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Volumn 1819, Issue 7, 2012, Pages 700-706

Coupling polymerase pausing and chromatin landscapes for precise regulation of transcription

Author keywords

Chromatin; Nucleosome; Pausing; Transcription

Indexed keywords

RNA POLYMERASE II;

EID: 84861855149     PISSN: 18749399     EISSN: 18764320     Source Type: Journal    
DOI: 10.1016/j.bbagrm.2012.02.015     Document Type: Review
Times cited : (24)

References (52)
  • 1
    • 0028068714 scopus 로고
    • Facilitated binding of TATA-binding protein to nucleosomal DNA
    • Imbalzano A.N., Kwon H., Green M.R., Kingston R.E. Facilitated binding of TATA-binding protein to nucleosomal DNA. Nature 1994, 370:481-485.
    • (1994) Nature , vol.370 , pp. 481-485
    • Imbalzano, A.N.1    Kwon, H.2    Green, M.R.3    Kingston, R.E.4
  • 2
    • 0025239781 scopus 로고
    • Nucleosome positioning modulates accessibility of regulatory proteins to the mouse mammary tumor virus promoter
    • Pina B., Bruggemeier U., Beato M. Nucleosome positioning modulates accessibility of regulatory proteins to the mouse mammary tumor virus promoter. Cell 1990, 60:719-731.
    • (1990) Cell , vol.60 , pp. 719-731
    • Pina, B.1    Bruggemeier, U.2    Beato, M.3
  • 3
    • 1542328277 scopus 로고    scopus 로고
    • Anatomy of a hypersensitive site
    • Reinke H., Horz W. Anatomy of a hypersensitive site. Biochim. Biophys. Acta 2004, 1677:24-29.
    • (2004) Biochim. Biophys. Acta , vol.1677 , pp. 24-29
    • Reinke, H.1    Horz, W.2
  • 4
    • 2942574467 scopus 로고    scopus 로고
    • Removal of promoter nucleosomes by disassembly rather than sliding in vivo
    • Boeger H., Griesenbeck J., Strattan J.S., Kornberg R.D. Removal of promoter nucleosomes by disassembly rather than sliding in vivo. Mol. Cell 2004, 14:667-673.
    • (2004) Mol. Cell , vol.14 , pp. 667-673
    • Boeger, H.1    Griesenbeck, J.2    Strattan, J.S.3    Kornberg, R.D.4
  • 5
    • 0038094502 scopus 로고    scopus 로고
    • Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter
    • Reinke H., Horz W. Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol. Cell 2003, 11:1599-1607.
    • (2003) Mol. Cell , vol.11 , pp. 1599-1607
    • Reinke, H.1    Horz, W.2
  • 6
    • 34548717647 scopus 로고    scopus 로고
    • Chromatin disassembly from the PHO5 promoter is essential for the recruitment of the general transcription machinery and coactivators
    • Adkins M.W., Williams S.K., Linger J., Tyler J.K. Chromatin disassembly from the PHO5 promoter is essential for the recruitment of the general transcription machinery and coactivators. Mol. Cell. Biol. 2007, 27:6372-6382.
    • (2007) Mol. Cell. Biol. , vol.27 , pp. 6372-6382
    • Adkins, M.W.1    Williams, S.K.2    Linger, J.3    Tyler, J.K.4
  • 7
    • 0019303186 scopus 로고
    • The 5' ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I
    • Wu C. The 5' ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature 1980, 286:854-860.
    • (1980) Nature , vol.286 , pp. 854-860
    • Wu, C.1
  • 8
    • 0019401409 scopus 로고
    • DNase I hypersensitive sites in Drosophila chromatin occur at the 5' ends of regions of transcription
    • Keene M.A., Corces V., Lowenhaupt K., Elgin S.C. DNase I hypersensitive sites in Drosophila chromatin occur at the 5' ends of regions of transcription. Proc. Natl. Acad. Sci. U. S. A. 1981, 78:143-146.
    • (1981) Proc. Natl. Acad. Sci. U. S. A. , vol.78 , pp. 143-146
    • Keene, M.A.1    Corces, V.2    Lowenhaupt, K.3    Elgin, S.C.4
  • 9
    • 0021271338 scopus 로고
    • Chromatin structure of hsp 70 genes, activated by heat shock: selective removal of histones from the coding region and their absence from the 5' region
    • Karpov V.L., Preobrazhenskaya O.V., Mirzabekov A.D. Chromatin structure of hsp 70 genes, activated by heat shock: selective removal of histones from the coding region and their absence from the 5' region. Cell 1984, 36:423-431.
    • (1984) Cell , vol.36 , pp. 423-431
    • Karpov, V.L.1    Preobrazhenskaya, O.V.2    Mirzabekov, A.D.3
  • 10
    • 0024282827 scopus 로고
    • The RNA polymerase II molecule at the 5' end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged
    • Rougvie A.E., Lis J.T. The RNA polymerase II molecule at the 5' end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged. Cell 1988, 54:795-804.
    • (1988) Cell , vol.54 , pp. 795-804
    • Rougvie, A.E.1    Lis, J.T.2
  • 11
    • 0022817308 scopus 로고
    • RNA polymerase II interacts with the promoter region of the noninduced hsp70 gene in Drosophila melanogaster cells
    • Gilmour D.S., Lis J.T. RNA polymerase II interacts with the promoter region of the noninduced hsp70 gene in Drosophila melanogaster cells. Mol. Cell. Biol. 1986, 6:3984-3989.
    • (1986) Mol. Cell. Biol. , vol.6 , pp. 3984-3989
    • Gilmour, D.S.1    Lis, J.T.2
  • 12
    • 0032459466 scopus 로고    scopus 로고
    • Promoter-associated pausing in promoter architecture and postinitiation transcriptional regulation
    • Lis J. Promoter-associated pausing in promoter architecture and postinitiation transcriptional regulation. Cold Spring Harb. Symp. Quant. Biol. 1998, 63:347-356.
    • (1998) Cold Spring Harb. Symp. Quant. Biol. , vol.63 , pp. 347-356
    • Lis, J.1
  • 15
    • 57849109058 scopus 로고    scopus 로고
    • Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
    • Core L.J., Waterfall J.J., Lis J.T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 2008, 322:1845-1848.
    • (2008) Science , vol.322 , pp. 1845-1848
    • Core, L.J.1    Waterfall, J.J.2    Lis, J.T.3
  • 16
    • 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
  • 19
    • 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
  • 20
    • 79954562232 scopus 로고    scopus 로고
    • Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells
    • Min I.M., Waterfall J.J., Core L.J., Munroe R.J., Schimenti J., Lis J.T. Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells. Genes Dev. 2011, 25:742-754.
    • (2011) Genes Dev. , vol.25 , pp. 742-754
    • Min, I.M.1    Waterfall, J.J.2    Core, L.J.3    Munroe, R.J.4    Schimenti, J.5    Lis, J.T.6
  • 21
    • 47549090254 scopus 로고    scopus 로고
    • NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly
    • Gilchrist D.A., Nechaev S., Lee C., Ghosh S.K., Collins J.B., Li L., Gilmour D.S., Adelman K. NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly. Genes Dev. 2008, 22:1921-1933.
    • (2008) Genes Dev. , vol.22 , pp. 1921-1933
    • Gilchrist, D.A.1    Nechaev, S.2    Lee, C.3    Ghosh, S.K.4    Collins, J.B.5    Li, L.6    Gilmour, D.S.7    Adelman, K.8
  • 22
    • 0028055116 scopus 로고
    • ATP-dependent nucleosome disruption at a heat-shock promoter mediated by binding of GAGA transcription factor
    • Tsukiyama T., Becker P.B., Wu C. ATP-dependent nucleosome disruption at a heat-shock promoter mediated by binding of GAGA transcription factor. Nature 1994, 367:525-532.
    • (1994) Nature , vol.367 , pp. 525-532
    • Tsukiyama, T.1    Becker, P.B.2    Wu, C.3
  • 23
    • 0029562736 scopus 로고
    • Purification and properties of an ATP-dependent nucleosome remodeling factor
    • Tsukiyama T., Wu C. Purification and properties of an ATP-dependent nucleosome remodeling factor. Cell 1995, 83:1011-1020.
    • (1995) Cell , vol.83 , pp. 1011-1020
    • Tsukiyama, T.1    Wu, C.2
  • 25
    • 0031306557 scopus 로고    scopus 로고
    • Role of nucleosome remodeling factor NURF in transcriptional activation of chromatin
    • Mizuguchi G., Tsukiyama T., Wisniewski J., Wu C. Role of nucleosome remodeling factor NURF in transcriptional activation of chromatin. Mol. Cell 1997, 1:141-150.
    • (1997) Mol. Cell , vol.1 , pp. 141-150
    • Mizuguchi, G.1    Tsukiyama, T.2    Wisniewski, J.3    Wu, C.4
  • 27
    • 34047111213 scopus 로고    scopus 로고
    • Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome
    • Albert I., Mavrich T.N., Tomsho L.P., Qi J., Zanton S.J., Schuster S.C., Pugh B.F. Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 2007, 446:572-576.
    • (2007) Nature , vol.446 , pp. 572-576
    • Albert, I.1    Mavrich, T.N.2    Tomsho, L.P.3    Qi, J.4    Zanton, S.J.5    Schuster, S.C.6    Pugh, B.F.7
  • 34
    • 75149135277 scopus 로고    scopus 로고
    • G+C content dominates intrinsic nucleosome occupancy
    • Tillo D., Hughes T.R. G+C content dominates intrinsic nucleosome occupancy. BMC Bioinforma. 2009, 10:442.
    • (2009) BMC Bioinforma. , vol.10 , pp. 442
    • Tillo, D.1    Hughes, T.R.2
  • 36
    • 74949110964 scopus 로고    scopus 로고
    • High-resolution nucleosome mapping reveals transcription-dependent promoter packaging
    • Weiner A., Hughes A., Yassour M., Rando O.J., Friedman N. High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res. 2010, 20:90-100.
    • (2010) Genome Res. , vol.20 , pp. 90-100
    • Weiner, A.1    Hughes, A.2    Yassour, M.3    Rando, O.J.4    Friedman, N.5
  • 37
    • 43749088127 scopus 로고    scopus 로고
    • Two strategies for gene regulation by promoter nucleosomes
    • Tirosh I., Barkai N. Two strategies for gene regulation by promoter nucleosomes. Genome Res. 2008, 18:1084-1091.
    • (2008) Genome Res. , vol.18 , pp. 1084-1091
    • Tirosh, I.1    Barkai, N.2
  • 38
    • 68149150830 scopus 로고    scopus 로고
    • H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions
    • Jin C., Zang C., Wei G., Cui K., Peng W., Zhao K., Felsenfeld G. H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. Nat. Genet. 2009, 41:941-945.
    • (2009) Nat. Genet. , vol.41 , pp. 941-945
    • Jin, C.1    Zang, C.2    Wei, G.3    Cui, K.4    Peng, W.5    Zhao, K.6    Felsenfeld, G.7
  • 40
    • 0029026719 scopus 로고
    • Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure
    • Iyer V., Struhl K. Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO J. 1995, 14:2570-2579.
    • (1995) EMBO J. , vol.14 , pp. 2570-2579
    • Iyer, V.1    Struhl, K.2
  • 42
    • 40549111302 scopus 로고    scopus 로고
    • All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues
    • Rozenberg J.M., Shlyakhtenko A., Glass K., Rishi V., Myakishev M.V., FitzGerald P.C., Vinson C. All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues. BMC Genomics 2008, 9:67.
    • (2008) BMC Genomics , vol.9 , pp. 67
    • Rozenberg, J.M.1    Shlyakhtenko, A.2    Glass, K.3    Rishi, V.4    Myakishev, M.V.5    FitzGerald, P.C.6    Vinson, C.7
  • 43
    • 46149108345 scopus 로고    scopus 로고
    • Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 loci
    • Petesch S.J., Lis J.T. Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 loci. Cell 2008, 134:74-84.
    • (2008) Cell , vol.134 , pp. 74-84
    • Petesch, S.J.1    Lis, J.T.2
  • 44
    • 0032519352 scopus 로고    scopus 로고
    • Nucleosomes are not necessary for promoter-proximal pausing in vitro on the Drosophila hsp70 promoter
    • Benjamin L.R., Gilmour D.S. Nucleosomes are not necessary for promoter-proximal pausing in vitro on the Drosophila hsp70 promoter. Nucleic Acids Res. 1998, 26:1051-1055.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 1051-1055
    • Benjamin, L.R.1    Gilmour, D.S.2
  • 45
    • 70350013550 scopus 로고    scopus 로고
    • Biased chromatin signatures around polyadenylation sites and exons
    • Spies N., Nielsen C.B., Padgett R.A., Burge C.B. Biased chromatin signatures around polyadenylation sites and exons. Molecular cell 2009, 36:245-254.
    • (2009) Molecular cell , vol.36 , pp. 245-254
    • Spies, N.1    Nielsen, C.B.2    Padgett, R.A.3    Burge, C.B.4
  • 47
    • 70349333201 scopus 로고    scopus 로고
    • Nucleosomes are well positioned in exons and carry characteristic histone modifications
    • Andersson R., Enroth S., Rada-Iglesias A., Wadelius C., Komorowski J. Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res. 2009, 19:1732-1741.
    • (2009) Genome Res. , vol.19 , pp. 1732-1741
    • Andersson, R.1    Enroth, S.2    Rada-Iglesias, A.3    Wadelius, C.4    Komorowski, J.5
  • 48
    • 69949132191 scopus 로고    scopus 로고
    • Chromatin organization marks exon-intron structure
    • Schwartz S., Meshorer E., Ast G. Chromatin organization marks exon-intron structure. Nat. Struct. Mol. Biol. 2009, 16:990-995.
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 990-995
    • Schwartz, S.1    Meshorer, E.2    Ast, G.3
  • 49
    • 34047262671 scopus 로고    scopus 로고
    • Transcriptional regulation by chromatin disassembly and reassembly
    • Williams S.K., Tyler J.K. Transcriptional regulation by chromatin disassembly and reassembly. Curr. Opin. Genet. Dev. 2007, 17:88-93.
    • (2007) Curr. Opin. Genet. Dev. , vol.17 , pp. 88-93
    • Williams, S.K.1    Tyler, J.K.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.