메뉴 건너뛰기




Volumn 53, Issue 5, 2014, Pages 819-830

Nucleosomes are context-specific, H2A.Z-Modulated barriers to RNA polymerase

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE H2AZ; NUCLEOTIDE; RNA POLYMERASE II;

EID: 84896786505     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2014.02.014     Document Type: Article
Times cited : (290)

References (55)
  • 1
    • 84871699564 scopus 로고    scopus 로고
    • Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans
    • Adelman K., Lis J.T. Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nat. Rev. Genet. 2012, 13:720-731.
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 720-731
    • Adelman, K.1    Lis, J.T.2
  • 2
    • 11344268432 scopus 로고    scopus 로고
    • Efficient release from promoter-proximal stall sites requires transcript cleavage factor TFIIS
    • Adelman K., Marr M.T., Werner J., Saunders A., Ni Z., Andrulis E.D., Lis J.T. Efficient release from promoter-proximal stall sites requires transcript cleavage factor TFIIS. Mol. Cell 2005, 17:103-112.
    • (2005) Mol. Cell , vol.17 , pp. 103-112
    • Adelman, K.1    Marr, M.T.2    Werner, J.3    Saunders, A.4    Ni, Z.5    Andrulis, E.D.6    Lis, J.T.7
  • 5
    • 84870575235 scopus 로고    scopus 로고
    • Histone H2A variants in nucleosomes and chromatin: more or less stable?
    • Bönisch C., Hake S.B. Histone H2A variants in nucleosomes and chromatin: more or less stable?. Nucleic Acids Res. 2012, 40:10719-10741.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 10719-10741
    • Bönisch, C.1    Hake, S.B.2
  • 7
    • 0023138161 scopus 로고
    • Transcription initiation by RNA polymerase II invitro. Properties of preinitiation, initiation, and elongation complexes
    • Cai H., Luse D.S. Transcription initiation by RNA polymerase II invitro. Properties of preinitiation, initiation, and elongation complexes. J.Biol. Chem. 1987, 262:298-304.
    • (1987) J.Biol. Chem. , vol.262 , pp. 298-304
    • Cai, H.1    Luse, D.S.2
  • 8
    • 70249121045 scopus 로고    scopus 로고
    • The logic of chromatin architecture and remodelling at promoters
    • Cairns B.R. The logic of chromatin architecture and remodelling at promoters. Nature 2009, 461:193-198.
    • (2009) Nature , vol.461 , pp. 193-198
    • Cairns, B.R.1
  • 10
    • 78751659330 scopus 로고    scopus 로고
    • Nascent transcript sequencing visualizes transcription at nucleotide resolution
    • Churchman L.S., Weissman J.S. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 2011, 469:368-373.
    • (2011) Nature , vol.469 , pp. 368-373
    • Churchman, L.S.1    Weissman, J.S.2
  • 11
    • 84864094076 scopus 로고    scopus 로고
    • Native elongating transcript sequencing (NET-seq)
    • Unit 4.14, 11-17, Chapter 4
    • Churchman L.S., Weissman J.S. Native elongating transcript sequencing (NET-seq). Curr. Protoc. Mol. Biol. 2012, Chapter 4. Unit 4.14, 11-17.
    • (2012) Curr. Protoc. Mol. Biol.
    • Churchman, L.S.1    Weissman, J.S.2
  • 12
    • 84868122260 scopus 로고    scopus 로고
    • Deposition of histone variant H2A.Z within gene bodies regulates responsive genes
    • Coleman-Derr D., Zilberman D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genet. 2012, 8:e1002988.
    • (2012) PLoS Genet. , vol.8
    • Coleman-Derr, D.1    Zilberman, D.2
  • 14
    • 77952996319 scopus 로고    scopus 로고
    • Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones
    • Deal R.B., Henikoff J.G., Henikoff S. Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones. Science 2010, 328:1161-1164.
    • (2010) Science , vol.328 , pp. 1161-1164
    • Deal, R.B.1    Henikoff, J.G.2    Henikoff, S.3
  • 15
    • 78149477660 scopus 로고    scopus 로고
    • Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation
    • Gilchrist D.A., Dos Santos G., Fargo D.C., Xie B., Gao Y., Li L., Adelman K. Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation. Cell 2010, 143:540-551.
    • (2010) Cell , vol.143 , pp. 540-551
    • Gilchrist, D.A.1    Dos Santos, G.2    Fargo, D.C.3    Xie, B.4    Gao, Y.5    Li, L.6    Adelman, K.7
  • 16
    • 77951169141 scopus 로고    scopus 로고
    • Chromatin remodeling by imitation switch (ISWI) class ATP-dependent remodelers is stimulated by histone variant H2A.Z
    • Goldman J.A., Garlick J.D., Kingston R.E. Chromatin remodeling by imitation switch (ISWI) class ATP-dependent remodelers is stimulated by histone variant H2A.Z. J.Biol. Chem. 2010, 285:4645-4651.
    • (2010) J.Biol. Chem. , vol.285 , pp. 4645-4651
    • Goldman, J.A.1    Garlick, J.D.2    Kingston, R.E.3
  • 17
    • 77954738659 scopus 로고    scopus 로고
    • Roles for H2A.Z and its acetylation in GAL1 transcription and gene induction, but not GAL1-transcriptional memory
    • Halley J.E., Kaplan T., Wang A.Y., Kobor M.S., Rine J. Roles for H2A.Z and its acetylation in GAL1 transcription and gene induction, but not GAL1-transcriptional memory. PLoS Biol. 2010, 8:e1000401.
    • (2010) PLoS Biol. , vol.8
    • Halley, J.E.1    Kaplan, T.2    Wang, A.Y.3    Kobor, M.S.4    Rine, J.5
  • 18
    • 25844491702 scopus 로고    scopus 로고
    • Global regulation of X chromosomal genes by the MSL complex in Drosophila melanogaster
    • Hamada F.N., Park P.J., Gordadze P.R., Kuroda M.I. Global regulation of X chromosomal genes by the MSL complex in Drosophila melanogaster. Genes Dev. 2005, 19:2289-2294.
    • (2005) Genes Dev. , vol.19 , pp. 2289-2294
    • Hamada, F.N.1    Park, P.J.2    Gordadze, P.R.3    Kuroda, M.I.4
  • 20
    • 60349089645 scopus 로고    scopus 로고
    • Nucleosome positioning and gene regulation: advances through genomics
    • Jiang C.Z., Pugh B.F. Nucleosome positioning and gene regulation: advances through genomics. Nat. Rev. Genet. 2009, 10:161-172.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 161-172
    • Jiang, C.Z.1    Pugh, B.F.2
  • 21
    • 34250745886 scopus 로고    scopus 로고
    • Nucleosome stability mediated by histone variants H3.3 and H2A.Z
    • Jin C., Felsenfeld G. Nucleosome stability mediated by histone variants H3.3 and H2A.Z. Genes Dev. 2007, 21:1519-1529.
    • (2007) Genes Dev. , vol.21 , pp. 1519-1529
    • Jin, C.1    Felsenfeld, G.2
  • 23
    • 0032808150 scopus 로고    scopus 로고
    • Quantitation of RNA polymerase II and its transcription factors in an HeLa cell: little soluble holoenzyme but significant amounts of polymerases attached to the nuclear substructure
    • Kimura H., Tao Y., Roeder R.G., Cook P.R. Quantitation of RNA polymerase II and its transcription factors in an HeLa cell: little soluble holoenzyme but significant amounts of polymerases attached to the nuclear substructure. Mol. Cell. Biol. 1999, 19:5383-5392.
    • (1999) Mol. Cell. Biol. , vol.19 , pp. 5383-5392
    • Kimura, H.1    Tao, Y.2    Roeder, R.G.3    Cook, P.R.4
  • 25
    • 0030950638 scopus 로고    scopus 로고
    • RNA polymerase switches between inactivated and activated states by translocating back and forth along the DNA and the RNA
    • Komissarova N., Kashlev M. RNA polymerase switches between inactivated and activated states by translocating back and forth along the DNA and the RNA. J.Biol. Chem. 1997, 272:15329-15338.
    • (1997) J.Biol. Chem. , vol.272 , pp. 15329-15338
    • Komissarova, N.1    Kashlev, M.2
  • 28
    • 84874175008 scopus 로고    scopus 로고
    • Precise maps of RNA polymerase reveal how promoters direct initiation and pausing
    • Kwak H., Fuda N.J., Core L.J., Lis J.T. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 2013, 339:950-953.
    • (2013) Science , vol.339 , pp. 950-953
    • Kwak, H.1    Fuda, N.J.2    Core, L.J.3    Lis, J.T.4
  • 31
    • 0033756308 scopus 로고    scopus 로고
    • Chromatin association of human origin recognition complex, cdc6, and minichromosome maintenance proteins during the cell cycle: assembly of prereplication complexes in late mitosis
    • Méndez J., Stillman B. Chromatin association of human origin recognition complex, cdc6, and minichromosome maintenance proteins during the cell cycle: assembly of prereplication complexes in late mitosis. Mol. Cell. Biol. 2000, 20:8602-8612.
    • (2000) Mol. Cell. Biol. , vol.20 , pp. 8602-8612
    • Méndez, J.1    Stillman, B.2
  • 32
    • 74549132843 scopus 로고    scopus 로고
    • Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila
    • Nechaev S., Fargo D.C., dos Santos G., Liu L., Gao Y., Adelman K. Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science 2010, 327:335-338.
    • (2010) Science , vol.327 , pp. 335-338
    • Nechaev, S.1    Fargo, D.C.2    dos Santos, G.3    Liu, L.4    Gao, Y.5    Adelman, K.6
  • 34
    • 84871700533 scopus 로고    scopus 로고
    • Mediator-regulated transcription through the+1 nucleosome
    • Nock A., Ascano J.M., Barrero M.J., Malik S. Mediator-regulated transcription through the+1 nucleosome. Mol. Cell 2012, 48:837-848.
    • (2012) Mol. Cell , vol.48 , pp. 837-848
    • Nock, A.1    Ascano, J.M.2    Barrero, M.J.3    Malik, S.4
  • 35
    • 0031552174 scopus 로고    scopus 로고
    • The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase
    • Nudler E., Mustaev A., Lukhtanov E., Goldfarb A. The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell 1997, 89:33-41.
    • (1997) Cell , vol.89 , pp. 33-41
    • Nudler, E.1    Mustaev, A.2    Lukhtanov, E.3    Goldfarb, A.4
  • 36
    • 84858165145 scopus 로고    scopus 로고
    • Genome-wide structure and organization of eukaryotic pre-initiation complexes
    • Rhee H.S., Pugh B.F. Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature 2012, 483:295-301.
    • (2012) Nature , vol.483 , pp. 295-301
    • Rhee, H.S.1    Pugh, B.F.2
  • 37
    • 0029790806 scopus 로고    scopus 로고
    • Translocation and transcriptional arrest during transcript elongation by RNA polymerase II
    • Samkurashvili I., Luse D.S. Translocation and transcriptional arrest during transcript elongation by RNA polymerase II. J.Biol. Chem. 1996, 271:23495-23505.
    • (1996) J.Biol. Chem. , vol.271 , pp. 23495-23505
    • Samkurashvili, I.1    Luse, D.S.2
  • 38
    • 79955432482 scopus 로고    scopus 로고
    • Histone variant H2A.Z and RNA polymerase II transcription elongation
    • Santisteban M.S., Hang M., Smith M.M. Histone variant H2A.Z and RNA polymerase II transcription elongation. Mol. Cell. Biol. 2011, 31:1848-1860.
    • (2011) Mol. Cell. Biol. , vol.31 , pp. 1848-1860
    • Santisteban, M.S.1    Hang, M.2    Smith, M.M.3
  • 40
    • 84885660614 scopus 로고    scopus 로고
    • Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss
    • Sheinin M.Y., Li M., Soltani M., Luger K., Wang M.D. Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss. Nat. Commun. 2013, 4:2579.
    • (2013) Nat. Commun. , vol.4 , pp. 2579
    • Sheinin, M.Y.1    Li, M.2    Soltani, M.3    Luger, K.4    Wang, M.D.5
  • 41
    • 77950998789 scopus 로고    scopus 로고
    • Evidence that transcript cleavage is essential for RNA polymerase II transcription and cell viability
    • Sigurdsson S., Dirac-Svejstrup A.B., Svejstrup J.Q. Evidence that transcript cleavage is essential for RNA polymerase II transcription and cell viability. Mol. Cell 2010, 38:202-210.
    • (2010) Mol. Cell , vol.38 , pp. 202-210
    • Sigurdsson, S.1    Dirac-Svejstrup, A.B.2    Svejstrup, J.Q.3
  • 42
    • 0033664380 scopus 로고    scopus 로고
    • Crystal structure of a nucleosome core particle containing the variant histone H2A.Z
    • Suto R.K., Clarkson M.J., Tremethick D.J., Luger K. Crystal structure of a nucleosome core particle containing the variant histone H2A.Z. Nat. Struct. Biol. 2000, 7:1121-1124.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 1121-1124
    • Suto, R.K.1    Clarkson, M.J.2    Tremethick, D.J.3    Luger, K.4
  • 43
    • 77949874234 scopus 로고    scopus 로고
    • Histone variants-ancient wrap artists of the epigenome
    • Talbert P.B., Henikoff S. Histone variants-ancient wrap artists of the epigenome. Nat. Rev. Mol. Cell Biol. 2010, 11:264-275.
    • (2010) Nat. Rev. Mol. Cell Biol. , vol.11 , pp. 264-275
    • Talbert, P.B.1    Henikoff, S.2
  • 44
    • 81055135515 scopus 로고    scopus 로고
    • Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide
    • Teves S.S., Henikoff S. Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide. Genes Dev. 2011, 25:2387-2397.
    • (2011) Genes Dev. , vol.25 , pp. 2387-2397
    • Teves, S.S.1    Henikoff, S.2
  • 45
    • 84893755427 scopus 로고    scopus 로고
    • Transcription-generated torsional stress destabilizes nucleosomes
    • Teves S.S., Henikoff S. Transcription-generated torsional stress destabilizes nucleosomes. Nat. Struct. Mol. Biol. 2014, 21:88-94.
    • (2014) Nat. Struct. Mol. Biol. , vol.21 , pp. 88-94
    • Teves, S.S.1    Henikoff, S.2
  • 46
    • 77952378219 scopus 로고    scopus 로고
    • Histone variant H2A.Z inhibits transcription in reconstituted nucleosomes
    • Thakar A., Gupta P., McAllister W.T., Zlatanova J. Histone variant H2A.Z inhibits transcription in reconstituted nucleosomes. Biochemistry 2010, 49:4018-4026.
    • (2010) Biochemistry , vol.49 , pp. 4018-4026
    • Thakar, A.1    Gupta, P.2    McAllister, W.T.3    Zlatanova, J.4
  • 48
    • 78649884849 scopus 로고    scopus 로고
    • H2A.Z nucleosomes enriched over active genes are homotypic
    • Weber C.M., Henikoff J.G., Henikoff S. H2A.Z nucleosomes enriched over active genes are homotypic. Nat. Struct. Mol. Biol. 2010, 17:1500-1507.
    • (2010) Nat. Struct. Mol. Biol. , vol.17 , pp. 1500-1507
    • Weber, C.M.1    Henikoff, J.G.2    Henikoff, S.3
  • 49
    • 28544442465 scopus 로고    scopus 로고
    • Swc2 is a widely conserved H2AZ-binding module essential for ATP-dependent histone exchange
    • Wu W.H., Alami S., Luk E., Wu C.H., Sen S., Mizuguchi G., Wei D., Wu C. Swc2 is a widely conserved H2AZ-binding module essential for ATP-dependent histone exchange. Nat. Struct. Mol. Biol. 2005, 12:1064-1071.
    • (2005) Nat. Struct. Mol. Biol. , vol.12 , pp. 1064-1071
    • Wu, W.H.1    Alami, S.2    Luk, E.3    Wu, C.H.4    Sen, S.5    Mizuguchi, G.6    Wei, D.7    Wu, C.8
  • 50
    • 0028090567 scopus 로고
    • Physical isolation of nascent RNA chains transcribed by RNA polymerase II: evidence for cotranscriptional splicing
    • Wuarin J., Schibler U. Physical isolation of nascent RNA chains transcribed by RNA polymerase II: evidence for cotranscriptional splicing. Mol. Cell. Biol. 1994, 14:7219-7225.
    • (1994) Mol. Cell. Biol. , vol.14 , pp. 7219-7225
    • Wuarin, J.1    Schibler, U.2
  • 51
    • 0035019156 scopus 로고    scopus 로고
    • Loss of HCF-1-chromatin association precedes temperature-induced growth arrest of tsBN67 cells
    • Wysocka J., Reilly P.T., Herr W. Loss of HCF-1-chromatin association precedes temperature-induced growth arrest of tsBN67 cells. Mol. Cell. Biol. 2001, 21:3820-3829.
    • (2001) Mol. Cell. Biol. , vol.21 , pp. 3820-3829
    • Wysocka, J.1    Reilly, P.T.2    Herr, W.3
  • 52
    • 84872393129 scopus 로고    scopus 로고
    • Transcription elongation factors DSIF and NELF: promoter-proximal pausing and beyond
    • Yamaguchi Y., Shibata H., Handa H. Transcription elongation factors DSIF and NELF: promoter-proximal pausing and beyond. Biochim. Biophys. Acta 2013, 1829:98-104.
    • (2013) Biochim. Biophys. Acta , vol.1829 , pp. 98-104
    • Yamaguchi, Y.1    Shibata, H.2    Handa, H.3
  • 53
    • 84875149194 scopus 로고    scopus 로고
    • Regulation of nucleosome dynamics by histone modifications
    • Zentner G.E., Henikoff S. Regulation of nucleosome dynamics by histone modifications. Nat. Struct. Mol. Biol. 2013, 20:259-266.
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 259-266
    • Zentner, G.E.1    Henikoff, S.2
  • 54
    • 79956316470 scopus 로고    scopus 로고
    • A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome
    • Zhang Z., Wippo C.J., Wal M., Ward E., Korber P., Pugh B.F. A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. Science 2011, 332:977-980.
    • (2011) Science , vol.332 , pp. 977-980
    • Zhang, Z.1    Wippo, C.J.2    Wal, M.3    Ward, E.4    Korber, P.5    Pugh, B.F.6
  • 55
    • 38949091078 scopus 로고    scopus 로고
    • H2A.Z: view from the top
    • Zlatanova J., Thakar A. H2A.Z: view from the top. Structure 2008, 16:166-179.
    • (2008) Structure , vol.16 , pp. 166-179
    • Zlatanova, J.1    Thakar, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.