메뉴 건너뛰기




Volumn 19, Issue 10, 2009, Pages 1732-1741

Nucleosomes are well positioned in exons and carry characteristic histone modifications

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE;

EID: 70349333201     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.092353.109     Document Type: Article
Times cited : (265)

References (53)
  • 1
    • 44449158814 scopus 로고    scopus 로고
    • Splicing, transcription, and chromatin: A ménage à trois
    • DOI 10.1016/j.gde.2008.01.006, PII S0959437X08000105
    • Allemand E, Batsche E, Muchardt C. 2008. Splicing, transcription, and chromatin: A ménage à trois. Curr Opin Genet Dev 18: 145-151. (Pubitemid 351756536)
    • (2008) Current Opinion in Genetics and Development , vol.18 , Issue.2 , pp. 145-151
    • Allemand, E.1    Batsche, E.2    Muchardt, C.3
  • 2
    • 0030575777 scopus 로고    scopus 로고
    • Naturally occurring nucleosome positioning signals in human exons and introns
    • DOI 10.1006/jmbi.1996.0592
    • Baldi P, Brunak S, Chauvin Y, Krogh A. 1996. Naturally occurring nucleosome positioning signals in human exons and introns. J Mol Biol 263: 503-510. (Pubitemid 26382069)
    • (1996) Journal of Molecular Biology , vol.263 , Issue.4 , pp. 503-510
    • Baldi, P.1    Brunak, S.2    Chauvin, Y.3    Krogh, A.4
  • 4
    • 34249026300 scopus 로고    scopus 로고
    • High-Resolution Profiling of Histone Methylations in the Human Genome
    • DOI 10.1016/j.cell.2007.05.009, PII S0092867407006009
    • Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. 2007. High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837. (Pubitemid 46802390)
    • (2007) Cell , vol.129 , Issue.4 , pp. 823-837
    • Barski, A.1    Cuddapah, S.2    Cui, K.3    Roh, T.-Y.4    Schones, D.E.5    Wang, Z.6    Wei, G.7    Chepelev, I.8    Zhao, K.9
  • 5
    • 30044441988 scopus 로고    scopus 로고
    • The human SWI/SNF subunit Brm is a regulator of alternative splicing
    • DOI 10.1038/nsmb1030
    • Batsche E, Yaniv M, Muchardt C. 2006. The human SWI/SNF subunit Brm is a regulator of alternative splicing. Nat Struct Mol Biol 13: 22-29. (Pubitemid 43049398)
    • (2006) Nature Structural and Molecular Biology , vol.13 , Issue.1 , pp. 22-29
    • Batsche, E.1    Yaniv, M.2    Muchardt, C.3
  • 6
    • 0026027087 scopus 로고
    • Splice junctions follow a 205-base ladder
    • Beckmann JS, Trifonov EN. 1991. Splice junctions follow a 205-base ladder. Proc Natl Acad Sci 88: 2380-2383.
    • (1991) Proc Natl Acad Sci , vol.88 , pp. 2380-2383
    • Beckmann, J.S.1    Trifonov, E.N.2
  • 7
    • 0028895417 scopus 로고
    • Exon recognition in vertebrate splicing
    • Berget SM. 1995. Exon recognition in vertebrate splicing. J Biol Chem 270: 2411-2414.
    • (1995) J Biol Chem , vol.270 , pp. 2411-2414
    • Berget, S.M.1
  • 8
    • 0024021747 scopus 로고
    • Splice site selection, rate of splicing, and alternative splicing on nascent transcripts
    • Beyer AL, Osheim YN. 1988. Splice site selection, rate of splicing, and alternative splicing on nascent transcripts. Genes & Dev 2: 754-765.
    • (1988) Genes & Dev , vol.2 , pp. 754-765
    • Beyer, A.L.1    Osheim, Y.N.2
  • 10
    • 27744577727 scopus 로고    scopus 로고
    • Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription
    • DOI 10.1016/j.cell.2005.10.023, PII S0092867405011566
    • Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK, Shia WJ, Anderson S, Yates J, Washburn MP, et al. 2005. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123: 581-592. (Pubitemid 41608462)
    • (2005) Cell , vol.123 , Issue.4 , pp. 581-592
    • Carrozza, M.J.1    Li, B.2    Florens, L.3    Suganuma, T.4    Swanson, S.K.5    Lee, K.K.6    Shia, W.-J.7    Anderson, S.8    Yates, J.9    Washburn, M.P.10    Workman, J.L.11
  • 13
    • 0033178886 scopus 로고    scopus 로고
    • Intron-exon structures of eukaryotic model organisms
    • DOI 10.1093/nar/27.15.3219
    • Deutsch M, Long M. 1999. Intron-exon structures of eukaryotic model organisms. Nucleic Acids Res 27: 3219-3228. (Pubitemid 29355739)
    • (1999) Nucleic Acids Research , vol.27 , Issue.15 , pp. 3219-3228
    • Deutsch, M.1    Long, M.2
  • 14
    • 38549139593 scopus 로고    scopus 로고
    • Dynamic histone H3 methylation during gene induction: HYPB/Setd2 mediates all H3K36 trimethylation
    • Edmunds JW, Mahadevan LC, Clayton AL. 2008. Dynamic histone H3 methylation during gene induction: HYPB/Setd2 mediates all H3K36 trimethylation. EMBO J 27: 406-420.
    • (2008) EMBO J , vol.27 , pp. 406-420
    • Edmunds, J.W.1    Mahadevan, L.C.2    Clayton, A.L.3
  • 15
    • 66749175352 scopus 로고    scopus 로고
    • Transcription-associated recombination in eukaryotes: Link between transcription, replication, and recombination
    • Gottipati P, Helleday T. 2009. Transcription-associated recombination in eukaryotes: Link between transcription, replication, and recombination. Mutagenesis 24: 203-210.
    • (2009) Mutagenesis , vol.24 , pp. 203-210
    • Gottipati, P.1    Helleday, T.2
  • 16
    • 33847076248 scopus 로고    scopus 로고
    • Chromatin Challenges during DNA Replication and Repair
    • DOI 10.1016/j.cell.2007.01.030, PII S0092867407001298
    • Groth A, Rocha W, Verreault A, Almouzni G. 2007. Chromatin challenges during DNA replication and repair. Cell 128: 721-733. (Pubitemid 46273574)
    • (2007) Cell , vol.128 , Issue.4 , pp. 721-733
    • Groth, A.1    Rocha, W.2    Verreault, A.3    Almouzni, G.4
  • 18
    • 38349127601 scopus 로고    scopus 로고
    • Combinatorial control of exon recognition
    • Hertel KJ. 2008. Combinatorial control of exon recognition. J Biol Chem 283: 1211-1215.
    • (2008) J Biol Chem , vol.283 , pp. 1211-1215
    • Hertel, K.J.1
  • 21
    • 38649129366 scopus 로고    scopus 로고
    • Diverse roles of hnRNP L in mammalian mRNA processing: A combined microarray and RNAi analysis
    • DOI 10.1261/rna.725208
    • Hung LH, Heiner M, Hui J, Schreiner S, Benes V, Bindereif A. 2008. Diverse roles of hnRNP L in mammalian mRNA processing: A combined microarray and RNAi analysis. RNA 14: 284-296. (Pubitemid 351171589)
    • (2008) RNA , vol.14 , Issue.2 , pp. 284-296
    • Hung, L.-H.1    Heiner, M.2    Hui, J.3    Schreiner, S.4    Benes, V.5    Bindereif, A.6
  • 23
    • 60349089645 scopus 로고    scopus 로고
    • Nucleosome positioning and gene regulation: Advances through genomics
    • Jiang C, Pugh BF. 2009. Nucleosome positioning and gene regulation: Advances through genomics. Nat Rev Genet 10: 161-172.
    • (2009) Nat Rev Genet , vol.10 , pp. 161-172
    • Jiang, C.1    Pugh, B.F.2
  • 24
    • 20444429051 scopus 로고    scopus 로고
    • Gene splice sites correlate with nucleosome positions
    • DOI 10.1016/j.gene.2005.03.004, PII S0378111905001071
    • Kogan S, Trifonov EN. 2005. Gene splice sites correlate with nucleosome positions. Gene 352: 57-62. (Pubitemid 40804971)
    • (2005) Gene , vol.352 , Issue.1-2 , pp. 57-62
    • Kogan, S.1    Trifonov, E.N.2
  • 26
    • 30044440197 scopus 로고    scopus 로고
    • Chromatin, transcript elongation, and alternative splicing
    • Kornblihtt AR. 2006. Chromatin, transcript elongation, and alternative splicing. Nat Struct Mol Biol 13: 5-7.
    • (2006) Nat Struct Mol Biol , vol.13 , pp. 5-7
    • Kornblihtt, A.R.1
  • 27
    • 42449089029 scopus 로고    scopus 로고
    • Coupling transcription and alternative splicing
    • Kornblihtt AR. 2007. Coupling transcription and alternative splicing. Adv Exp Med Biol 623: 175-189.
    • (2007) Adv Exp Med Biol , vol.623 , pp. 175-189
    • Kornblihtt, A.R.1
  • 30
    • 35348993743 scopus 로고    scopus 로고
    • Demethylation of H3K27 regulates polycomb recruitment and H2A ubiquitination
    • DOI 10.1126/science.1149042
    • Lee MG, Villa R, Trojer P, Norman J, Yan KP, Reinberg D, Di Croce L, Shiekhattar R. 2007. Demethylation of H3K27 regulates polycomb recruitment and H2A ubiquitination. Science 318: 447-450. (Pubitemid 47614529)
    • (2007) Science , vol.318 , Issue.5849 , pp. 447-450
    • Min, G.L.1    Villa, R.2    Trojer, P.3    Norman, J.4    Yan, K.-P.5    Reinberg, D.6    Di Croce, L.7    Shiekhattar, R.8
  • 31
    • 33847070442 scopus 로고    scopus 로고
    • The role of chromatin during transcription
    • Li B, Carey M, Workman JL. 2007. The role of chromatin during transcription. Cell 128: 707-719.
    • (2007) Cell , vol.128 , pp. 707-719
    • Li, B.1    Carey, M.2    Workman, J.L.3
  • 32
    • 4744355045 scopus 로고    scopus 로고
    • The WW domain-containing proteins interact with the early spliceosome and participate in pre-mRNA splicing in vivo
    • Lin KT, Lu RM, Tarn WY. 2004. The WW domain-containing proteins interact with the early spliceosome and participate in pre-mRNA splicing in vivo. Mol Cell Biol 24: 9176-9185.
    • (2004) Mol Cell Biol , vol.24 , pp. 9176-9185
    • Lin, K.T.1    Lu, R.M.2    Tarn, W.Y.3
  • 34
    • 0034704145 scopus 로고    scopus 로고
    • The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II
    • Morris DP, Greenleaf AL. 2000. The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II. J Biol Chem 275: 39935-39943.
    • (2000) J Biol Chem , vol.275 , pp. 39935-39943
    • Morris, D.P.1    Greenleaf, A.L.2
  • 35
    • 0037107547 scopus 로고    scopus 로고
    • On the importance of being co-transcriptional
    • Neugebauer KM. 2002. On the importance of being co-transcriptional. J Cell Sci 115: 3865-3871.
    • (2002) J Cell Sci , vol.115 , pp. 3865-3871
    • Neugebauer, K.M.1
  • 36
    • 48749100692 scopus 로고    scopus 로고
    • Regulation of CD45 alternative splicing by heterogeneous ribonucleoprotein, hnRNPLL
    • Oberdoerffer S, Moita LF, Neems D, Freitas RP, Hacohen N, Rao A. 2008. Regulation of CD45 alternative splicing by heterogeneous ribonucleoprotein, hnRNPLL. Science 321: 686-691.
    • (2008) Science , vol.321 , pp. 686-691
    • Oberdoerffer, S.1    Moita, L.F.2    Neems, D.3    Freitas, R.P.4    Hacohen, N.5    Rao, A.6
  • 37
    • 44649196386 scopus 로고    scopus 로고
    • Functional integration of transcriptional and RNA processing machineries
    • Pandit S, Wang D, Fu XD. 2008. Functional integration of transcriptional and RNA processing machineries. Curr Opin Cell Biol 20: 260-265.
    • (2008) Curr Opin Cell Biol , vol.20 , pp. 260-265
    • Pandit, S.1    Wang, D.2    Fu, X.D.3
  • 39
    • 5344244656 scopus 로고    scopus 로고
    • R Development Core Team. R Foundation for Statistical Computing, Vienna, Austria
    • R Development Core Team. 2008. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
    • (2008) R: A Language and Environment for Statistical Computing
  • 41
    • 39449088572 scopus 로고    scopus 로고
    • Genome-wide approaches to studying chromatin modifications
    • DOI 10.1038/nrg2270, PII NRG2270
    • Schones DE, Zhao K. 2008. Genome-wide approaches to studying chromatin modifications. Nat Rev Genet 9: 179-191. (Pubitemid 351271798)
    • (2008) Nature Reviews Genetics , vol.9 , Issue.3 , pp. 179-191
    • Schones, D.E.1    Zhao, K.2
  • 42
    • 39749145198 scopus 로고    scopus 로고
    • Dynamic Regulation of Nucleosome Positioning in the Human Genome
    • DOI 10.1016/j.cell.2008.02.022, PII S0092867408002705
    • Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. 2008. Dynamic regulation of nucleosome positioning in the human genome. Cell 132: 887-898. (Pubitemid 351312809)
    • (2008) Cell , vol.132 , Issue.5 , pp. 887-898
    • Schones, D.E.1    Cui, K.2    Cuddapah, S.3    Roh, T.-Y.4    Barski, A.5    Wang, Z.6    Wei, G.7    Zhao, K.8
  • 44
    • 19344363599 scopus 로고    scopus 로고
    • Quality control of messenger ribonucleoprotein particles in the nucleus and at the pore
    • DOI 10.1016/j.ceb.2005.04.007, PII S0955067405000499, Nucleus and Gene Expression
    • Sommer P, Nehrbass U. 2005. Quality control of messenger ribonucleoprotein particles in the nucleus and at the pore. Curr Opin Cell Biol 17: 294-301. (Pubitemid 40719920)
    • (2005) Current Opinion in Cell Biology , vol.17 , Issue.3 , pp. 294-301
    • Sommer, P.1    Nehrbass, U.2
  • 48
    • 57149100569 scopus 로고    scopus 로고
    • The impact of the nucleosome code on protein-coding sequence evolution in yeast
    • Warnecke T, Batada NN, Hurst LD. 2008. The impact of the nucleosome code on protein-coding sequence evolution in yeast. PLoS Genet 4: e1000250.
    • (2008) PLoS Genet , vol.4
    • Warnecke, T.1    Batada, N.N.2    Hurst, L.D.3
  • 49
    • 56649089682 scopus 로고    scopus 로고
    • Evolutionary footprints of nucleosome positions in yeast
    • Washietl S, Machne R, Goldman N. 2008. Evolutionary footprints of nucleosome positions in yeast. Trends Genet 24: 583-587.
    • (2008) Trends Genet , vol.24 , pp. 583-587
    • Washietl, S.1    Machne, R.2    Goldman, N.3
  • 50
    • 33846525436 scopus 로고    scopus 로고
    • The Spt6 SH2 domain binds Ser2-P RNAPII to direct Iws1-dependent mRNA splicing and export
    • DOI 10.1101/gad.1503107
    • Yoh SM, Cho H, Pickle L, Evans RM, Jones KA. 2007. The Spt6 SH2 domain binds Ser2-P RNAPII to direct Iws1-dependent mRNA splicing and export. Genes & Dev 21: 160-174. (Pubitemid 46155810)
    • (2007) Genes and Development , vol.21 , Issue.2 , pp. 160-174
    • Yoh, S.M.1    Cho, H.2    Pickle, L.3    Evans, R.M.4    Jones, K.A.5
  • 51
    • 58049206591 scopus 로고    scopus 로고
    • The Iws1:Spt6:CTD complex controls cotranscriptional mRNA biosynthesis and HYPB/Setd2-mediated histone H3K36 methylation
    • Yoh SM, Lucas JS, Jones KA. 2008. The Iws1:Spt6:CTD complex controls cotranscriptional mRNA biosynthesis and HYPB/Setd2-mediated histone H3K36 methylation. Genes & Dev 22: 3422-3434.
    • (2008) Genes & Dev , vol.22 , pp. 3422-3434
    • Yoh, S.M.1    Lucas, J.S.2    Jones, K.A.3
  • 53
    • 67650120109 scopus 로고    scopus 로고
    • Heterogeneous nuclear Rribonucleoprotein L is a subunit of human KMT3a/Set2 complex required for H3 Lys-36 trimethylation activity in vivo
    • Yuan W, Xie J, Long C, Erdjument-Bromage H, Ding X, Zheng Y, Tempst P, Chen S, Zhu B, Reinberg D. 2009. Heterogeneous nuclear Rribonucleoprotein L is a subunit of human KMT3a/Set2 complex required for H3 Lys-36 trimethylation activity in vivo. J Biol Chem 284: 15701-15707.
    • (2009) J Biol Chem , vol.284 , pp. 15701-15707
    • Yuan, W.1    Xie, J.2    Long, C.3    Erdjument-Bromage, H.4    Ding, X.5    Zheng, Y.6    Tempst, P.7    Chen, S.8    Zhu, B.9    Reinberg, D.10


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.