메뉴 건너뛰기




Volumn 11, Issue 8, 2013, Pages

Linking Stochastic Fluctuations in Chromatin Structure and Gene Expression

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMATIN STRUCTURE; CONTROLLED STUDY; ELECTRON MICROSCOPY; FUNGAL GENE; GENE ACTIVATION; GENE EXPRESSION; GENE REPRESSION; MATHEMATICAL COMPUTING; NONHUMAN; NUCLEOSOME; PHO5 GENE; PROMOTER REGION; STATISTICS; STEADY STATE; YEAST;

EID: 84883138228     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.1001621     Document Type: Article
Times cited : (100)

References (54)
  • 2
    • 0036790975 scopus 로고    scopus 로고
    • Intrinsic and extrinsic contributions to stochasticity in gene expression
    • Swain PS, Elowitz MB, Siggia ED, (2002) Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc Natl Acad Sci U S A 99: 12795-12800.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 12795-12800
    • Swain, P.S.1    Elowitz, M.B.2    Siggia, E.D.3
  • 3
    • 84859641038 scopus 로고    scopus 로고
    • Using gene expression noise to understand gene regulation
    • Munsky B, Neuert G, van Oudenaarden A, (2012) Using gene expression noise to understand gene regulation. Science 336: 183-187.
    • (2012) Science , vol.336 , pp. 183-187
    • Munsky, B.1    Neuert, G.2    van Oudenaarden, A.3
  • 4
    • 2942718723 scopus 로고    scopus 로고
    • Control of stochasticity in eukaryotic gene expression
    • Raser JM, O'Shea EK, (2004) Control of stochasticity in eukaryotic gene expression. Science 304: 1811-1814.
    • (2004) Science , vol.304 , pp. 1811-1814
    • Raser, J.M.1    O'Shea, E.K.2
  • 5
    • 79251603722 scopus 로고    scopus 로고
    • Non-genetic heterogeneity from stochastic partitioning at cell division
    • Huh D, Paulsson J, (2011) Non-genetic heterogeneity from stochastic partitioning at cell division. Nat Genet 43: 95-100.
    • (2011) Nat Genet , vol.43 , pp. 95-100
    • Huh, D.1    Paulsson, J.2
  • 6
    • 79952287917 scopus 로고    scopus 로고
    • Occlusion of regulatory sequences by promoter nucleosomes in vivo
    • doi: 10.1371/journal.pone.0017521
    • Mao C, Brown CR, Griesenbeck J, Boeger H, (2011) Occlusion of regulatory sequences by promoter nucleosomes in vivo. PLoS One 6: e17521 doi:10.1371/journal.pone.0017521.
    • (2011) PLoS One , vol.6
    • Mao, C.1    Brown, C.R.2    Griesenbeck, J.3    Boeger, H.4
  • 7
    • 0028791330 scopus 로고
    • Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation
    • Polach KJ, Widom J, (1995) Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation. J Mol Biol 254: 130-149.
    • (1995) J Mol Biol , vol.254 , pp. 130-149
    • Polach, K.J.1    Widom, J.2
  • 8
    • 0023661185 scopus 로고
    • Binding of transcription factor TFIID to the major late promoter during in vitro nucleosome assembly potentiates subsequent initiation by RNA polymerase II
    • Workman JL, Roeder RG, (1987) Binding of transcription factor TFIID to the major late promoter during in vitro nucleosome assembly potentiates subsequent initiation by RNA polymerase II. Cell 51: 613-622.
    • (1987) Cell , vol.51 , pp. 613-622
    • Workman, J.L.1    Roeder, R.G.2
  • 9
    • 68149120313 scopus 로고    scopus 로고
    • Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II
    • Hodges C, Bintu L, Lubkowska L, Kashlev M, Bustamante C, (2009) Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II. Science 325: 626-628.
    • (2009) Science , vol.325 , pp. 626-628
    • Hodges, C.1    Bintu, L.2    Lubkowska, L.3    Kashlev, M.4    Bustamante, C.5
  • 10
    • 0024261583 scopus 로고
    • Nucleosome loss activates yeast downstream promoters in vivo
    • Han M, Grunstein M, (1988) Nucleosome loss activates yeast downstream promoters in vivo. Cell 55: 1137-1145.
    • (1988) Cell , vol.55 , pp. 1137-1145
    • Han, M.1    Grunstein, M.2
  • 11
    • 0041828953 scopus 로고    scopus 로고
    • Transcription elongation factors repress transcription initiation from cryptic sites
    • Kaplan CD, Laprade L, Winston F, (2003) Transcription elongation factors repress transcription initiation from cryptic sites. Science 301: 1096-1099.
    • (2003) Science , vol.301 , pp. 1096-1099
    • Kaplan, C.D.1    Laprade, L.2    Winston, F.3
  • 12
    • 0022799080 scopus 로고
    • Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements
    • Almer A, Rudolph H, Hinnen A, Horz W, (1986) Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements. Embo J 5: 2689-2696.
    • (1986) Embo J , vol.5 , pp. 2689-2696
    • Almer, A.1    Rudolph, H.2    Hinnen, A.3    Horz, W.4
  • 13
    • 43049157587 scopus 로고    scopus 로고
    • Nucleosome retention and the stochastic nature of promoter chromatin remodeling for transcription
    • Boeger H, Griesenbeck J, Kornberg RD, (2008) Nucleosome retention and the stochastic nature of promoter chromatin remodeling for transcription. Cell 133: 716-726.
    • (2008) Cell , vol.133 , pp. 716-726
    • Boeger, H.1    Griesenbeck, J.2    Kornberg, R.D.3
  • 14
    • 0038094501 scopus 로고    scopus 로고
    • Nucleosomes unfold completely at a transcriptionally active promoter
    • Boeger H, Griesenbeck J, Strattan JS, Kornberg RD, (2003) Nucleosomes unfold completely at a transcriptionally active promoter. Mol Cell 11: 1587-1598.
    • (2003) Mol Cell , vol.11 , pp. 1587-1598
    • Boeger, H.1    Griesenbeck, J.2    Strattan, J.S.3    Kornberg, R.D.4
  • 16
    • 84875214621 scopus 로고    scopus 로고
    • Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise
    • Dadiani M, van Dijk D, Segal B, Field Y, Ben-Artzi G, et al. (2013) Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise. Genome Res 23: 966-976.
    • (2013) Genome Res , vol.23 , pp. 966-976
    • Dadiani, M.1    van Dijk, D.2    Segal, B.3    Field, Y.4    Ben-Artzi, G.5
  • 18
    • 0344629430 scopus 로고    scopus 로고
    • Affinity purification of specific chromatin segments from chromosomal loci in yeast
    • Griesenbeck J, Boeger H, Strattan JS, Kornberg RD, (2003) Affinity purification of specific chromatin segments from chromosomal loci in yeast. Mol Cell Biol 23: 9275-9282.
    • (2003) Mol Cell Biol , vol.23 , pp. 9275-9282
    • Griesenbeck, J.1    Boeger, H.2    Strattan, J.S.3    Kornberg, R.D.4
  • 20
    • 0017736647 scopus 로고
    • Cross-linking of DNA with trimethylpsoralen is a probe for chromatin structure
    • Cech T, Pardue ML, (1977) Cross-linking of DNA with trimethylpsoralen is a probe for chromatin structure. Cell 11: 631-640.
    • (1977) Cell , vol.11 , pp. 631-640
    • Cech, T.1    Pardue, M.L.2
  • 21
    • 0024517893 scopus 로고
    • The two positively acting regulatory proteins PHO2 and PHO4 physically interact with PHO5 upstream activation regions
    • Vogel K, Horz W, Hinnen A, (1989) The two positively acting regulatory proteins PHO2 and PHO4 physically interact with PHO5 upstream activation regions. Mol Cell Biol 9: 2050-2057.
    • (1989) Mol Cell Biol , vol.9 , pp. 2050-2057
    • Vogel, K.1    Horz, W.2    Hinnen, A.3
  • 22
    • 33644794061 scopus 로고    scopus 로고
    • Active PHO5 chromatin encompasses variable numbers of nucleosomes at individual promoters
    • Jessen WJ, Hoose SA, Kilgore JA, Kladde MP, (2006) Active PHO5 chromatin encompasses variable numbers of nucleosomes at individual promoters. Nat Struct Mol Biol 13: 256-263.
    • (2006) Nat Struct Mol Biol , vol.13 , pp. 256-263
    • Jessen, W.J.1    Hoose, S.A.2    Kilgore, J.A.3    Kladde, M.P.4
  • 23
    • 78650930357 scopus 로고    scopus 로고
    • Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast
    • Miller C, Schwalb B, Maier K, Schulz D, Dumcke S, et al. (2011) Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol 7: 458.
    • (2011) Mol Syst Biol , vol.7 , pp. 458
    • Miller, C.1    Schwalb, B.2    Maier, K.3    Schulz, D.4    Dumcke, S.5
  • 24
    • 33645453254 scopus 로고    scopus 로고
    • Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
    • Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637-643.
    • (2006) Nature , vol.440 , pp. 637-643
    • Krogan, N.J.1    Cagney, G.2    Yu, H.3    Zhong, G.4    Guo, X.5
  • 25
    • 0035193294 scopus 로고    scopus 로고
    • Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations
    • Kepler TB, Elston TC, (2001) Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. Biophys J 81: 3116-3136.
    • (2001) Biophys J , vol.81 , pp. 3116-3136
    • Kepler, T.B.1    Elston, T.C.2
  • 26
    • 0000111447 scopus 로고
    • Markovian modeling of gene product synthesis
    • Peccoud J, Ycart B, (1995) Markovian modeling of gene product synthesis. Theor Popul Biol 48: 222-234.
    • (1995) Theor Popul Biol , vol.48 , pp. 222-234
    • Peccoud, J.1    Ycart, B.2
  • 27
    • 20344389483 scopus 로고    scopus 로고
    • Models of stochastic gene expression
    • Paulsson J, (2005) Models of stochastic gene expression. Physics of Life Reviews 2: 157-175.
    • (2005) Physics of Life Reviews , vol.2 , pp. 157-175
    • Paulsson, J.1
  • 28
    • 84874770600 scopus 로고    scopus 로고
    • Formation and fate of a complete 31-protein RNA polymerase II transcription preinitiation complex
    • Murakami K, Calero G, Brown CR, Liu X, Davis RE, et al. (2013) Formation and fate of a complete 31-protein RNA polymerase II transcription preinitiation complex. J Biol Chem 288: 6325-6332.
    • (2013) J Biol Chem , vol.288 , pp. 6325-6332
    • Murakami, K.1    Calero, G.2    Brown, C.R.3    Liu, X.4    Davis, R.E.5
  • 29
    • 57149101122 scopus 로고    scopus 로고
    • Single-RNA counting reveals alternative modes of gene expression in yeast
    • Zenklusen D, Larson DR, Singer RH, (2008) Single-RNA counting reveals alternative modes of gene expression in yeast. Nat Struct Mol Biol 15: 1263-1271.
    • (2008) Nat Struct Mol Biol , vol.15 , pp. 1263-1271
    • Zenklusen, D.1    Larson, D.R.2    Singer, R.H.3
  • 30
    • 0018290840 scopus 로고
    • Post-replicative nonribosomal transcription units in D. melanogaster embryos
    • McKnight SL, Miller OL Jr, (1979) Post-replicative nonribosomal transcription units in D. melanogaster embryos. Cell 17: 551-563.
    • (1979) Cell , vol.17 , pp. 551-563
    • McKnight, S.L.1    Miller Jr., O.L.2
  • 31
    • 84866083176 scopus 로고    scopus 로고
    • Dynamics of protein noise can distinguish between alternate sources of gene-expression variability
    • Singh A, Razooky BS, Dar RD, Weinberger LS, (2012) Dynamics of protein noise can distinguish between alternate sources of gene-expression variability. Mol Syst Biol 8: 607.
    • (2012) Mol Syst Biol , vol.8 , pp. 607
    • Singh, A.1    Razooky, B.S.2    Dar, R.D.3    Weinberger, L.S.4
  • 32
    • 79957608918 scopus 로고    scopus 로고
    • General properties of transcriptional time series in Escherichia coli
    • So LH, Ghosh A, Zong C, Sepulveda LA, Segev R, et al. (2011) General properties of transcriptional time series in Escherichia coli. Nat Genet 43: 554-560.
    • (2011) Nat Genet , vol.43 , pp. 554-560
    • So, L.H.1    Ghosh, A.2    Zong, C.3    Sepulveda, L.A.4    Segev, R.5
  • 33
    • 77952566675 scopus 로고    scopus 로고
    • SWI/SNF has intrinsic nucleosome disassembly activity that is dependent on adjacent nucleosomes
    • Dechassa ML, Sabri A, Pondugula S, Kassabov SR, Chatterjee N, et al. (2010) SWI/SNF has intrinsic nucleosome disassembly activity that is dependent on adjacent nucleosomes. Mol Cell 38: 590-602.
    • (2010) Mol Cell , vol.38 , pp. 590-602
    • Dechassa, M.L.1    Sabri, A.2    Pondugula, S.3    Kassabov, S.R.4    Chatterjee, N.5
  • 34
    • 81755171464 scopus 로고    scopus 로고
    • In vivo role for the chromatin-remodeling enzyme SWI/SNF in the removal of promoter nucleosomes by disassembly rather than sliding
    • Brown CR, Mao C, Falkovskaia E, Law JK, Boeger H, (2011) In vivo role for the chromatin-remodeling enzyme SWI/SNF in the removal of promoter nucleosomes by disassembly rather than sliding. J Biol Chem 286: 40556-40565.
    • (2011) J Biol Chem , vol.286 , pp. 40556-40565
    • Brown, C.R.1    Mao, C.2    Falkovskaia, E.3    Law, J.K.4    Boeger, H.5
  • 35
    • 0035265922 scopus 로고    scopus 로고
    • A transient histone hyperacetylation signal marks nucleosomes for remodeling at the PHO8 promoter in vivo
    • Reinke H, Gregory PD, Horz W, (2001) A transient histone hyperacetylation signal marks nucleosomes for remodeling at the PHO8 promoter in vivo. Mol Cell 7: 529-538.
    • (2001) Mol Cell , vol.7 , pp. 529-538
    • Reinke, H.1    Gregory, P.D.2    Horz, W.3
  • 36
    • 33947137710 scopus 로고    scopus 로고
    • Dynamics of replication-independent histone turnover in budding yeast
    • Dion MF, Kaplan T, Kim M, Buratowski S, Friedman N, et al. (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
  • 37
    • 84859582058 scopus 로고    scopus 로고
    • Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function
    • Lickwar CR, Mueller F, Hanlon SE, McNally JG, Lieb JD, (2012) Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function. Nature 484: 251-255.
    • (2012) Nature , vol.484 , pp. 251-255
    • Lickwar, C.R.1    Mueller, F.2    Hanlon, S.E.3    McNally, J.G.4    Lieb, J.D.5
  • 38
    • 31544446038 scopus 로고    scopus 로고
    • Transcriptional activators are dispensable for transcription in the absence of Spt6-mediated chromatin reassembly of promoter regions
    • Adkins MW, Tyler JK, (2006) Transcriptional activators are dispensable for transcription in the absence of Spt6-mediated chromatin reassembly of promoter regions. Mol Cell 21: 405-416.
    • (2006) Mol Cell , vol.21 , pp. 405-416
    • Adkins, M.W.1    Tyler, J.K.2
  • 39
    • 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 DC, dos Santos G, Liu L, Gao Y, et al. (2010) Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science 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
  • 41
    • 36549013619 scopus 로고    scopus 로고
    • RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo
    • Zeitlinger J, Stark A, Kellis M, Hong JW, Nechaev S, et al. (2007) RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet 39: 1512-1516.
    • (2007) Nat Genet , vol.39 , pp. 1512-1516
    • Zeitlinger, J.1    Stark, A.2    Kellis, M.3    Hong, J.W.4    Nechaev, S.5
  • 42
    • 34447098370 scopus 로고    scopus 로고
    • A chromatin landmark and transcription initiation at most promoters in human cells
    • Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA, (2007) A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130: 77-88.
    • (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
  • 43
    • 3542998667 scopus 로고    scopus 로고
    • Nucleosomes facilitate their own invasion
    • Li G, Widom J, (2004) Nucleosomes facilitate their own invasion. Nat Struct Mol Biol 11: 763-769.
    • (2004) Nat Struct Mol Biol , vol.11 , pp. 763-769
    • Li, G.1    Widom, J.2
  • 44
    • 0028872728 scopus 로고
    • Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative
    • Adams CC, Workman JL, (1995) Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative. Mol Cell Biol 15: 1405-1421.
    • (1995) Mol Cell Biol , vol.15 , pp. 1405-1421
    • Adams, C.C.1    Workman, J.L.2
  • 45
    • 55549113874 scopus 로고    scopus 로고
    • A quantitative model of transcription factor-activated gene expression
    • Kim HD, O'Shea EK, (2008) A quantitative model of transcription factor-activated gene expression. Nat Struct Mol Biol 15: 1192-1198.
    • (2008) Nat Struct Mol Biol , vol.15 , pp. 1192-1198
    • Kim, H.D.1    O'Shea, E.K.2
  • 46
    • 0025977162 scopus 로고
    • A functional role for nucleosomes in the repression of a yeast promoter
    • Straka C, Horz W, (1991) A functional role for nucleosomes in the repression of a yeast promoter. Embo J 10: 361-368.
    • (1991) Embo J , vol.10 , pp. 361-368
    • Straka, C.1    Horz, W.2
  • 47
    • 84862624197 scopus 로고    scopus 로고
    • The lac repressor displays facilitated diffusion in living cells
    • Hammar P, Leroy P, Mahmutovic A, Marklund EG, Berg OG, et al. (2012) The lac repressor displays facilitated diffusion in living cells. Science 336: 1595-1598.
    • (2012) Science , vol.336 , pp. 1595-1598
    • Hammar, P.1    Leroy, P.2    Mahmutovic, A.3    Marklund, E.G.4    Berg, O.G.5
  • 48
    • 0021674214 scopus 로고
    • A bacterial repressor protein or a yeast transcriptional terminator can block upstream activation of a yeast gene
    • Brent R, Ptashne M, (1984) A bacterial repressor protein or a yeast transcriptional terminator can block upstream activation of a yeast gene. Nature 312: 612-615.
    • (1984) Nature , vol.312 , pp. 612-615
    • Brent, R.1    Ptashne, M.2
  • 49
    • 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
  • 51
    • 2942574467 scopus 로고    scopus 로고
    • Removal of promoter nucleosomes by disassembly rather than sliding in vivo
    • Boeger H, Griesenbeck J, Strattan JS, Kornberg RD, (2004) Removal of promoter nucleosomes by disassembly rather than sliding in vivo. Mol Cell 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
  • 52
    • 0024455692 scopus 로고
    • Electron microscopy of chromatin
    • Sogo JM, Thoma F, (1989) Electron microscopy of chromatin. Methods Enzymol 170: 142-165.
    • (1989) Methods Enzymol , vol.170 , pp. 142-165
    • Sogo, J.M.1    Thoma, F.2
  • 53
    • 0023800064 scopus 로고
    • DNA sequence specificity of 4,5′,8-trimethylpsoralen cross-linking. Effect of neighboring bases on cross-linking the 5′-TA dinucleotide
    • Esposito F, Brankamp RG, Sinden RR, (1988) DNA sequence specificity of 4,5′,8-trimethylpsoralen cross-linking. Effect of neighboring bases on cross-linking the 5′-TA dinucleotide. JBC 263: 11466-11472.
    • (1988) JBC , vol.263 , pp. 11466-11472
    • Esposito, F.1    Brankamp, R.G.2    Sinden, R.R.3
  • 54
    • 0031957859 scopus 로고    scopus 로고
    • A topological approach to nucleosome structure and dynamics: the linking number paradox and other issues
    • Prunell A, (1998) A topological approach to nucleosome structure and dynamics: the linking number paradox and other issues. Biophys J 74: 2531-2544.
    • (1998) Biophys J , vol.74 , pp. 2531-2544
    • Prunell, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.