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For: Hornung G, Bar-Ziv R, Rosin D, Tokuriki N, Tawfik DS, Oren M, Barkai N. Noise-mean relationship in mutated promoters. Genome Res 2012;22:2409-17. [PMID: 22820945 DOI: 10.1101/gr.139378.112] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Number Cited by Other Article(s)
1
McQueen E, Yang B, Wittkopp PJ. Epistatic impacts of cis- and trans-regulatory mutations on the distribution of mutational effects for gene expression in Saccharomyces cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.26.645465. [PMID: 40196697 PMCID: PMC11974906 DOI: 10.1101/2025.03.26.645465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
2
Kozubowski L, Berman J. The impact of phenotypic heterogeneity on fungal pathogenicity and drug resistance. FEMS Microbiol Rev 2025;49:fuaf001. [PMID: 39809571 PMCID: PMC11756289 DOI: 10.1093/femsre/fuaf001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 11/26/2024] [Accepted: 01/13/2025] [Indexed: 01/16/2025]  Open
3
Zhou L, Chen H, Zhang J, Zhang J, Qiu H, Zhou T. Exact burst-size distributions for gene-expression models with complex promoter structure. Biosystems 2024;246:105337. [PMID: 39299486 DOI: 10.1016/j.biosystems.2024.105337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 09/14/2024] [Accepted: 09/14/2024] [Indexed: 09/22/2024]
4
Shi C, Yang X, Zhou T, Zhang J. Nascent RNA kinetics with complex promoter architecture: Analytic results and parameter inference. Phys Rev E 2024;110:034413. [PMID: 39425372 DOI: 10.1103/physreve.110.034413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 09/11/2024] [Indexed: 10/21/2024]
5
Schofield JA, Hahn S. Transcriptional noise, gene activation, and roles of SAGA and Mediator Tail measured using nucleotide recoding single-cell RNA-seq. Cell Rep 2024;43:114593. [PMID: 39102335 PMCID: PMC11405135 DOI: 10.1016/j.celrep.2024.114593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 06/29/2024] [Accepted: 07/22/2024] [Indexed: 08/07/2024]  Open
6
Pal S, Dhar R. Living in a noisy world-origins of gene expression noise and its impact on cellular decision-making. FEBS Lett 2024;598:1673-1691. [PMID: 38724715 DOI: 10.1002/1873-3468.14898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/23/2024] [Accepted: 03/27/2024] [Indexed: 07/23/2024]
7
Breimann L, Bahry E, Zouinkhi M, Kolyvanov K, Street LA, Preibisch S, Ercan S. Analysis of developmental gene expression using smFISH and in silico staging of C. elegans embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594414. [PMID: 38798598 PMCID: PMC11118362 DOI: 10.1101/2024.05.15.594414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
8
Jiao Y, Nigam D, Barry K, Daum C, Yoshinaga Y, Lipzen A, Khan A, Parasa SP, Wei S, Lu Z, Tello-Ruiz MK, Dhiman P, Burow G, Hayes C, Chen J, Brandizzi F, Mortimer J, Ware D, Xin Z. A large sequenced mutant library - valuable reverse genetic resource that covers 98% of sorghum genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024;117:1543-1557. [PMID: 38100514 DOI: 10.1111/tpj.16582] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/08/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023]
9
Meeussen JVW, Lenstra TL. Time will tell: comparing timescales to gain insight into transcriptional bursting. Trends Genet 2024;40:160-174. [PMID: 38216391 PMCID: PMC10860890 DOI: 10.1016/j.tig.2023.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 01/14/2024]
10
Kleinschmidt H, Xu C, Bai L. Using Synthetic DNA Libraries to Investigate Chromatin and Gene Regulation. Chromosoma 2023;132:167-189. [PMID: 37184694 PMCID: PMC10542970 DOI: 10.1007/s00412-023-00796-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/16/2023]
11
Weidemann DE, Holehouse J, Singh A, Grima R, Hauf S. The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian. SCIENCE ADVANCES 2023;9:eadh5138. [PMID: 37556551 PMCID: PMC10411910 DOI: 10.1126/sciadv.adh5138] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/07/2023] [Indexed: 08/11/2023]
12
Wittkopp PJ. Contributions of mutation and selection to regulatory variation: lessons from the Saccharomyces cerevisiae TDH3 gene. Philos Trans R Soc Lond B Biol Sci 2023;378:20220057. [PMID: 37004723 PMCID: PMC10067266 DOI: 10.1098/rstb.2022.0057] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/16/2023] [Indexed: 04/04/2023]  Open
13
Schofield JA, Hahn S. Broad compatibility between yeast UAS elements and core promoters and identification of promoter elements that determine cofactor specificity. Cell Rep 2023;42:112387. [PMID: 37058407 PMCID: PMC10567116 DOI: 10.1016/j.celrep.2023.112387] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/30/2023] [Accepted: 03/28/2023] [Indexed: 04/15/2023]  Open
14
Kumar DK, Jonas F, Jana T, Brodsky S, Carmi M, Barkai N. Complementary strategies for directing in vivo transcription factor binding through DNA binding domains and intrinsically disordered regions. Mol Cell 2023;83:1462-1473.e5. [PMID: 37116493 DOI: 10.1016/j.molcel.2023.04.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/17/2023] [Accepted: 01/30/2023] [Indexed: 04/30/2023]
15
Weidemann DE, Singh A, Grima R, Hauf S. The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531283. [PMID: 36945401 PMCID: PMC10028819 DOI: 10.1101/2023.03.06.531283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
16
Lambert É, Puwakdandawa K, Tao YF, Robert F. From structure to molecular condensates: emerging mechanisms for Mediator function. FEBS J 2023;290:286-309. [PMID: 34698446 DOI: 10.1111/febs.16250] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 02/05/2023]
17
Luo S, Wang Z, Zhang Z, Zhou T, Zhang J. Genome-wide inference reveals that feedback regulations constrain promoter-dependent transcriptional burst kinetics. Nucleic Acids Res 2022;51:68-83. [PMID: 36583343 PMCID: PMC9874261 DOI: 10.1093/nar/gkac1204] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/06/2022] [Accepted: 12/06/2022] [Indexed: 12/31/2022]  Open
18
Parab L, Pal S, Dhar R. Transcription factor binding process is the primary driver of noise in gene expression. PLoS Genet 2022;18:e1010535. [PMID: 36508455 PMCID: PMC9779669 DOI: 10.1371/journal.pgen.1010535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/22/2022] [Accepted: 11/16/2022] [Indexed: 12/14/2022]  Open
19
Jayaraman V, Toledo‐Patiño S, Noda‐García L, Laurino P. Mechanisms of protein evolution. Protein Sci 2022;31:e4362. [PMID: 35762715 PMCID: PMC9214755 DOI: 10.1002/pro.4362] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/11/2022] [Accepted: 05/14/2022] [Indexed: 11/06/2022]
20
Gene regulation in Escherichia coli is commonly selected for both high plasticity and low noise. Nat Ecol Evol 2022;6:1165-1179. [PMID: 35726087 DOI: 10.1038/s41559-022-01783-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 05/03/2022] [Indexed: 11/08/2022]
21
Cancer: More than a geneticist’s Pandora’s box. J Biosci 2022. [DOI: 10.1007/s12038-022-00254-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
22
Yang X, Wang Z, Wu Y, Zhou T, Zhang J. Kinetic characteristics of transcriptional bursting in a complex gene model with cyclic promoter structure. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022;19:3313-3336. [PMID: 35341253 DOI: 10.3934/mbe.2022153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
23
Yang X, Luo S, Zhang Z, Wang Z, Zhou T, Zhang J. Silent transcription intervals and translational bursting lead to diverse phenotypic switching. Phys Chem Chem Phys 2022;24:26600-26608. [DOI: 10.1039/d2cp03703c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
24
Chen M, Luo S, Cao M, Guo C, Zhou T, Zhang J. Exact distributions for stochastic gene expression models with arbitrary promoter architecture and translational bursting. Phys Rev E 2022;105:014405. [PMID: 35193181 DOI: 10.1103/physreve.105.014405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/14/2021] [Indexed: 11/07/2022]
25
Yokoshi M, Kawasaki K, Cambón M, Fukaya T. Dynamic modulation of enhancer responsiveness by core promoter elements in living Drosophila embryos. Nucleic Acids Res 2021;50:92-107. [PMID: 34897508 PMCID: PMC8754644 DOI: 10.1093/nar/gkab1177] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 11/12/2022]  Open
26
Gerhardt KP, Rao SD, Olson EJ, Igoshin OA, Tabor JJ. Independent control of mean and noise by convolution of gene expression distributions. Nat Commun 2021;12:6957. [PMID: 34845228 PMCID: PMC8630168 DOI: 10.1038/s41467-021-27070-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 11/03/2021] [Indexed: 11/28/2022]  Open
27
Bohrer CH, Larson DR. The Stochastic Genome and Its Role in Gene Expression. Cold Spring Harb Perspect Biol 2021;13:a040386. [PMID: 33903158 PMCID: PMC8485747 DOI: 10.1101/cshperspect.a040386] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
28
Chen M, Zhou T, Zhang J. Correlation between external regulators governs the mean-noise relationship in stochastic gene expression. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021;18:4713-4730. [PMID: 34198461 DOI: 10.3934/mbe.2021239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
29
Yang X, Chen Y, Zhou T, Zhang J. Exploring dissipative sources of non-Markovian biochemical reaction systems. Phys Rev E 2021;103:052411. [PMID: 34134237 DOI: 10.1103/physreve.103.052411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/29/2021] [Indexed: 11/07/2022]
30
Das S, Barik D. Scaling of intrinsic noise in an autocratic reaction network. Phys Rev E 2021;103:042403. [PMID: 34006004 DOI: 10.1103/physreve.103.042403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/16/2021] [Indexed: 11/07/2022]
31
Capp J. Interplay between genetic, epigenetic, and gene expression variability: Considering complexity in evolvability. Evol Appl 2021;14:893-901. [PMID: 33897810 PMCID: PMC8061278 DOI: 10.1111/eva.13204] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 12/11/2022]  Open
32
Ramalingam V, Natarajan M, Johnston J, Zeitlinger J. TATA and paused promoters active in differentiated tissues have distinct expression characteristics. Mol Syst Biol 2021;17:e9866. [PMID: 33543829 PMCID: PMC7863008 DOI: 10.15252/msb.20209866] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/22/2020] [Accepted: 01/07/2021] [Indexed: 12/18/2022]  Open
33
Qiu H, Zhang B, Zhou T. Explicit effect of stochastic reaction delay on gene expression. Phys Rev E 2020;101:012405. [PMID: 32069597 DOI: 10.1103/physreve.101.012405] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Indexed: 11/07/2022]
34
Zhang T, Foreman R, Wollman R. Identifying chromatin features that regulate gene expression distribution. Sci Rep 2020;10:20566. [PMID: 33239733 PMCID: PMC7688950 DOI: 10.1038/s41598-020-77638-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/10/2020] [Indexed: 12/17/2022]  Open
35
Reines D. Recent advances in understanding RNA polymerase II structure and function. Fac Rev 2020;9:11. [PMID: 33659943 PMCID: PMC7886063 DOI: 10.12703/b/9-11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
36
Capturing and Understanding the Dynamics and Heterogeneity of Gene Expression in the Living Cell. Int J Mol Sci 2020;21:ijms21218278. [PMID: 33167354 PMCID: PMC7663833 DOI: 10.3390/ijms21218278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 11/21/2022]  Open
37
Liu Y, Li L, Qi H, Que H, Wang W, Zhang G. Regulation Between HSF1 Isoforms and HSPs Contributes to the Variation in Thermal Tolerance Between Two Oyster Congeners. Front Genet 2020;11:581725. [PMID: 33193707 PMCID: PMC7652795 DOI: 10.3389/fgene.2020.581725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/06/2020] [Indexed: 01/09/2023]  Open
38
Arede L, Pina C. Buffering noise: KAT2A modular contributions to stabilization of transcription and cell identity in cancer and development. Exp Hematol 2020;93:25-37. [PMID: 33223444 DOI: 10.1016/j.exphem.2020.10.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 02/07/2023]
39
Cortijo S, Locke JCW. Does Gene Expression Noise Play a Functional Role in Plants? TRENDS IN PLANT SCIENCE 2020;25:1041-1051. [PMID: 32467064 DOI: 10.1016/j.tplants.2020.04.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/22/2020] [Accepted: 04/28/2020] [Indexed: 05/20/2023]
40
Hoppe C, Bowles JR, Minchington TG, Sutcliffe C, Upadhyai P, Rattray M, Ashe HL. Modulation of the Promoter Activation Rate Dictates the Transcriptional Response to Graded BMP Signaling Levels in the Drosophila Embryo. Dev Cell 2020;54:727-741.e7. [PMID: 32758422 PMCID: PMC7527239 DOI: 10.1016/j.devcel.2020.07.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 05/13/2020] [Accepted: 07/11/2020] [Indexed: 01/08/2023]
41
SIR2 Expression Noise Can Generate Heterogeneity in Viability but Does Not Affect Cell-to-Cell Epigenetic Silencing of Subtelomeric URA3 in Yeast. G3-GENES GENOMES GENETICS 2020;10:3435-3443. [PMID: 32727919 PMCID: PMC7466964 DOI: 10.1534/g3.120.401589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
42
Stochastic allelic expression as trigger for contractile imbalance in hypertrophic cardiomyopathy. Biophys Rev 2020;12:1055-1064. [PMID: 32661905 PMCID: PMC7429642 DOI: 10.1007/s12551-020-00719-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 07/02/2020] [Indexed: 12/17/2022]  Open
43
Triqueneaux G, Burny C, Symmons O, Janczarski S, Gruffat H, Yvert G. Cell-to-cell expression dispersion of B-cell surface proteins is linked to genetic variants in humans. Commun Biol 2020;3:346. [PMID: 32620900 PMCID: PMC7335051 DOI: 10.1038/s42003-020-1075-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 06/12/2020] [Indexed: 01/02/2023]  Open
44
Rodriguez J, Larson DR. Transcription in Living Cells: Molecular Mechanisms of Bursting. Annu Rev Biochem 2020;89:189-212. [DOI: 10.1146/annurev-biochem-011520-105250] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
45
Dhillon N, Shelansky R, Townshend B, Jain M, Boeger H, Endy D, Kamakaka R. Permutational analysis of Saccharomyces cerevisiae regulatory elements. Synth Biol (Oxf) 2020;5:ysaa007. [PMID: 32775697 PMCID: PMC7402160 DOI: 10.1093/synbio/ysaa007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/12/2020] [Accepted: 05/29/2020] [Indexed: 01/24/2023]  Open
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Ochiai H, Hayashi T, Umeda M, Yoshimura M, Harada A, Shimizu Y, Nakano K, Saitoh N, Liu Z, Yamamoto T, Okamura T, Ohkawa Y, Kimura H, Nikaido I. Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells. SCIENCE ADVANCES 2020;6:eaaz6699. [PMID: 32596448 PMCID: PMC7299619 DOI: 10.1126/sciadv.aaz6699] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 03/25/2020] [Indexed: 05/03/2023]
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Dhar R. Role of Mitochondria in Generation of Phenotypic Heterogeneity in Yeast. J Indian Inst Sci 2020. [DOI: 10.1007/s41745-020-00176-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Engl C, Jovanovic G, Brackston RD, Kotta-Loizou I, Buck M. The route to transcription initiation determines the mode of transcriptional bursting in E. coli. Nat Commun 2020;11:2422. [PMID: 32415118 PMCID: PMC7229158 DOI: 10.1038/s41467-020-16367-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 04/24/2020] [Indexed: 11/20/2022]  Open
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Sun M, Zhang J. Allele-specific single-cell RNA sequencing reveals different architectures of intrinsic and extrinsic gene expression noises. Nucleic Acids Res 2020;48:533-547. [PMID: 31799601 PMCID: PMC6954418 DOI: 10.1093/nar/gkz1134] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/19/2019] [Accepted: 11/20/2019] [Indexed: 01/13/2023]  Open
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Ham L, Brackston RD, Stumpf MPH. Extrinsic Noise and Heavy-Tailed Laws in Gene Expression. PHYSICAL REVIEW LETTERS 2020;124:108101. [PMID: 32216388 DOI: 10.1103/physrevlett.124.108101] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
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