-
1
-
-
79952638264
-
Cellular decision making and biological noise: From microbes to mammals
-
Balazsi 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
-
-
Balazsi, G.1
Van Oudenaarden, A.2
Collins, J.J.3
-
2
-
-
67650328126
-
Imaging transcription in living cells
-
Darzacq X et al (2009) Imaging transcription in living cells. Annu Rev Biophys 38: 173-196
-
(2009)
Annu Rev Biophys
, vol.38
, pp. 173-196
-
-
Darzacq, X.1
-
3
-
-
64749116742
-
Using movies to analyse gene circuit dynamics in single cells
-
Locke JC, Elowitz MB (2009) Using movies to analyse gene circuit dynamics in single cells. Nat Rev Microbiol 7: 383-392
-
(2009)
Nat Rev Microbiol
, vol.7
, pp. 383-392
-
-
Locke, J.C.1
Elowitz, M.B.2
-
4
-
-
77956651529
-
Bursts and pulses: Insights from single cell studies into transcriptional mechanisms
-
Chubb JR, Liverpool TB (2010) Bursts and pulses: insights from single cell studies into transcriptional mechanisms. Curr Opin Genet Dev 20: 478-484
-
(2010)
Curr Opin Genet Dev
, vol.20
, pp. 478-484
-
-
Chubb, J.R.1
Liverpool, T.B.2
-
5
-
-
0032562720
-
Visualization of single RNA transcripts in situ
-
DOI 10.1126/science.280.5363.585
-
Femino AM, Fay FS, Fogarty K, Singer RH (1998) Visualization of single RNA transcripts in situ. Science 280: 585-590 (Pubitemid 28227761)
-
(1998)
Science
, vol.280
, Issue.5363
, pp. 585-590
-
-
Femino, A.M.1
Fay, F.S.2
Fogarty, K.3
Singer, R.H.4
-
6
-
-
33748994704
-
Stochastic mRNA synthesis in mammalian cells
-
Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S (2006) Stochastic mRNA synthesis in mammalian cells. PLoS Biol 4: e309
-
(2006)
PLoS Biol
, vol.4
-
-
Raj, A.1
Peskin, C.S.2
Tranchina, D.3
Vargas, D.Y.4
Tyagi, S.5
-
7
-
-
77249114260
-
Variability in gene expression underlies incomplete penetrance
-
Raj A, Rifkin SA, Andersen E, van Oudenaarden A (2010) Variability in gene expression underlies incomplete penetrance. Nature 463: 913-918
-
(2010)
Nature
, vol.463
, pp. 913-918
-
-
Raj, A.1
Rifkin, S.A.2
Andersen, E.3
Van Oudenaarden, A.4
-
8
-
-
79957608918
-
General properties of transcriptional time series in Escherichia coli
-
So LH, Ghosh A, Zong C, Sepulveda LA, Segev R, Golding I (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
Golding, I.6
-
9
-
-
77955174763
-
Single-allele analysis of transcription kinetics in living mammalian cells
-
Yunger S, Rosenfeld L, Garini Y, Shav-Tal Y (2010) Single-allele analysis of transcription kinetics in living mammalian cells. Nat Methods 7: 631-633
-
(2010)
Nat Methods
, vol.7
, pp. 631-633
-
-
Yunger, S.1
Rosenfeld, L.2
Garini, Y.3
Shav-Tal, Y.4
-
10
-
-
57149101122
-
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
-
11
-
-
0032185810
-
Localization of ASH1 mRNA particles in living yeast
-
Bertrand E, Chartrand P, Schaefer M, Shenoy SM, Singer RH, Long RM (1998) Localization of ASH1 mRNA particles in living yeast. Mol Cell 2: 437-445 (Pubitemid 128381296)
-
(1998)
Molecular Cell
, vol.2
, Issue.4
, pp. 437-445
-
-
Bertrand, E.1
Chartrand, P.2
Schaefer, M.3
Shenoy, S.M.4
Singer, R.H.5
Long, R.M.6
-
12
-
-
79551537838
-
A transgenic mouse for in vivo detection of endogenous labeled mRNA
-
Lionnet T, Czaplinski K, Darzacq X, Shav-Tal Y, Wells AL, Chao JA, Park HY, de Turris V, Lopez-Jones M, Singer RH (2011) A transgenic mouse for in vivo detection of endogenous labeled mRNA. Nat Methods 8: 165-170
-
(2011)
Nat Methods
, vol.8
, pp. 165-170
-
-
Lionnet, T.1
Czaplinski, K.2
Darzacq, X.3
Shav-Tal, Y.4
Wells, A.L.5
Chao, J.A.6
Park, H.Y.7
De Turris, V.8
Lopez-Jones, M.9
Singer, R.H.10
-
13
-
-
79955407832
-
Real-time observation of transcription initiation and elongation on an endogenous yeast gene
-
Larson DR, Zenklusen D, Wu B, Chao JA, Singer RH (2011) Real-time observation of transcription initiation and elongation on an endogenous yeast gene. Science 332: 475-478
-
(2011)
Science
, vol.332
, pp. 475-478
-
-
Larson, D.R.1
Zenklusen, D.2
Wu, B.3
Chao, J.A.4
Singer, R.H.5
-
14
-
-
34548507690
-
In vivo dynamics of RNA polymerase II transcription
-
DOI 10.1038/nsmb1280, PII NSMB1280
-
Darzacq X, Shav-Tal Y, de Turris V, Brody Y, Shenoy SM, Phair RD, Singer RH (2007) In vivo dynamics of RNA polymerase II transcription. Nat Struct Mol Biol 14: 796-806 (Pubitemid 47373828)
-
(2007)
Nature Structural and Molecular Biology
, vol.14
, Issue.9
, pp. 796-806
-
-
Darzacq, X.1
Shav-Tal, Y.2
De Turris, V.3
Brody, Y.4
Shenoy, S.M.5
Phair, R.D.6
Singer, R.H.7
-
15
-
-
12144289862
-
From silencing to gene expression: Real-time analysis in single cells
-
DOI 10.1016/S0092-8674(04)00171-0, PII S0092867404001710
-
Janicki SM et al (2004) From silencing to gene expression: real-time analysis in single cells. Cell 116: 683-698 (Pubitemid 38326727)
-
(2004)
Cell
, vol.116
, Issue.5
, pp. 683-698
-
-
Janicki, S.M.1
Tsukamoto, T.2
Salghetti, S.E.3
Tansey, W.P.4
Sachidanandam, R.5
Prasanth, K.V.6
Ried, T.7
Shav-Tal, Y.8
Bertrand, E.9
Singer, R.H.10
Spector, D.L.11
-
16
-
-
33646591544
-
Transcriptional Pulsing of a Developmental Gene
-
DOI 10.1016/j.cub.2006.03.092, PII S0960982206014266
-
Chubb JR, Trcek T, Shenoy SM, Singer RH (2006) Transcriptional pulsing of a developmental gene. Curr Biol 16: 1018-1025 (Pubitemid 43728209)
-
(2006)
Current Biology
, vol.16
, Issue.10
, pp. 1018-1025
-
-
Chubb, J.R.1
Trcek, T.2
Shenoy, S.M.3
Singer, R.H.4
-
17
-
-
28944434119
-
Real-time kinetics of gene activity in individual bacteria
-
DOI 10.1016/j.cell.2005.09.031, PII S0092867405010378
-
Golding I, Paulsson J, Zawilski SM, Cox EC (2005) Real-time kinetics of gene activity in individual bacteria. Cell 123: 1025-1036 (Pubitemid 41785418)
-
(2005)
Cell
, vol.123
, Issue.6
, pp. 1025-1036
-
-
Golding, I.1
Paulsson, J.2
Zawilski, S.M.3
Cox, E.C.4
-
18
-
-
65449131152
-
Imaging intracellular RNA distribution and dynamics in living cells
-
Tyagi S (2009) Imaging intracellular RNA distribution and dynamics in living cells. Nat Methods 6: 331-338
-
(2009)
Nat Methods
, vol.6
, pp. 331-338
-
-
Tyagi, S.1
-
19
-
-
22744432208
-
Precise temporal modulation in the response of the SOS DNA repair network in individual bacteria
-
Friedman N, Vardi S, Ronen M, Alon U, Stavans J (2005) Precise temporal modulation in the response of the SOS DNA repair network in individual bacteria. PLoS Biol 3: e238
-
(2005)
PLoS Biol
, vol.3
-
-
Friedman, N.1
Vardi, S.2
Ronen, M.3
Alon, U.4
Stavans, J.5
-
20
-
-
0842332406
-
Dynamics of the p53-Mdm2 feedback loop in individual cells
-
DOI 10.1038/ng1293
-
Lahav G, Rosenfeld N, Sigal A, Geva-Zatorsky N, Levine AJ, Elowitz MB, Alon U (2004) Dynamics of the p53-Mdm2 feedback loop in individual cells. Nat Genet 36: 147-150 (Pubitemid 38174372)
-
(2004)
Nature Genetics
, vol.36
, Issue.2
, pp. 147-150
-
-
Lahav, G.1
Rosenfeld, N.2
Sigal, A.3
Geva-Zatorsky, N.4
Levine, A.J.5
Elowitz, M.B.6
Alon, U.7
-
21
-
-
80054837496
-
Stochastic pulse regulation in bacterial stress response
-
Locke JC, Young JW, Fontes M, Hernandez Jimenez MJ, Elowitz MB (2011) Stochastic pulse regulation in bacterial stress response. Science 334: 366-369
-
(2011)
Science
, vol.334
, pp. 366-369
-
-
Locke, J.C.1
Young, J.W.2
Fontes, M.3
Hernandez Jimenez, M.J.4
Elowitz, M.B.5
-
22
-
-
33645027986
-
Stochastic protein expression in individual cells at the single molecule level
-
Cai L, Friedman N, Xie XS (2006) Stochastic protein expression in individual cells at the single molecule level. Nature 440: 358-362
-
(2006)
Nature
, vol.440
, pp. 358-362
-
-
Cai, L.1
Friedman, N.2
Xie, X.S.3
-
23
-
-
33645033645
-
Probing gene expression in live cells, one protein molecule at a time
-
Yu J, Xiao J, Ren X, Lao K, Xie XS (2006) Probing gene expression in live cells, one protein molecule at a time. Science 311: 1600-1603
-
(2006)
Science
, vol.311
, pp. 1600-1603
-
-
Yu, J.1
Xiao, J.2
Ren, X.3
Lao, K.4
Xie, X.S.5
-
24
-
-
79955488304
-
Dynamic analysis of stochastic transcription cycles
-
Harper CV et al (2011) Dynamic analysis of stochastic transcription cycles. PLoS Biol 9: e1000607
-
(2011)
PLoS Biol
, vol.9
-
-
Harper, C.V.1
-
25
-
-
79955381895
-
Mammalian genes are transcribed with widely different bursting kinetics
-
Suter DM, Molina N, Gatfield D, Schneider K, Schibler U, Naef F (2011) Mammalian genes are transcribed with widely different bursting kinetics. Science 332: 472-474
-
(2011)
Science
, vol.332
, pp. 472-474
-
-
Suter, D.M.1
Molina, N.2
Gatfield, D.3
Schneider, K.4
Schibler, U.5
Naef, F.6
-
26
-
-
0242416539
-
Noise in eukaryotic gene expression
-
DOI 10.1038/nature01546
-
Blake WJ, Kaern M, Cantor CR, Collins JJ (2003) Noise in eukaryotic gene expression. Nature 422: 633-637 (Pubitemid 36460419)
-
(2003)
Nature
, vol.422
, Issue.6932
, pp. 633-637
-
-
Blake, W.J.1
Kaern, M.2
Cantor, C.R.3
Collins, J.J.4
-
27
-
-
71649113974
-
Visualization of individual Scr mRNAs during Drosophila embryogenesis yields evidence for transcriptional bursting
-
Pare A, Lemons D, Kosman D, Beaver W, Freund Y, McGinnis W (2009) Visualization of individual Scr mRNAs during Drosophila embryogenesis yields evidence for transcriptional bursting. Curr Biol 19: 2037-2042
-
(2009)
Curr Biol
, vol.19
, pp. 2037-2042
-
-
Pare, A.1
Lemons, D.2
Kosman, D.3
Beaver, W.4
Freund, Y.5
McGinnis, W.6
-
28
-
-
53349161901
-
Imaging individual mRNA molecules using multiple singly labeled probes
-
Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S (2008) Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods 5: 877-879
-
(2008)
Nat Methods
, vol.5
, pp. 877-879
-
-
Raj, A.1
Van Den Bogaard, P.2
Rifkin, S.A.3
Van Oudenaarden, A.4
Tyagi, S.5
-
29
-
-
0032167516
-
Transcription occurs in pulses in muscle fibers
-
Newlands S, Levitt LK, Robinson CS, Karpf AB, Hodgson VR, Wade RP, Hardeman EC (1998) Transcription occurs in pulses in muscle fibers. Genes Dev 12: 2748-2758 (Pubitemid 28420654)
-
(1998)
Genes and Development
, vol.12
, Issue.17
, pp. 2748-2758
-
-
Newlands, S.1
Levitt, L.K.2
Robinson, C.S.3
Karpf, A.B.C.4
Hodgson, V.R.M.5
Wade, R.P.6
Hardeman, E.C.7
-
30
-
-
43449111772
-
Modulation of RNA polymerase assembly dynamics in transcriptional regulation
-
DOI 10.1016/j.molcel.2008.04.021, PII S1097276508003237
-
Gorski SA, Snyder SK, John S, Grummt I, Misteli T (2008) Modulation of RNA polymerase assembly dynamics in transcriptional regulation. Mol Cell 30: 486-497 (Pubitemid 351672375)
-
(2008)
Molecular Cell
, vol.30
, Issue.4
, pp. 486-497
-
-
Gorski, S.A.1
Snyder, S.K.2
John, S.3
Grummt, I.4
Misteli, T.5
-
31
-
-
77951101695
-
Transcript counting in single cells reveals dynamics of rDNA transcription
-
Tan RZ, van Oudenaarden A (2010) Transcript counting in single cells reveals dynamics of rDNA transcription. Mol Syst Biol 6: 358
-
(2010)
Mol Syst Biol
, vol.6
, pp. 358
-
-
Tan, R.Z.1
Van Oudenaarden, A.2
-
32
-
-
33745287724
-
Noise in protein expression scales with natural protein abundance
-
DOI 10.1038/ng1807, PII N1807
-
Bar-Even A, Paulsson J, Maheshri N, Carmi M, O'Shea E, Pilpel Y, Barkai N (2006) Noise in protein expression scales with natural protein abundance. Nat Genet 38: 636-643 (Pubitemid 43927304)
-
(2006)
Nature Genetics
, vol.38
, Issue.6
, pp. 636-643
-
-
Bar-Even, A.1
Paulsson, J.2
Maheshri, N.3
Carmi, M.4
O'Shea, E.5
Pilpel, Y.6
Barkai, N.7
-
33
-
-
38549126635
-
Concurrent fast and slow cycling of a transcriptional activator at an endogenous promoter
-
DOI 10.1126/science.1150559
-
Karpova TS, Kim MJ, Spriet C, Nalley K, Stasevich TJ, Kherrouche Z, Heliot L, McNally JG (2008) Concurrent fast and slow cycling of a transcriptional activator at an endogenous promoter. Science 319: 466-469 (Pubitemid 351160580)
-
(2008)
Science
, vol.319
, Issue.5862
, pp. 466-469
-
-
Karpova, T.S.1
Kim, M.J.2
Spriet, C.3
Nalley, K.4
Stasevich, T.J.5
Kherrouche, Z.6
Heliot, L.7
McNally, J.G.8
-
34
-
-
77955102352
-
Quantifying e coli proteome and transcriptome with single-molecule sensitivity in single cells
-
Taniguchi Y, Choi PJ, Li GW, Chen H, Babu M, Hearn J, Emili A, Xie XS (2010) Quantifying E coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329: 533-538
-
(2010)
Science
, vol.329
, pp. 533-538
-
-
Taniguchi, Y.1
Choi, P.J.2
Li, G.W.3
Chen, H.4
Babu, M.5
Hearn, J.6
Emili, A.7
Xie, X.S.8
-
35
-
-
80052398196
-
Nuclear physics: Quantitative single-cell approaches to nuclear organization and gene expression
-
Lionnet T, Wu B, Grunwald D, Singer RH, Larson DR (2011) Nuclear physics: quantitative single-cell approaches to nuclear organization and gene expression. Cold Spring Harbor Symp Quant Biol 75: 113-126
-
(2011)
Cold Spring Harbor Symp Quant Biol
, vol.75
, pp. 113-126
-
-
Lionnet, T.1
Wu, B.2
Grunwald, D.3
Singer, R.H.4
Larson, D.R.5
-
37
-
-
78650216734
-
Transcription by the numbers redux: Experiments and calculations that surprise
-
Garcia HG, Sanchez A, Kuhlman T, Kondev J, Phillips R (2010) Transcription by the numbers redux: experiments and calculations that surprise. Trends Cell Biol 20: 723-733
-
(2010)
Trends Cell Biol
, vol.20
, pp. 723-733
-
-
Garcia, H.G.1
Sanchez, A.2
Kuhlman, T.3
Kondev, J.4
Phillips, R.5
-
38
-
-
20344389483
-
Models of stochastic gene expression
-
DOI 10.1016/j.plrev.2005.03.003, PII S1571064505000138
-
Paulsson J (2005) Models of stochastic gene expression. Phys Life Rev 2: 157-175 (Pubitemid 40792434)
-
(2005)
Physics of Life Reviews
, vol.2
, Issue.2
, pp. 157-175
-
-
Paulsson, J.1
-
39
-
-
79952672993
-
Impulse control: Temporal dynamics in gene transcription
-
Yosef N, Regev A (2011) Impulse control: temporal dynamics in gene transcription. Cell 144: 886-896
-
(2011)
Cell
, vol.144
, pp. 886-896
-
-
Yosef, N.1
Regev, A.2
-
40
-
-
0034688173
-
A synthetic oscillatory network of transcriptional regulators
-
DOI 10.1038/35002125
-
Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403: 335-338 (Pubitemid 30062393)
-
(2000)
Nature
, vol.403
, Issue.6767
, pp. 335-338
-
-
Elowitz, M.B.1
Leibier, S.2
-
41
-
-
79961051673
-
Separating intrinsic from extrinsic fluctuations in dynamic biological systems
-
Hilfinger A, Paulsson J (2011) Separating intrinsic from extrinsic fluctuations in dynamic biological systems. Proc Natl Acad Sci USA 108: 12167-12172
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 12167-12172
-
-
Hilfinger, A.1
Paulsson, J.2
-
42
-
-
79051469396
-
Burstiness and memory in complex systems
-
Goh KI, Barabasi A (2008) Burstiness and memory in complex systems. Europhysics Lett 81: 48002
-
(2008)
Europhysics Lett
, vol.81
, pp. 48002
-
-
Goh, K.I.1
Barabasi, A.2
-
43
-
-
77954541844
-
Single-cell NF-κB dynamics reveal digital activation and analogue information processing
-
Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW (2010) Single-cell NF-κB dynamics reveal digital activation and analogue information processing. Nature 466: 267-271
-
(2010)
Nature
, vol.466
, pp. 267-271
-
-
Tay, S.1
Hughey, J.J.2
Lee, T.K.3
Lipniacki, T.4
Quake, S.R.5
Covert, M.W.6
-
45
-
-
79251603722
-
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
-
46
-
-
76449108997
-
Digital nature of the immediate-early transcriptional response
-
Stevense M, Muramoto T, Muller I, Chubb JR (2010) Digital nature of the immediate-early transcriptional response. Development 137: 579-584
-
(2010)
Development
, vol.137
, pp. 579-584
-
-
Stevense, M.1
Muramoto, T.2
Muller, I.3
Chubb, J.R.4
-
47
-
-
0034667792
-
Orchestrated response: A symphony of transcription factors for gene control
-
Lemon B, Tjian R (2000) Orchestrated response: a symphony of transcription factors for gene control. Genes Dev 14: 2551-2569
-
(2000)
Genes Dev
, vol.14
, pp. 2551-2569
-
-
Lemon, B.1
Tjian, R.2
-
48
-
-
66049096618
-
The basal initiation machinery: Beyond the general transcription factors
-
Sikorski TW, Buratowski S (2009) The basal initiation machinery: beyond the general transcription factors. Curr Opin Cell Biol 21: 344-351
-
(2009)
Curr Opin Cell Biol
, vol.21
, pp. 344-351
-
-
Sikorski, T.W.1
Buratowski, S.2
-
49
-
-
82355190137
-
Assembly of the transcription machinery: Ordered and stable, random and dynamic, or both?
-
Stasevich TJ, McNally JG (2011) Assembly of the transcription machinery: ordered and stable, random and dynamic, or both? Chromosoma 120: 533-545
-
(2011)
Chromosoma
, vol.120
, pp. 533-545
-
-
Stasevich, T.J.1
McNally, J.G.2
-
50
-
-
2942718723
-
Control of stochasticity in eukaryotic gene expression
-
DOI 10.1126/science.1098641
-
Raser JM, O'Shea EK (2004) Control of stochasticity in eukaryotic gene expression. Science 304: 1811-1814 (Pubitemid 38787899)
-
(2004)
Science
, vol.304
, Issue.5678
, pp. 1811-1814
-
-
Raser, J.M.1
O'Shea, E.K.2
-
51
-
-
60349089645
-
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
-
52
-
-
57149119464
-
Distinct modes of regulation by chromatin encoded through nucleosome positioning signals
-
Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, Lubling Y, Widom J, Segal E (2008) Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol 4: e1000216
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Field, Y.1
Kaplan, N.2
Fondufe-Mittendorf, Y.3
Moore, I.K.4
Sharon, E.5
Lubling, Y.6
Widom, J.7
Segal, E.8
-
53
-
-
43749088127
-
Two strategies for gene regulation by promoter nucleosomes
-
DOI 10.1101/gr.076059.108
-
Tirosh I, Barkai N (2008) Two strategies for gene regulation by promoter nucleosomes. Genome Res 18: 1084-1091 (Pubitemid 351931159)
-
(2008)
Genome Research
, vol.18
, Issue.7
, pp. 1084-1091
-
-
Tirosh, I.1
Barkai, N.2
-
54
-
-
70249121045
-
The logic of chromatin architecture and remodelling at promoters
-
Cairns BR (2009) The logic of chromatin architecture and remodelling at promoters. Nature 461: 193-198
-
(2009)
Nature
, vol.461
, pp. 193-198
-
-
Cairns, B.R.1
-
55
-
-
77951902484
-
Nucleosome-depleted regions in cell-cycle-regulated promoters ensure reliable gene expression in every cell cycle
-
Bai L, Charvin G, Siggia ED, Cross FR (2010) Nucleosome-depleted regions in cell-cycle-regulated promoters ensure reliable gene expression in every cell cycle. Dev Cell 18: 544-555
-
(2010)
Dev Cell
, vol.18
, pp. 544-555
-
-
Bai, L.1
Charvin, G.2
Siggia, E.D.3
Cross, F.R.4
-
56
-
-
43449096915
-
Chromatin decouples promoter threshold from dynamic range
-
DOI 10.1038/nature06867, PII NATURE06867
-
Lam FH, Steger DJ, O'Shea EK (2008) Chromatin decouples promoter threshold from dynamic range. Nature 453: 246-250 (Pubitemid 351667976)
-
(2008)
Nature
, vol.453
, Issue.7192
, pp. 246-250
-
-
Lam, F.H.1
Steger, D.J.2
O'Shea, E.K.3
-
57
-
-
84855306788
-
A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast
-
Zaugg JB, Luscombe NM (2012) A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast. Genome Res 22: 84-94
-
(2012)
Genome Res
, vol.22
, pp. 84-94
-
-
Zaugg, J.B.1
Luscombe, N.M.2
-
59
-
-
82455199121
-
What do expression dynamics tell us about the mechanism of transcription?
-
Larson DR (2011) What do expression dynamics tell us about the mechanism of transcription? Curr Opin Genet Dev 21: 591-599
-
(2011)
Curr Opin Genet Dev
, vol.21
, pp. 591-599
-
-
Larson, D.R.1
-
60
-
-
2642544592
-
Estrogen receptor-α directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter
-
DOI 10.1016/S0092-8674(03)00934-6
-
Metivier R, Penot G, Hubner MR, Reid G, Brand H, Kos M, Gannon F (2003) Estrogen receptor-α directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115: 751-763 (Pubitemid 38030303)
-
(2003)
Cell
, vol.115
, Issue.6
, pp. 751-763
-
-
Metivier, R.1
Penot, G.2
Hubner, M.R.3
Reid, G.4
Brand, H.5
Kos, M.6
Gannon, F.7
-
61
-
-
77649140924
-
Methylation of H3K4 is required for inheritance of active transcriptional states
-
Muramoto T, Muller I, Thomas G, Melvin A, Chubb JR (2010) Methylation of H3K4 is required for inheritance of active transcriptional states. Curr Biol 20: 397-406
-
(2010)
Curr Biol
, vol.20
, pp. 397-406
-
-
Muramoto, T.1
Muller, I.2
Thomas, G.3
Melvin, A.4
Chubb, J.R.5
-
62
-
-
73649118540
-
Transcriptional memory: Staying in the loop
-
Brickner JH (2010) Transcriptional memory: staying in the loop. Curr Biol 20: R20-R21
-
(2010)
Curr Biol
, vol.20
-
-
Brickner, J.H.1
-
63
-
-
33748304273
-
Dynamics of heat shock factor association with native gene loci in living cells
-
DOI 10.1038/nature05025, PII NATURE05025
-
Yao J, Munson KM, Webb WW, Lis JT (2006) Dynamics of heat shock factor association with native gene loci in living cells. Nature 442: 1050-1053 (Pubitemid 44330263)
-
(2006)
Nature
, vol.442
, Issue.7106
, pp. 1050-1053
-
-
Yao, J.1
Munson, K.M.2
Webb, W.W.3
Lis, J.T.4
-
64
-
-
67649766870
-
Transcription factories: Gene expression in unions?
-
Sutherland H, Bickmore WA (2009) Transcription factories: gene expression in unions? Nat Rev Genet 10: 457-466
-
(2009)
Nat Rev Genet
, vol.10
, pp. 457-466
-
-
Sutherland, H.1
Bickmore, W.A.2
-
65
-
-
57849109058
-
Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
-
Core LJ, Waterfall JJ, Lis JT (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322: 1845-1848
-
(2008)
Science
, vol.322
, pp. 1845-1848
-
-
Core, L.J.1
Waterfall, J.J.2
Lis, J.T.3
-
66
-
-
36549061004
-
RNA polymerase is poised for activation across the genome
-
DOI 10.1038/ng.2007.21, PII NG200721
-
Muse GW, Gilchrist DA, Nechaev S, Shah R, Parker JS, Grissom SF, Zeitlinger J, Adelman K (2007) RNA polymerase is poised for activation across the genome. Nat Genet 39: 1507-1511 (Pubitemid 350191341)
-
(2007)
Nature Genetics
, vol.39
, Issue.12
, pp. 1507-1511
-
-
Muse, G.W.1
Gilchrist, D.A.2
Nechaev, S.3
Shah, R.4
Parker, J.S.5
Grissom, S.F.6
Zeitlinger, J.7
Adelman, K.8
-
67
-
-
78149477660
-
Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation
-
Gilchrist DA, Dos Santos G, Fargo DC, Xie B, Gao Y, Li L, Adelman K (2010) Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation. Cell 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
-
68
-
-
67749106610
-
Synchronous and stochastic patterns of gene activation in the Drosophila embryo
-
Boettiger AN, Levine M (2009) Synchronous and stochastic patterns of gene activation in the Drosophila embryo. Science 325: 471-473
-
(2009)
Science
, vol.325
, pp. 471-473
-
-
Boettiger, A.N.1
Levine, M.2
-
69
-
-
80555157616
-
Negative elongation factor accelerates the rate at which heat shock genes are shut off by facilitating dissociation of heat shock factor
-
Ghosh SK, Missra A, Gilmour DS (2011) Negative elongation factor accelerates the rate at which heat shock genes are shut off by facilitating dissociation of heat shock factor. Mol Cell Biol 31: 4232-4243
-
(2011)
Mol Cell Biol
, vol.31
, pp. 4232-4243
-
-
Ghosh, S.K.1
Missra, A.2
Gilmour, D.S.3
-
71
-
-
77954815037
-
FRAP and kinetic modeling in the analysis of nuclear protein dynamics: What do we really know?
-
Mueller F, Mazza D, Stasevich TJ, McNally JG (2010) FRAP and kinetic modeling in the analysis of nuclear protein dynamics: what do we really know? Curr Opin Cell Biol 22: 403-411
-
(2010)
Curr Opin Cell Biol
, vol.22
, pp. 403-411
-
-
Mueller, F.1
Mazza, D.2
Stasevich, T.J.3
McNally, J.G.4
-
72
-
-
82555205173
-
Fast transcription rates of RNA polymerase II in human cells
-
Maiuri P, Knezevich A, De Marco A, Mazza D, Kula A, McNally JG, Marcello A (2011) Fast transcription rates of RNA polymerase II in human cells. EMBO Rep 12: 1280-1285
-
(2011)
EMBO Rep
, vol.12
, pp. 1280-1285
-
-
Maiuri, P.1
Knezevich, A.2
De Marco, A.3
Mazza, D.4
Kula, A.5
McNally, J.G.6
Marcello, A.7
-
73
-
-
62449302589
-
Elongation dynamics shape bursty transcription and translation
-
Dobrzynski M, Bruggeman FJ (2009) Elongation dynamics shape bursty transcription and translation. Proc Natl Acad Sci USA 106: 2583-2588
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 2583-2588
-
-
Dobrzynski, M.1
Bruggeman, F.J.2
-
74
-
-
15244358670
-
Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo
-
DOI 10.1016/j.molcel.2005.02.017
-
Mason PB, Struhl K (2005) Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo. Mol Cell 17: 831-840 (Pubitemid 40386944)
-
(2005)
Molecular Cell
, vol.17
, Issue.6
, pp. 831-840
-
-
Mason, P.B.1
Struhl, K.2
-
75
-
-
0141888375
-
A slow RNA polymerase II affects alternative splicing in vivo
-
DOI 10.1016/j.molcel.2003.08.001
-
de la Mata M, Alonso CR, Kadener S, Fededa JP, Blaustein M, Pelisch F, Cramer P, Bentley D, Kornblihtt AR (2003) A slow RNA polymerase II affects alternative splicing in vivo. Mol Cell 12: 525-532 (Pubitemid 37238937)
-
(2003)
Molecular Cell
, vol.12
, Issue.2
, pp. 525-532
-
-
De La Mata, M.1
Alonso, C.R.2
Kadener, S.3
Fededa, J.P.4
Blaustein, M.5
Pelisch, F.6
Cramer, P.7
Bentley, D.8
Kornblihtt, A.R.9
-
76
-
-
35548988487
-
The transcriptional cycle of HIV-1 in real-time and live cells
-
DOI 10.1083/jcb.200706018
-
Boireau S, Maiuri P, Basyuk E, de la Mata M, Knezevich A, Pradet-Balade B, Backer V, Kornblihtt A, Marcello A, Bertrand E (2007) The transcriptional cycle of HIV-1 in real-time and live cells. J Cell Biol 179: 291-304 (Pubitemid 350004893)
-
(2007)
Journal of Cell Biology
, vol.179
, Issue.2
, pp. 291-304
-
-
Boireau, S.1
Maiuri, P.2
Basyuk, E.3
De La Mata, M.4
Knezevich, A.5
Pradet-Balade, B.6
Backer, V.7
Kornblihtt, A.8
Marcello, A.9
Bertrand, E.10
-
77
-
-
48949092575
-
A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation
-
Lian Z, Karpikov A, Lian J, Mahajan MC, Hartman S, Gerstein M, Snyder M, Weissman SM (2008) A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation. Genome Res 18: 1224-1237
-
(2008)
Genome Res
, vol.18
, pp. 1224-1237
-
-
Lian, Z.1
Karpikov, A.2
Lian, J.3
Mahajan, M.C.4
Hartman, S.5
Gerstein, M.6
Snyder, M.7
Weissman, S.M.8
-
78
-
-
52949098296
-
Frequency-modulated nuclear localization bursts coordinate gene regulation
-
Cai L, Dalal CK, Elowitz MB (2008) Frequency-modulated nuclear localization bursts coordinate gene regulation. Nature 455: 485-490
-
(2008)
Nature
, vol.455
, pp. 485-490
-
-
Cai, L.1
Dalal, C.K.2
Elowitz, M.B.3
-
79
-
-
33745451921
-
Oscillations and variability in the p53 system
-
2006 0033
-
Geva-Zatorsky N et al (2006) Oscillations and variability in the p53 system. Mol Syst Biol 2: 2006 0033
-
(2006)
Mol Syst Biol
, vol.2
-
-
Geva-Zatorsky, N.1
-
80
-
-
0029155607
-
Enhancers increase the probability but not the level of gene expression
-
Walters MC, Fiering S, Eidemiller J, Magis W, Groudine M, Martin DI (1995) Enhancers increase the probability but not the level of gene expression. Proc Natl Acad Sci USA 92: 7125-7129
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 7125-7129
-
-
Walters, M.C.1
Fiering, S.2
Eidemiller, J.3
Magis, W.4
Groudine, M.5
Martin, D.I.6
-
81
-
-
33746228114
-
Interchromosomal Interactions and Olfactory Receptor Choice
-
DOI 10.1016/j.cell.2006.06.035, PII S0092867406008555
-
Lomvardas S, Barnea G, Pisapia DJ, Mendelsohn M, Kirkland J, Axel R (2006) Interchromosomal interactions and olfactory receptor choice. Cell 126: 403-413 (Pubitemid 44092961)
-
(2006)
Cell
, vol.126
, Issue.2
, pp. 403-413
-
-
Lomvardas, S.1
Barnea, G.2
Pisapia, D.J.3
Mendelsohn, M.4
Kirkland, J.5
Axel, R.6
-
82
-
-
81055125638
-
Regulation of the probability of mouse odorant receptor gene choice
-
Khan M, Vaes E, Mombaerts P (2011) Regulation of the probability of mouse odorant receptor gene choice. Cell 147: 907-921
-
(2011)
Cell
, vol.147
, pp. 907-921
-
-
Khan, M.1
Vaes, E.2
Mombaerts, P.3
-
83
-
-
79960980390
-
Variegated gene expression caused by cell-specific long-range DNA interactions
-
Noordermeer D, de Wit E, Klous P, van de Werken H, Simonis M, Lopez-Jones M, Eussen B, de Klein A, Singer RH, de Laat W (2011) Variegated gene expression caused by cell-specific long-range DNA interactions. Nat Cell Biol 13: 944-951
-
(2011)
Nat Cell Biol
, vol.13
, pp. 944-951
-
-
Noordermeer, D.1
De Wit, E.2
Klous, P.3
Van De Werken, H.4
Simonis, M.5
Lopez-Jones, M.6
Eussen, B.7
De Klein, A.8
Singer, R.H.9
De Laat, W.10
-
84
-
-
65549104157
-
Histone modifications at human enhancers reflect global cell-type-specific gene expression
-
Heintzman ND et al (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459: 108-112
-
(2009)
Nature
, vol.459
, pp. 108-112
-
-
Heintzman, N.D.1
-
85
-
-
58049191558
-
Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation
-
Cui K, Zang C, Roh TY, Schones DE, Childs RW, Peng W, Zhao K (2009) Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell 4: 80-93
-
(2009)
Cell Stem Cell
, vol.4
, pp. 80-93
-
-
Cui, K.1
Zang, C.2
Roh, T.Y.3
Schones, D.E.4
Childs, R.W.5
Peng, W.6
Zhao, K.7
-
86
-
-
77956520011
-
Functional roles for noise in genetic circuits
-
Eldar A, Elowitz MB (2010) Functional roles for noise in genetic circuits. Nature 467: 167-173
-
(2010)
Nature
, vol.467
, pp. 167-173
-
-
Eldar, A.1
Elowitz, M.B.2
-
87
-
-
79953044960
-
Genome-wide transcription factor binding: Beyond direct target regulation
-
MacQuarrie KL, Fong AP, Morse RH, Tapscott SJ (2011) Genome-wide transcription factor binding: beyond direct target regulation. Trends Genet 27: 141-148
-
(2011)
Trends Genet
, vol.27
, pp. 141-148
-
-
MacQuarrie, K.L.1
Fong, A.P.2
Morse, R.H.3
Tapscott, S.J.4
-
88
-
-
78650747491
-
Discovery and characterization of chromatin states for systematic annotation of the human genome
-
Ernst J, Kellis M (2010) Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 28: 817-825
-
(2010)
Nat Biotechnol
, vol.28
, pp. 817-825
-
-
Ernst, J.1
Kellis, M.2
-
89
-
-
77957776228
-
Systematic protein location mapping reveals five principal chromatin types in Drosophila cells
-
Filion GJ et al (2010) Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 143: 212-224
-
(2010)
Cell
, vol.143
, pp. 212-224
-
-
Filion, G.J.1
-
90
-
-
78751659330
-
Nascent transcript sequencing visualizes transcription at nucleotide resolution
-
Churchman LS, Weissman JS (2011) Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 469: 368-373
-
(2011)
Nature
, vol.469
, pp. 368-373
-
-
Churchman, L.S.1
Weissman, J.S.2
-
91
-
-
34748826166
-
A high-resolution atlas of nucleosome occupancy in yeast
-
DOI 10.1038/ng2117, PII NG2117
-
Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C (2007) A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet 39: 1235-1244 (Pubitemid 47482684)
-
(2007)
Nature Genetics
, vol.39
, Issue.10
, pp. 1235-1244
-
-
Lee, W.1
Tillo, D.2
Bray, N.3
Morse, R.H.4
Davis, R.W.5
Hughes, T.R.6
Nislow, C.7
-
92
-
-
76449108997
-
Digital nature of the immediate-early transcriptional response
-
Stevense M, Muramoto T, Müller I, Chubb JR (2010) Digital nature of the immediate-early transcriptional response. Development 137: 579-584
-
(2010)
Development
, vol.137
, pp. 579-584
-
-
Stevense, M.1
Muramoto, T.2
Müller, I.3
Chubb, J.R.4
|