메뉴 건너뛰기




Volumn 42, Issue 3, 2014, Pages 1619-1627

Analysis of the mechanism of nucleosome survival during transcription

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE I; HISTONE; RNA POLYMERASE II;

EID: 84896721102     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1120     Document Type: Article
Times cited : (38)

References (40)
  • 1
    • 27744533201 scopus 로고    scopus 로고
    • Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae
    • Martens, J.A., Wu, P.Y. and Winston, F. (2005) Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae. Genes Dev., 19, 2695-2704.
    • (2005) Genes Dev , vol.19 , pp. 2695-2704
    • Martens, J.A.1    Wu, P.Y.2    Winston, F.3
  • 2
    • 56849114880 scopus 로고    scopus 로고
    • Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome
    • Cheung, V., Chua, G., Batada, N.N., Landry, C.R., Michnick, S.W., Hughes, T.R. and Winston, F. (2008) Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome. PLoS Biol., 6, e277.
    • (2008) PLoS Biol , vol.6
    • Cheung, V.1    Chua, G.2    Batada, N.N.3    Landry, C.R.4    Michnick, S.W.5    Hughes, T.R.6    Winston, F.7
  • 4
    • 9144274420 scopus 로고    scopus 로고
    • Evidence for distinct mechanisms facilitating transcript elongation through chromatin in vivo
    • Kristjuhan, A. and Svejstrup, J.Q. (2004) Evidence for distinct mechanisms facilitating transcript elongation through chromatin in vivo. EMBO J., 23, 4243-4252.
    • (2004) EMBO J , vol.23 , pp. 4243-4252
    • Kristjuhan, A.1    Svejstrup, J.Q.2
  • 5
    • 3543023310 scopus 로고    scopus 로고
    • Evidence for nucleosome depletion at active regulatory regions genome-wide
    • Lee, C.K., Shibata, Y., Rao, B., Strahl, B.D. and Lieb, J.D. (2004) Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat. Genet., 36, 900-905.
    • (2004) Nat. Genet , vol.36 , pp. 900-905
    • Lee, C.K.1    Shibata, Y.2    Rao, B.3    Strahl, B.D.4    Lieb, J.D.5
  • 6
    • 8644287437 scopus 로고    scopus 로고
    • Evidence for eviction and rapid deposition of histones upon transcriptional elongation by RNA polymerase II
    • Schwabish, M.A. and Struhl, K. (2004) Evidence for eviction and rapid deposition of histones upon transcriptional elongation by RNA polymerase II. Mol. Cell. Biol., 24, 10111-10117.
    • (2004) Mol. Cell. Biol , vol.24 , pp. 10111-10117
    • Schwabish, M.A.1    Struhl, K.2
  • 7
    • 26444545490 scopus 로고    scopus 로고
    • Domain-wide displacement of histones by activated heat shock factor occurs independently of Swi/Snf and is not correlated with RNA polymerase II density
    • Zhao, J., Herrera-Diaz, J. and Gross, D.S. (2005) Domain-wide displacement of histones by activated heat shock factor occurs independently of Swi/Snf and is not correlated with RNA polymerase II density. Mol. Cell. Biol., 25, 8985-8999.
    • (2005) Mol. Cell. Biol , vol.25 , pp. 8985-8999
    • Zhao, J.1    Herrera-Diaz, J.2    Gross, D.S.3
  • 8
    • 23744460663 scopus 로고    scopus 로고
    • Variant histone H3.3 is deposited at sites of nucleosomal displacement throughout transcribed genes while active histone modifications show a promoter-proximal bias
    • Wirbelauer, C., Bell, O. and Schubeler, D. (2005) Variant histone H3.3 is deposited at sites of nucleosomal displacement throughout transcribed genes while active histone modifications show a promoter-proximal bias. Genes Dev., 19, 1761-1766.
    • (2005) Genes Dev , vol.19 , pp. 1761-1766
    • Wirbelauer, C.1    Bell, O.2    Schubeler, D.3
  • 9
    • 17044394787 scopus 로고    scopus 로고
    • Transcriptional activation triggers deposition and removal of the histone variant H3.3
    • Schwartz, B.E. and Ahmad, K. (2005) Transcriptional activation triggers deposition and removal of the histone variant H3.3. Genes Dev., 19, 804-814.
    • (2005) Genes Dev , vol.19 , pp. 804-814
    • Schwartz, B.E.1    Ahmad, K.2
  • 10
    • 15444376394 scopus 로고    scopus 로고
    • Replication-independent core histone dynamics at transcriptionally active loci in vivo
    • Thiriet, C. and Hayes, J.J. (2005) Replication-independent core histone dynamics at transcriptionally active loci in vivo. Genes Dev., 19, 677-682.
    • (2005) Genes Dev , vol.19 , pp. 677-682
    • Thiriet, C.1    Hayes, J.J.2
  • 11
    • 33947137710 scopus 로고    scopus 로고
    • Dynamics of replication-independent histone turnover in budding yeast
    • Dion, M.F., Kaplan, T., Kim, M., Buratowski, S., Friedman, N. and Rando, O.J. (2007) Dynamics of replication-independent histone turnover in budding yeast. Science, 315, 1405-1408.
    • (2007) Science , vol.315 , pp. 1405-1408
    • Dion, M.F.1    Kaplan, T.2    Kim, M.3    Buratowski, S.4    Friedman, N.5    Rando, O.J.6
  • 12
    • 34547277498 scopus 로고    scopus 로고
    • Genome-wide replication-independent histone H3 exchange occurs predominantly at promoters and implicates H3 K56 acetylation and Asf1
    • Rufiange, A., Jacques, P.E., Bhat, W., Robert, F. and Nourani, A. (2007) Genome-wide replication-independent histone H3 exchange occurs predominantly at promoters and implicates H3 K56 acetylation and Asf1. Mol. Cell, 27, 393-405.
    • (2007) Mol. Cell , vol.27 , pp. 393-405
    • Rufiange, A.1    Jacques, P.E.2    Bhat, W.3    Robert, F.4    Nourani, A.5
  • 13
    • 33846663256 scopus 로고    scopus 로고
    • Continuous histone H2B and transcription-dependent histone H3 exchange in yeast cells outside of replication
    • Jamai, A., Imoberdorf, R.M. and Strubin, M. (2007) Continuous histone H2B and transcription-dependent histone H3 exchange in yeast cells outside of replication. Mol. Cell, 25, 345-355.
    • (2007) Mol. Cell , vol.25 , pp. 345-355
    • Jamai, A.1    Imoberdorf, R.M.2    Strubin, M.3
  • 14
    • 34247328546 scopus 로고    scopus 로고
    • Histone dynamics during transcription: Exchange of H2A/H2B dimers and H3/H4 tetramers during pol II elongation
    • Thiriet, C. and Hayes, J.J. (2006) Histone dynamics during transcription: exchange of H2A/H2B dimers and H3/H4 tetramers during pol II elongation. Results Probl. Cell Differ., 41, 77-90.
    • (2006) Results Probl. Cell Differ , vol.41 , pp. 77-90
    • Thiriet, C.1    Hayes, J.J.2
  • 16
    • 0036203807 scopus 로고    scopus 로고
    • Nucleosome remodeling induced by RNA polymerase II: Loss of the H2A/H2B dimer during transcription
    • Kireeva, M.L., Walter, W., Tchernajenko, V., Bondarenko, V., Kashlev, M. and Studitsky, V.M. (2002) Nucleosome remodeling induced by RNA polymerase II: loss of the H2A/H2B dimer during transcription. Mol. Cell, 9, 541-552.
    • (2002) Mol. Cell , vol.9 , pp. 541-552
    • Kireeva, M.L.1    Walter, W.2    Tchernajenko, V.3    Bondarenko, V.4    Kashlev, M.5    Studitsky, V.M.6
  • 19
    • 77954934291 scopus 로고    scopus 로고
    • RNA polymerase complexes cooperate to relieve the nucleosomal barrier and evict histones
    • Kulaeva, O.I., Hsieh, F.K. and Studitsky, V.M. (2010) RNA polymerase complexes cooperate to relieve the nucleosomal barrier and evict histones. Proc. Natl Acad. Sci. USA, 107, 11325-11330.
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 11325-11330
    • Kulaeva, O.I.1    Hsieh, F.K.2    Studitsky, V.M.3
  • 22
    • 77957252758 scopus 로고    scopus 로고
    • Crystal structures of nucleosome core particles containing the 601 strong positioning sequence
    • Vasudevan, D., Chua, E.Y. and Davey, C.A. (2010) Crystal structures of nucleosome core particles containing the 601 strong positioning sequence. J. Mol. Biol., 403, 1-10.
    • (2010) J. Mol. Biol , vol.403 , pp. 1-10
    • Vasudevan, D.1    Chua, E.Y.2    Davey, C.A.3
  • 23
    • 10944232674 scopus 로고    scopus 로고
    • Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS
    • Kettenberger, H., Armache, K.J. and Cramer, P. (2004) Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol. Cell, 16, 955-965.
    • (2004) Mol. Cell , vol.16 , pp. 955-965
    • Kettenberger, H.1    Armache, K.J.2    Cramer, P.3
  • 24
    • 67849110013 scopus 로고    scopus 로고
    • 3D-DART: A DNA structure modelling server
    • van Dijk, M. and Bonvin, A.M. (2009) 3D-DART: a DNA structure modelling server. Nucleic Acids Res., 37, W235-W239.
    • (2009) Nucleic Acids Res , vol.37
    • Van Dijk, M.1    Bonvin, A.M.2
  • 26
    • 0035964342 scopus 로고    scopus 로고
    • Electrostatics of nanosystems: Application to microtubules and the ribosome
    • Baker, N.A., Sept, D., Joseph, S., Holst, M.J. and McCammon, J.A. (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl Acad. Sci. USA, 98, 10037-10041.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 10037-10041
    • Baker, N.A.1    Sept, D.2    Joseph, S.3    Holst, M.J.4    McCammon, J.A.5
  • 27
    • 0347381303 scopus 로고    scopus 로고
    • Preparation and characterization of recombinant Thermus aquaticus RNA polymerase
    • Kuznedelov, K., Minakhin, L. and Severinov, K. (2003) Preparation and characterization of recombinant Thermus aquaticus RNA polymerase. Methods Enzymol., 370, 94-108.
    • (2003) Methods Enzymol , vol.370 , pp. 94-108
    • Kuznedelov, K.1    Minakhin, L.2    Severinov, K.3
  • 28
  • 29
    • 0034051171 scopus 로고    scopus 로고
    • The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex
    • Kireeva, M.L., Komissarova, N., Waugh, D.S. and Kashlev, M. (2000) The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex. J. Biol. Chem., 275, 6530-6536.
    • (2000) J. Biol. Chem , vol.275 , pp. 6530-6536
    • Kireeva, M.L.1    Komissarova, N.2    Waugh, D.S.3    Kashlev, M.4
  • 30
    • 0016593453 scopus 로고
    • Sequence of the PR promoter of phage lambda
    • Walz, A. and Pirrotta, V. (1975) Sequence of the PR promoter of phage lambda. Nature, 254, 118-121.
    • (1975) Nature , vol.254 , pp. 118-121
    • Walz, A.1    Pirrotta, V.2
  • 31
    • 0036307707 scopus 로고    scopus 로고
    • Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution
    • Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W. and Richmond, T.J. (2002) Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. J. Mol. Biol., 319, 1097-1113.
    • (2002) J. Mol. Biol , vol.319 , pp. 1097-1113
    • Davey, C.A.1    Sargent, D.F.2    Luger, K.3    Maeder, A.W.4    Richmond, T.J.5
  • 32
    • 0141704307 scopus 로고    scopus 로고
    • Bacterial polymerase and yeast polymerase II use similar mechanisms for transcription through nucleosomes
    • Walter, W., Kireeva, M.L., Studitsky, V.M. and Kashlev, M. (2003) Bacterial polymerase and yeast polymerase II use similar mechanisms for transcription through nucleosomes. J. Biol. Chem., 278, 36148-36156.
    • (2003) J. Biol. Chem , vol.278 , pp. 36148-36156
    • Walter, W.1    Kireeva, M.L.2    Studitsky, V.M.3    Kashlev, M.4
  • 33
    • 0033578701 scopus 로고    scopus 로고
    • Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution
    • Zhang, G., Campbell, E.A., Minakhin, L., Richter, C., Severinov, K. and Darst, S.A. (1999) Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution. Cell, 98, 811-824.
    • (1999) Cell , vol.98 , pp. 811-824
    • Zhang, G.1    Campbell, E.A.2    Minakhin, L.3    Richter, C.4    Severinov, K.5    Darst, S.A.6
  • 35
    • 77956231587 scopus 로고    scopus 로고
    • Histone Sin mutations promote nucleosome traversal and histone displacement by RNA polymerase II
    • Hsieh, F.K., Fisher, M., Ujvari, A., Studitsky, V.M. and Luse, D.S. (2010) Histone Sin mutations promote nucleosome traversal and histone displacement by RNA polymerase II. EMBO Rep., 11, 705-710.
    • (2010) EMBO Rep , vol.11 , pp. 705-710
    • Hsieh, F.K.1    Fisher, M.2    Ujvari, A.3    Studitsky, V.M.4    Luse, D.S.5
  • 36
    • 0039837085 scopus 로고    scopus 로고
    • Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences
    • Thastrom, A., Lowary, P.T., Widlund, H.R., Cao, H., Kubista, M. and Widom, J. (1999) Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences. J. Mol. Biol., 288, 213-229.
    • (1999) J. Mol. Biol , vol.288 , pp. 213-229
    • Thastrom, A.1    Lowary, P.T.2    Widlund, H.R.3    Cao, H.4    Kubista, M.5    Widom, J.6
  • 37
    • 0027960539 scopus 로고
    • A highly conserved domain of RNA polymerase II shares a functional element with acidic activation domains of upstream transcription factors
    • Xiao, H., Friesen, J.D. and Lis, J.T. (1994) A highly conserved domain of RNA polymerase II shares a functional element with acidic activation domains of upstream transcription factors. Mol Cell. Biol., 14, 7507-7516.
    • (1994) Mol Cell. Biol , vol.14 , pp. 7507-7516
    • Xiao, H.1    Friesen, J.D.2    Lis, J.T.3
  • 38
    • 0031451329 scopus 로고    scopus 로고
    • Mechanism of transcription through the nucleosome by eukaryotic RNA polymerase
    • Studitsky, V.M., Kassavetis, G.A., Geiduschek, E.P. and Felsenfeld, G. (1997) Mechanism of transcription through the nucleosome by eukaryotic RNA polymerase. Science, 278, 1960-1963.
    • (1997) Science , vol.278 , pp. 1960-1963
    • Studitsky, V.M.1    Kassavetis, G.A.2    Geiduschek, E.P.3    Felsenfeld, G.4
  • 39
    • 0028850059 scopus 로고
    • Overcoming a nucleosomal barrier to transcription
    • Studitsky, V.M., Clark, D.J. and Felsenfeld, G. (1995) Overcoming a nucleosomal barrier to transcription. Cell, 83, 19-27.
    • (1995) Cell , vol.83 , pp. 19-27
    • Studitsky, V.M.1    Clark, D.J.2    Felsenfeld, G.3
  • 40
    • 0028125847 scopus 로고
    • A histone octamer can step around a transcribing polymerase without leaving the template
    • Studitsky, V.M., Clark, D.J. and Felsenfeld, G. (1994) A histone octamer can step around a transcribing polymerase without leaving the template. Cell, 76, 371-382.
    • (1994) Cell , vol.76 , pp. 371-382
    • Studitsky, V.M.1    Clark, D.J.2    Felsenfeld, G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.