메뉴 건너뛰기




Volumn 11, Issue 5, 2015, Pages

Orthogonal control of expression mean and variance by epigenetic features at different genomic loci

Author keywords

chromatin environment; gene expression noise; single cell biology; single molecule RNA FISH

Indexed keywords

MESSENGER RNA; CHROMATIN; PROTEIN;

EID: 84930202865     PISSN: None     EISSN: 17444292     Source Type: Journal    
DOI: 10.15252/msb.20145704     Document Type: Article
Times cited : (80)

References (55)
  • 1
    • 41349119880 scopus 로고    scopus 로고
    • Stochastic switching as a survival strategy in fluctuating environments
    • Acar M, Mettetal JT, van Oudenaarden A, (2008) Stochastic switching as a survival strategy in fluctuating environments. Nat Genet 40: 471-475
    • (2008) Nat Genet , vol.40 , pp. 471-475
    • Acar, M.1    Mettetal, J.T.2    Van Oudenaarden, A.3
  • 2
    • 0031879114 scopus 로고    scopus 로고
    • Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-Infected Escherichia coli cells
    • Arkin A, Ross J, McAdams HH, (1998) Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-Infected Escherichia coli cells. Genetics 149: 1633-1648
    • (1998) Genetics , vol.149 , pp. 1633-1648
    • Arkin, A.1    Ross, J.2    McAdams, H.H.3
  • 4
    • 79952638264 scopus 로고    scopus 로고
    • Cellular decision making and biological noise: From microbes to mammals
    • Balázsi G, van Oudenaarden A, Collins JJ, (2011) Cellular decision making and biological noise: from microbes to mammals. Cell 144: 910-925
    • (2011) Cell , vol.144 , pp. 910-925
    • Balázsi, G.1    Van Oudenaarden, A.2    Collins, J.J.3
  • 6
    • 34547519199 scopus 로고    scopus 로고
    • Evolution of chromosome organization driven by selection for reduced gene expression noise
    • Batada NN, Hurst LD, (2007) Evolution of chromosome organization driven by selection for reduced gene expression noise. Nat Genet 39: 945-949
    • (2007) Nat Genet , vol.39 , pp. 945-949
    • Batada, N.N.1    Hurst, L.D.2
  • 9
    • 44349162752 scopus 로고    scopus 로고
    • Transcriptome-wide noise controls lineage choice in mammalian progenitor cells
    • Chang HH, Hemberg M, Barahona M, Ingber DE, Huang S, (2008) Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature 453: 544-547
    • (2008) Nature , vol.453 , pp. 544-547
    • Chang, H.H.1    Hemberg, M.2    Barahona, M.3    Ingber, D.E.4    Huang, S.5
  • 13
    • 77952996319 scopus 로고    scopus 로고
    • Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones
    • Deal RB, Henikoff JG, Henikoff S, (2010) Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones. Science 328: 1161-1164
    • (2010) Science , vol.328 , pp. 1161-1164
    • Deal, R.B.1    Henikoff, J.G.2    Henikoff, S.3
  • 14
    • 84858065741 scopus 로고    scopus 로고
    • Mutual information analysis reveals coevolving residues in Tat that compensate for two distinct functions in HIV-1 gene expression
    • Dey SS, Xue Y, Joachimiak MP, Friedland GD, Burnett JC, Zhou Q, Arkin AP, Schaffer DV, (2012) Mutual information analysis reveals coevolving residues in Tat that compensate for two distinct functions in HIV-1 gene expression. J Biol Chem 287: 7945-7955
    • (2012) J Biol Chem , vol.287 , pp. 7945-7955
    • Dey, S.S.1    Xue, Y.2    Joachimiak, M.P.3    Friedland, G.D.4    Burnett, J.C.5    Zhou, Q.6    Arkin, A.P.7    Schaffer, D.V.8
  • 16
    • 84860324470 scopus 로고    scopus 로고
    • Roles for microRNAs in conferring robustness to biological processes
    • Ebert MS, Sharp PA, (2012) Roles for microRNAs in conferring robustness to biological processes. Cell 149: 515-524
    • (2012) Cell , vol.149 , pp. 515-524
    • Ebert, M.S.1    Sharp, P.A.2
  • 18
    • 33750247101 scopus 로고    scopus 로고
    • Linking stochastic dynamics to population distribution: An analytical framework of gene expression
    • Friedman N, Cai L, Xie XS, (2006) Linking stochastic dynamics to population distribution: an analytical framework of gene expression. Phys Rev Lett 97: 168302
    • (2006) Phys Rev Lett , vol.97 , pp. 168302
    • Friedman, N.1    Cai, L.2    Xie, X.S.3
  • 19
    • 28944434119 scopus 로고    scopus 로고
    • Real-time kinetics of gene activity in individual bacteria
    • Golding I, Paulsson J, Zawilski SM, Cox EC, (2005) Real-time kinetics of gene activity in individual bacteria. Cell 123: 1025-1036
    • (2005) Cell , vol.123 , pp. 1025-1036
    • Golding, I.1    Paulsson, J.2    Zawilski, S.M.3    Cox, E.C.4
  • 21
    • 84860710346 scopus 로고    scopus 로고
    • Nucleosome organization affects the sensitivity of gene expression to promoter mutations
    • Hornung G, Oren M, Barkai N, (2012) Nucleosome organization affects the sensitivity of gene expression to promoter mutations. Mol Cell 46: 362-368
    • (2012) Mol Cell , vol.46 , pp. 362-368
    • Hornung, G.1    Oren, M.2    Barkai, N.3
  • 22
    • 0035794637 scopus 로고    scopus 로고
    • The site of HIV-1 integration in the human genome determines basal transcriptional activity and response to Tat transactivation
    • Jordan A, Defechereux P, Verdin E, (2001) The site of HIV-1 integration in the human genome determines basal transcriptional activity and response to Tat transactivation. EMBO J 20: 1726-1738
    • (2001) EMBO J , vol.20 , pp. 1726-1738
    • Jordan, A.1    Defechereux, P.2    Verdin, E.3
  • 23
    • 19544379881 scopus 로고    scopus 로고
    • Stochasticity in gene expression: From theories to phenotypes
    • Kaern M, Elston TC, Blake WJ, Collins JJ, (2005) Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet 6: 451-464
    • (2005) Nat Rev Genet , vol.6 , pp. 451-464
    • Kaern, M.1    Elston, T.C.2    Blake, W.J.3    Collins, J.J.4
  • 24
    • 43449096915 scopus 로고    scopus 로고
    • Chromatin decouples promoter threshold from dynamic range
    • Lam FH, Steger DJ, O'Shea EK, (2008) Chromatin decouples promoter threshold from dynamic range. Nature 453: 246-250
    • (2008) Nature , vol.453 , pp. 246-250
    • Lam, F.H.1    Steger, D.J.2    O'Shea, E.K.3
  • 27
    • 84874405819 scopus 로고    scopus 로고
    • Chromatin accessibility at the HIV LTR promoter sets a threshold for NF-κB mediated viral gene expression
    • Miller-Jensen K, Dey SS, Pham N, Foley JE, Arkin AP, Schaffer DV, (2012) Chromatin accessibility at the HIV LTR promoter sets a threshold for NF-κB mediated viral gene expression. Integr Biol (Camb) 4: 661
    • (2012) Integr Biol (Camb) , vol.4 , pp. 661
    • Miller-Jensen, K.1    Dey, S.S.2    Pham, N.3    Foley, J.E.4    Arkin, A.P.5    Schaffer, D.V.6
  • 28
    • 80052809114 scopus 로고    scopus 로고
    • Varying virulence: Epigenetic control of expression noise and disease processes
    • Miller-Jensen K, Dey SS, Schaffer DV, Arkin AP, (2011) Varying virulence: epigenetic control of expression noise and disease processes. Trends Biotechnol 29: 517-525
    • (2011) Trends Biotechnol , vol.29 , pp. 517-525
    • Miller-Jensen, K.1    Dey, S.S.2    Schaffer, D.V.3    Arkin, A.P.4
  • 30
    • 0842285841 scopus 로고    scopus 로고
    • Summing up the noise in gene networks
    • Paulsson J, (2004) Summing up the noise in gene networks. Nature 427: 415-418
    • (2004) Nature , vol.427 , pp. 415-418
    • Paulsson, J.1
  • 31
    • 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
  • 32
    • 0034142332 scopus 로고    scopus 로고
    • A compilation of cellular transcription factor interactions with the HIV-1 LTR promoter
    • Pereira LA, Bentley K, Peeters A, Churchill MJ, Deacon NJ, (2000) A compilation of cellular transcription factor interactions with the HIV-1 LTR promoter. Nucleic Acids Res 28: 663-668
    • (2000) Nucleic Acids Res , vol.28 , pp. 663-668
    • Pereira, L.A.1    Bentley, K.2    Peeters, A.3    Churchill, M.J.4    Deacon, N.J.5
  • 33
    • 82455219436 scopus 로고    scopus 로고
    • Repressive LTR nucleosome positioning by the BAF complex is required for HIV latency
    • Rafati H, Parra M, Hakre S, Moshkin Y, Verdin E, Mahmoudi T, (2011) Repressive LTR nucleosome positioning by the BAF complex is required for HIV latency. PLoS Biol 9: e1001206
    • (2011) PLoS Biol , vol.9 , pp. e1001206
    • Rafati, H.1    Parra, M.2    Hakre, S.3    Moshkin, Y.4    Verdin, E.5    Mahmoudi, T.6
  • 36
    • 53549123008 scopus 로고    scopus 로고
    • Nature, nurture, or chance: Stochastic gene expression and its consequences
    • Raj A, van Oudenaarden A, (2008) Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135: 216-226
    • (2008) Cell , vol.135 , pp. 216-226
    • Raj, A.1    Van Oudenaarden, A.2
  • 37
    • 67650711140 scopus 로고    scopus 로고
    • Genome-wide views of chromatin structure
    • Rando OJ, Chang HY, (2009) Genome-wide views of chromatin structure. Annu Rev Biochem 78: 245-271
    • (2009) Annu Rev Biochem , vol.78 , pp. 245-271
    • Rando, O.J.1    Chang, H.Y.2
  • 38
    • 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
  • 39
    • 0037162715 scopus 로고    scopus 로고
    • HIV-1 integration in the human genome favors active genes and local hotspots
    • Schröder ARW, (2002) HIV-1 integration in the human genome favors active genes and local hotspots. Cell 110: 521-529
    • (2002) Cell , vol.110 , pp. 521-529
    • Schröder, A.R.W.1
  • 41
    • 77951604611 scopus 로고    scopus 로고
    • Transcriptional bursting from the HIV-1 promoter is a significant source of stochastic noise in HIV-1 gene expression
    • Singh A, Razooky B, Cox CD, Simpson ML, Weinberger LS, (2010a) Transcriptional bursting from the HIV-1 promoter is a significant source of stochastic noise in HIV-1 gene expression. Biophys J 98: L32-L34
    • (2010) Biophys J , vol.98 , pp. L32-L34
    • Singh, A.1    Razooky, B.2    Cox, C.D.3    Simpson, M.L.4    Weinberger, L.S.5
  • 42
    • 77952257945 scopus 로고    scopus 로고
    • Patterns of basal signaling heterogeneity can distinguish cellular populations with different drug sensitivities
    • Singh DK, Ku C-J, Wichaidit C, Steininger RJ, Wu LF, Altschuler SJ, (2010b) Patterns of basal signaling heterogeneity can distinguish cellular populations with different drug sensitivities. Mol Syst Biol 6: 369
    • (2010) Mol Syst Biol , vol.6 , pp. 369
    • Singh, D.K.1    Ku, C.-J.2    Wichaidit, C.3    Steininger, R.J.4    Wu, L.F.5    Altschuler, S.J.6
  • 43
    • 78049436913 scopus 로고    scopus 로고
    • HIV promoter integration site primarily modulates transcriptional burst size rather than frequency
    • Skupsky R, Burnett JC, Foley JE, Schaffer DV, Arkin AP, (2010) HIV promoter integration site primarily modulates transcriptional burst size rather than frequency. PLoS Comput Biol 6: e1000952
    • (2010) PLoS Comput Biol , vol.6 , pp. e1000952
    • Skupsky, R.1    Burnett, J.C.2    Foley, J.E.3    Schaffer, D.V.4    Arkin, A.P.5
  • 44
    • 66249136447 scopus 로고    scopus 로고
    • Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis
    • Spencer SL, Gaudet S, Albeck JG, Burke JM, Sorger PK, (2009) Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis. Nature 459: 428-432
    • (2009) Nature , vol.459 , pp. 428-432
    • Spencer, S.L.1    Gaudet, S.2    Albeck, J.G.3    Burke, J.M.4    Sorger, P.K.5
  • 45
    • 0017185026 scopus 로고
    • Non-genetic individuality: Chance in the single cell
    • Spudich JL, Koshland DE, (1976) Non-genetic individuality: chance in the single cell. Nature 262: 467-471
    • (1976) Nature , vol.262 , pp. 467-471
    • Spudich, J.L.1    Koshland, D.E.2
  • 48
    • 43749088127 scopus 로고    scopus 로고
    • Two strategies for gene regulation by promoter nucleosomes
    • Tirosh I, Barkai N, (2008) Two strategies for gene regulation by promoter nucleosomes. Genome Res 18: 1084-1091
    • (2008) Genome Res , vol.18 , pp. 1084-1091
    • Tirosh, I.1    Barkai, N.2
  • 49
    • 0027258123 scopus 로고
    • Chromatin disruption in the promoter of human immunodeficiency virus type 1 during transcriptional activation
    • Verdin E, Paras P Jr, Van Lint C, (1993) Chromatin disruption in the promoter of human immunodeficiency virus type 1 during transcriptional activation. EMBO J 12: 3249-3259
    • (1993) EMBO J , vol.12 , pp. 3249-3259
    • Verdin, E.1    Paras, Jr.P.2    Van Lint, C.3
  • 50
    • 84874149579 scopus 로고    scopus 로고
    • Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts
    • Viñuelas J, Kaneko G, Coulon A, Vallin E, Morin V, Mejia-Pous C, Kupiec J-J, Beslon G, Gandrillon O, (2013) Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts. BMC Biol 11: 15
    • (2013) BMC Biol , vol.11 , pp. 15
    • Viñuelas, J.1    Kaneko, G.2    Coulon, A.3    Vallin, E.4    Morin, V.5    Mejia-Pous, C.6    Kupiec, J.-J.7    Beslon, G.8    Gandrillon, O.9
  • 51
    • 34547635063 scopus 로고    scopus 로고
    • HIV integration site selection: Analysis by massively parallel pyrosequencing reveals association with epigenetic modifications
    • Wang GP, Ciuffi A, Leipzig J, Berry CC, Bushman FD, (2007) HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. Genome Res 17: 1186-1194
    • (2007) Genome Res , vol.17 , pp. 1186-1194
    • Wang, G.P.1    Ciuffi, A.2    Leipzig, J.3    Berry, C.C.4    Bushman, F.D.5
  • 53
    • 22744441386 scopus 로고    scopus 로고
    • Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 tat fluctuations drive phenotypic diversity
    • Weinberger LS, Burnett JC, Toettcher JE, Arkin AP, Schaffer DV, (2005) Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 tat fluctuations drive phenotypic diversity. Cell 122: 169-182
    • (2005) Cell , vol.122 , pp. 169-182
    • Weinberger, L.S.1    Burnett, J.C.2    Toettcher, J.E.3    Arkin, A.P.4    Schaffer, D.V.5
  • 54
    • 41349095731 scopus 로고    scopus 로고
    • Transient-mediated fate determination in a transcriptional circuit of HIV
    • Weinberger LS, Dar RD, Simpson ML, (2008) Transient-mediated fate determination in a transcriptional circuit of HIV. Nat Genet 40: 466-470
    • (2008) Nat Genet , vol.40 , pp. 466-470
    • Weinberger, L.S.1    Dar, R.D.2    Simpson, M.L.3
  • 55
    • 33644856456 scopus 로고    scopus 로고
    • Stochastic spineless expression creates the retinal mosaic for colour vision
    • Wernet MF, Mazzoni EO, Celik A, Duncan DM, Duncan I, Desplan C, (2006) Stochastic spineless expression creates the retinal mosaic for colour vision. Nature 440: 174-180
    • (2006) Nature , vol.440 , pp. 174-180
    • Wernet, M.F.1    Mazzoni, E.O.2    Celik, A.3    Duncan, D.M.4    Duncan, I.5    Desplan, C.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.