner, B.B.3    Mercer, T.R.4    Kolle, G.5    Nourbakhsh, E.6    Wani, S.7    Tang, D.8    Krishnan, K.9    Georgas, K.M.10
  • 24
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    • 10.1038/nprot.2012.016, 3334321, 22383036
    • Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012, 7:562-578. 10.1038/nprot.2012.016, 3334321, 22383036.
    • (2012) Nat Protoc , vol.7 , pp. 562-578
    • Trapnell, C.1    Roberts, A.2    Goff, L.3    Pertea, G.4    Kim, D.5    Kelley, D.R.6    Pimentel, H.7    Salzberg, S.L.8    Rinn, J.L.9    Pachter, L.10
  • 25
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • 10.1038/nbt.1621, 3146043, 20436464
    • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010, 28:511-515. 10.1038/nbt.1621, 3146043, 20436464.
    • (2010) Nat Biotechnol , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5    van Baren, M.J.6    Salzberg, S.L.7    Wold, B.J.8    Pachter, L.9
  • 26
    • 79959446962 scopus 로고    scopus 로고
    • PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions
    • 10.1093/bioinformatics/btr209, 3117341, 21685081
    • Lin MF, Jungreis I, Kellis M. PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics 2011, 27:i275-i282. 10.1093/bioinformatics/btr209, 3117341, 21685081.
    • (2011) Bioinformatics , vol.27
    • Lin, M.F.1    Jungreis, I.2    Kellis, M.3
  • 27
    • 84864251757 scopus 로고    scopus 로고
    • Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions
    • 10.1016/j.cell.2012.05.043, 3405548, 22817891
    • Bhatt DM, Pandya-Jones A, Tong AJ, Barozzi I, Lissner MM, Natoli G, Black DL, Smale ST. Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Cell 2012, 150:279-290. 10.1016/j.cell.2012.05.043, 3405548, 22817891.
    • (2012) Cell , vol.150 , pp. 279-290
    • Bhatt, D.M.1    Pandya-Jones, A.2    Tong, A.J.3    Barozzi, I.4    Lissner, M.M.5    Natoli, G.6    Black, D.L.7    Smale, S.T.8
  • 28
    • 37549010335 scopus 로고    scopus 로고
    • Launching the T-cell-lineage developmental programme
    • Rothenberg EV, Moore JE, Yui MA. Launching the T-cell-lineage developmental programme. NatRevImmunol 2008, 8:9-21.
    • (2008) NatRevImmunol , vol.8 , pp. 9-21
    • Rothenberg, E.V.1    Moore, J.E.2    Yui, M.A.3
  • 29
    • 67849130563 scopus 로고    scopus 로고
    • ToppGene Suite for gene list enrichment analysis and candidate gene prioritization
    • 10.1093/nar/gkp427, 2703978, 19465376
    • Chen J, Bardes EE, Aronow BJ, Jegga AG. ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res 2009, 37:W305-W311. 10.1093/nar/gkp427, 2703978, 19465376.
    • (2009) Nucleic Acids Res , vol.37
    • Chen, J.1    Bardes, E.E.2    Aronow, B.J.3    Jegga, A.G.4
  • 31
    • 33846505022 scopus 로고    scopus 로고
    • Key factors in the organized chaos of early T cell development
    • 10.1038/ni1436, 17242687
    • Hayday AC, Pennington DJ. Key factors in the organized chaos of early T cell development. Nat Immunol 2007, 8:137-144. 10.1038/ni1436, 17242687.
    • (2007) Nat Immunol , vol.8 , pp. 137-144
    • Hayday, A.C.1    Pennington, D.J.2
  • 33
    • 84859157183 scopus 로고    scopus 로고
    • Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity
    • 10.1016/j.cell.2012.01.056, 3336965, 22500808
    • Zhang JA, Mortazavi A, Williams BA, Wold BJ, Rothenberg EV. Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity. Cell 2012, 149:467-482. 10.1016/j.cell.2012.01.056, 3336965, 22500808.
    • (2012) Cell , vol.149 , pp. 467-482
    • Zhang, J.A.1    Mortazavi, A.2    Williams, B.A.3    Wold, B.J.4    Rothenberg, E.V.5
  • 35
    • 84858440747 scopus 로고    scopus 로고
    • Metazoan promoters: emerging characteristics and insights into transcriptional regulation
    • Lenhard B, Sandelin A, Carninci P. Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nat Rev Genet 2012, 13:233-245.
    • (2012) Nat Rev Genet , vol.13 , pp. 233-245
    • Lenhard, B.1    Sandelin, A.2    Carninci, P.3
  • 36
    • 78650304236 scopus 로고    scopus 로고
    • Charting histone modifications and the functional organization of mammalian genomes
    • Zhou VW, Goren A, Bernstein BE. Charting histone modifications and the functional organization of mammalian genomes. Nat Rev Genet 2011, 12:7-18.
    • (2011) Nat Rev Genet , vol.12 , pp. 7-18
    • Zhou, V.W.1    Goren, A.2    Bernstein, B.E.3
  • 39
    • 80051885764 scopus 로고    scopus 로고
    • Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types
    • 10.1016/j.immuni.2011.08.007, 3169184, 21867929
    • Wei G, Abraham BJ, Yagi R, Jothi R, Cui K, Sharma S, Narlikar L, Northrup DL, Tang Q, Paul WE, et al. Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types. Immunity 2011, 35:299-311. 10.1016/j.immuni.2011.08.007, 3169184, 21867929.
    • (2011) Immunity , vol.35 , pp. 299-311
    • Wei, G.1    Abraham, B.J.2    Yagi, R.3    Jothi, R.4    Cui, K.5    Sharma, S.6    Narlikar, L.7    Northrup, D.L.8    Tang, Q.9    Paul, W.E.10
  • 42
    • 84859087611 scopus 로고    scopus 로고
    • R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters
    • 10.1016/j.molcel.2012.01.017, 3319272, 22387027
    • Ginno PA, Lott PL, Christensen HC, Korf I, Chedin F. R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol Cell 2012, 45:814-825. 10.1016/j.molcel.2012.01.017, 3319272, 22387027.
    • (2012) Mol Cell , vol.45 , pp. 814-825
    • Ginno, P.A.1    Lott, P.L.2    Christensen, H.C.3    Korf, I.4    Chedin, F.5
  • 43
    • 84880510553 scopus 로고    scopus 로고
    • Promoter directionality is controlled by U1 snRNP and polyadenylation signals
    • 10.1038/nature12349, 23792564
    • Almada AE, Wu X, Kriz AJ, Burge CB, Sharp PA. Promoter directionality is controlled by U1 snRNP and polyadenylation signals. Nature 2013, 499:360-363. 10.1038/nature12349, 23792564.
    • (2013) Nature , vol.499 , pp. 360-363
    • Almada, A.E.1    Wu, X.2    Kriz, A.J.3    Burge, C.B.4    Sharp, P.A.5
  • 45
    • 84864303162 scopus 로고    scopus 로고
    • First exon length controls active chromatin signatures and transcription
    • 10.1016/j.celrep.2012.05.019, 22840397
    • Bieberstein NI, Carrillo Oesterreich F, Straube K, Neugebauer KM. First exon length controls active chromatin signatures and transcription. Cell Rep 2012, 2:62-68. 10.1016/j.celrep.2012.05.019, 22840397.
    • (2012) Cell Rep , vol.2 , pp. 62-68
    • Bieberstein, N.I.1    Carrillo Oesterreich, F.2    Straube, K.3    Neugebauer, K.M.4
  • 46
    • 78649836342 scopus 로고    scopus 로고
    • Reciprocal intronic and exonic histone modification regions in humans
    • 10.1038/nsmb.1924, 3057557, 21057525
    • Huff JT, Plocik AM, Guthrie C, Yamamoto KR. Reciprocal intronic and exonic histone modification regions in humans. Nat Struct Mol Biol 2010, 17:1495-1499. 10.1038/nsmb.1924, 3057557, 21057525.
    • (2010) Nat Struct Mol Biol , vol.17 , pp. 1495-1499
    • Huff, J.T.1    Plocik, A.M.2    Guthrie, C.3    Yamamoto, K.R.4
  • 47
    • 84872405841 scopus 로고
    • Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription
    • Heidemann M, Hintermair C, Voss K, Eick D. Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription. Biochim Biophys Acta 1829, 2013:55-62.
    • (1829) Biochim Biophys Acta , vol.2013 , pp. 55-62
    • Heidemann, M.1    Hintermair, C.2    Voss, K.3    Eick, D.4
  • 48
    • 84870566023 scopus 로고    scopus 로고
    • Long non-coding RNAs in C. elegans
    • 10.1101/gr.140475.112, 3514682, 22707570
    • Nam JW, Bartel D. Long non-coding RNAs in C. elegans. Genome Res 2012, 22(12):2529-2540. 10.1101/gr.140475.112, 3514682, 22707570.
    • (2012) Genome Res , vol.22 , Issue.12 , pp. 2529-2540
    • Nam, J.W.1    Bartel, D.2
  • 49
    • 84870485829 scopus 로고    scopus 로고
    • CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters
    • 10.1101/gr.138776.112, 3514669, 23100115
    • Fenouil R, Cauchy P, Koch F, Descostes N, Cabeza JZ, Innocenti C, Ferrier P, Spicuglia S, Gut M, Gut I, Andrau JC. CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters. Genome Res 2012, 22:2399-2408. 10.1101/gr.138776.112, 3514669, 23100115.
    • (2012) Genome Res , vol.22 , pp. 2399-2408
    • Fenouil, R.1    Cauchy, P.2    Koch, F.3    Descostes, N.4    Cabeza, J.Z.5    Innocenti, C.6    Ferrier, P.7    Spicuglia, S.8    Gut, M.9    Gut, I.10    Andrau, J.C.11
  • 50
    • 38649114329 scopus 로고    scopus 로고
    • Specific expression of long noncoding RNAs in the mouse brain
    • 10.1073/pnas.0706729105, 2206602, 18184812
    • Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS. Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A 2008, 105:716-721. 10.1073/pnas.0706729105, 2206602, 18184812.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 716-721
    • Mercer, T.R.1    Dinger, M.E.2    Sunkin, S.M.3    Mehler, M.F.4    Mattick, J.S.5
  • 51
    • 62249133709 scopus 로고    scopus 로고
    • Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    • 10.1038/nature07672, 2754849, 19182780
    • Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009, 458:223-227. 10.1038/nature07672, 2754849, 19182780.
    • (2009) Nature , vol.458 , pp. 223-227
    • Guttman, M.1    Amit, I.2    Garber, M.3    French, C.4    Lin, M.F.5    Feldser, D.6    Huarte, M.7    Zuk, O.8    Carey, B.W.9    Cassady, J.P.10
  • 52
    • 84867073340 scopus 로고    scopus 로고
    • Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage
    • 10.1016/j.cell.2012.07.035, 3462286, 22981692
    • Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico AR, Capra JA, et al. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell 2012, 151:206-220. 10.1016/j.cell.2012.07.035, 3462286, 22981692.
    • (2012) Cell , vol.151 , pp. 206-220
    • Wamstad, J.A.1    Alexander, J.M.2    Truty, R.M.3    Shrikumar, A.4    Li, F.5    Eilertson, K.E.6    Ding, H.7    Wylie, J.N.8    Pico, A.R.9    Capra, J.A.10
  • 53
    • 84879987789 scopus 로고    scopus 로고
    • LincRNAs: genomics, evolution, and mechanisms
    • 10.1016/j.cell.2013.06.020, 23827673
    • Ulitsky I, Bartel DP. lincRNAs: genomics, evolution, and mechanisms. Cell 2013, 154:26-46. 10.1016/j.cell.2013.06.020, 23827673.
    • (2013) Cell , vol.154 , pp. 26-46
    • Ulitsky, I.1    Bartel, D.P.2
  • 54
    • 84455206362 scopus 로고    scopus 로고
    • Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution
    • 10.1016/j.cell.2011.11.055, 3376356, 22196729
    • Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP. Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell 2011, 147:1537-1550. 10.1016/j.cell.2011.11.055, 3376356, 22196729.
    • (2011) Cell , vol.147 , pp. 1537-1550
    • Ulitsky, I.1    Shkumatava, A.2    Jan, C.H.3    Sive, H.4    Bartel, D.P.5
  • 55
    • 34248358308 scopus 로고    scopus 로고
    • Hyperconserved CpG domains underlie Polycomb-binding sites
    • 10.1073/pnas.0609746104, 1838490, 17376869
    • Tanay A, ODonnell AH, Damelin M, Bestor TH. Hyperconserved CpG domains underlie Polycomb-binding sites. Proc Natl Acad Sci U S A 2007, 104:5521-5526. 10.1073/pnas.0609746104, 1838490, 17376869.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 5521-5526
    • Tanay, A.1    Donnell, O.A.H.2    Damelin, M.3    Bestor, T.H.4
  • 56
    • 44449113335 scopus 로고    scopus 로고
    • Diversity of core promoter elements comprising human bidirectional promoters
    • Yang MQ, Elnitski LL. Diversity of core promoter elements comprising human bidirectional promoters. BMC Genomics 2008, 9(Suppl 2):S3.
    • (2008) BMC Genomics , vol.9 , Issue.SUPPL. 2
    • Yang, M.Q.1    Elnitski, L.L.2
  • 58
    • 33746093492 scopus 로고    scopus 로고
    • Cotranscriptional processes and their influence on genome stability
    • 10.1101/gad.1438306, 16847344
    • Li X, Manley JL. Cotranscriptional processes and their influence on genome stability. Genes Dev 2006, 20:1838-1847. 10.1101/gad.1438306, 16847344.
    • (2006) Genes Dev , vol.20 , pp. 1838-1847
    • Li, X.1    Manley, J.L.2
  • 59
    • 84855286267 scopus 로고    scopus 로고
    • Genome instability and transcription elongation impairment in human cells depleted of THO/TREX
    • 10.1371/journal.pgen.1002386, 3228816, 22144908
    • Dominguez-Sanchez MS, Barroso S, Gomez-Gonzalez B, Luna R, Aguilera A. Genome instability and transcription elongation impairment in human cells depleted of THO/TREX. PLoS Genet 2011, 7:e1002386. 10.1371/journal.pgen.1002386, 3228816, 22144908.
    • (2011) PLoS Genet , vol.7
    • Dominguez-Sanchez, M.S.1    Barroso, S.2    Gomez-Gonzalez, B.3    Luna, R.4    Aguilera, A.5
  • 60
    • 77954841539 scopus 로고    scopus 로고
    • Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis
    • 10.1101/gad.573310, 2904944, 20634320
    • El Hage A, French SL, Beyer AL, Tollervey D. Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis. Genes Dev 2010, 24:1546-1558. 10.1101/gad.573310, 2904944, 20634320.
    • (2010) Genes Dev , vol.24 , pp. 1546-1558
    • El Hage, A.1    French, S.L.2    Beyer, A.L.3    Tollervey, D.4
  • 61
    • 34447267682 scopus 로고    scopus 로고
    • Impairment of transcription elongation by R-loops in vitro
    • 10.1016/j.bbrc.2007.06.098, 17603014
    • Tous C, Aguilera A. Impairment of transcription elongation by R-loops in vitro. Biochem Biophys Res Commun 2007, 360:428-432. 10.1016/j.bbrc.2007.06.098, 17603014.
    • (2007) Biochem Biophys Res Commun , vol.360 , pp. 428-432
    • Tous, C.1    Aguilera, A.2
  • 62
    • 84863426816 scopus 로고    scopus 로고
    • Identification and characterization of a noncoding RNA at the mouse Pcna locus
    • 10.1007/s10059-012-2164-x, 22228179
    • Lee JY, Khan AA, Min H, Wang X, Kim MH. Identification and characterization of a noncoding RNA at the mouse Pcna locus. Mol Cells 2012, 33:111-116. 10.1007/s10059-012-2164-x, 22228179.
    • (2012) Mol Cells , vol.33 , pp. 111-116
    • Lee, J.Y.1    Khan, A.A.2    Min, H.3    Wang, X.4    Kim, M.H.5
  • 63
  • 64
    • 84871699564 scopus 로고    scopus 로고
    • Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans
    • 10.1038/nrg3293, 3552498, 22986266
    • Adelman K, Lis JT. Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nat Rev Genet 2012, 13:720-731. 10.1038/nrg3293, 3552498, 22986266.
    • (2012) Nat Rev Genet , vol.13 , pp. 720-731
    • Adelman, K.1    Lis, J.T.2
  • 65
    • 34447098370 scopus 로고    scopus 로고
    • A chromatin landmark and transcription initiation at most promoters in human cells
    • 10.1016/j.cell.2007.05.042, 3200295, 17632057
    • Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 2007, 130:77-88. 10.1016/j.cell.2007.05.042, 3200295, 17632057.
    • (2007) Cell , vol.130 , pp. 77-88
    • Guenther, M.G.1    Levine, S.S.2    Boyer, L.A.3    Jaenisch, R.4    Young, R.A.5
  • 66
    • 70849107088 scopus 로고    scopus 로고
    • Immediate mediators of the inflammatory response are poised for gene activation through RNA polymerase II stalling
    • 10.1073/pnas.0910177106, 2775335, 19820169
    • Adelman K, Kennedy MA, Nechaev S, Gilchrist DA, Muse GW, Chinenov Y, Rogatsky I. Immediate mediators of the inflammatory response are poised for gene activation through RNA polymerase II stalling. Proc Natl Acad Sci U S A 2009, 106:18207-18212. 10.1073/pnas.0910177106, 2775335, 19820169.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 18207-18212
    • Adelman, K.1    Kennedy, M.A.2    Nechaev, S.3    Gilchrist, D.A.4    Muse, G.W.5    Chinenov, Y.6    Rogatsky, I.7
  • 67
    • 67649648237 scopus 로고    scopus 로고
    • Control of inducible gene expression by signal-dependent transcriptional elongation
    • 10.1016/j.cell.2009.05.047, 2828818, 19596240
    • Hargreaves DC, Horng T, Medzhitov R. Control of inducible gene expression by signal-dependent transcriptional elongation. Cell 2009, 138:129-145. 10.1016/j.cell.2009.05.047, 2828818, 19596240.
    • (2009) Cell , vol.138 , pp. 129-145
    • Hargreaves, D.C.1    Horng, T.2    Medzhitov, R.3
  • 68
    • 44749094453 scopus 로고    scopus 로고
    • Genome-wide RNA polymerase II: not genes only!
    • 10.1016/j.tibs.2008.04.006, 18467100
    • Koch F, Jourquin F, Ferrier P, Andrau JC. Genome-wide RNA polymerase II: not genes only!. Trends Biochem Sci 2008, 33:265-273. 10.1016/j.tibs.2008.04.006, 18467100.
    • (2008) Trends Biochem Sci , vol.33 , pp. 265-273
    • Koch, F.1    Jourquin, F.2    Ferrier, P.3    Andrau, J.C.4
  • 70
    • 47649125318 scopus 로고    scopus 로고
    • Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation
    • Lopez-Maury L, Marguerat S, Bahler J. Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation. Nat Rev Genet 2008, 9:583-593.
    • (2008) Nat Rev Genet , vol.9 , pp. 583-593
    • Lopez-Maury, L.1    Marguerat, S.2    Bahler, J.3
  • 71
    • 29244476917 scopus 로고    scopus 로고
    • Filtering transcriptional noise during development: concepts and mechanisms
    • 10.1038/nrg1750, 16369570
    • Arias AM, Hayward P. Filtering transcriptional noise during development: concepts and mechanisms. Nat Rev Genet 2006, 7:34-44. 10.1038/nrg1750, 16369570.
    • (2006) Nat Rev Genet , vol.7 , pp. 34-44
    • Arias, A.M.1    Hayward, P.2
  • 74
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: a flexible suite of utilities for comparing genomic features
    • 10.1093/bioinformatics/btq033, 2832824, 20110278
    • Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26:841-842. 10.1093/bioinformatics/btq033, 2832824, 20110278.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 76
    • 77952567987 scopus 로고    scopus 로고
    • Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
    • 10.1016/j.molcel.2010.05.004, 2898526, 20513432
    • Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 2010, 38:576-589. 10.1016/j.molcel.2010.05.004, 2898526, 20513432.
    • (2010) Mol Cell , vol.38 , pp. 576-589
    • Heinz, S.1    Benner, C.2    Spann, N.3    Bertolino, E.4    Lin, Y.C.5    Laslo, P.6    Cheng, J.X.7    Murre, C.8    Singh, H.9    Glass, C.K.10
  • 77
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • da Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4:44-57.
    • (2009) Nat Protoc , vol.4 , pp. 44-57
    • da Huang, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 78
    • 84856340032 scopus 로고    scopus 로고
    • TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks
    • Lepoivre C, Bergon A, Lopez F, Perumal NB, Nguyen C, Imbert J, Puthier D. TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks. BMC Bioinf 2012, 13:19.
    • (2012) BMC Bioinf , vol.13 , pp. 19
    • Lepoivre, C.1    Bergon, A.2    Lopez, F.3    Perumal, N.B.4    Nguyen, C.5    Imbert, J.6    Puthier, D.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.