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For: Brown CR, Mao C, Falkovskaia E, Jurica MS, Boeger H. Linking stochastic fluctuations in chromatin structure and gene expression. PLoS Biol 2013;11:e1001621. [PMID: 23940458 DOI: 10.1371/journal.pbio.1001621] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 06/24/2013] [Indexed: 01/16/2023]  Open
Number Cited by Other Article(s)
1
Liu X, Chang Z, Sun P, Cao B, Wang Y, Fang J, Pei Y, Chen B, Zou W. MONITTR allows real-time imaging of transcription and endogenous proteins in C. elegans. J Cell Biol 2025;224:e202403198. [PMID: 39400293 PMCID: PMC11473600 DOI: 10.1083/jcb.202403198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 08/26/2024] [Accepted: 09/24/2024] [Indexed: 10/15/2024]  Open
2
Dhillon N, Kamakaka RT. Transcriptional silencing in Saccharomyces cerevisiae: known unknowns. Epigenetics Chromatin 2024;17:28. [PMID: 39272151 PMCID: PMC11401328 DOI: 10.1186/s13072-024-00553-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Accepted: 09/02/2024] [Indexed: 09/15/2024]  Open
3
Trzaskoma P, Jung S, Pękowska A, Bohrer CH, Wang X, Naz F, Dell’Orso S, Dubois WD, Olivera A, Vartak SV, Zhao Y, Nayak S, Overmiller A, Morasso MI, Sartorelli V, Larson DR, Chow CC, Casellas R, O’Shea JJ. 3D chromatin architecture, BRD4, and Mediator have distinct roles in regulating genome-wide transcriptional bursting and gene network. SCIENCE ADVANCES 2024;10:eadl4893. [PMID: 39121214 PMCID: PMC11313860 DOI: 10.1126/sciadv.adl4893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 07/08/2024] [Indexed: 08/11/2024]
4
Whitney PH, Lionnet T. The method in the madness: Transcriptional control from stochastic action at the single-molecule scale. Curr Opin Struct Biol 2024;87:102873. [PMID: 38954990 PMCID: PMC11373363 DOI: 10.1016/j.sbi.2024.102873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/07/2024] [Accepted: 06/05/2024] [Indexed: 07/04/2024]
5
Shelansky R, Abrahamsson S, Brown CR, Doody M, Lenstra TL, Larson DR, Boeger H. Single gene analysis in yeast suggests nonequilibrium regulatory dynamics for transcription. Nat Commun 2024;15:6226. [PMID: 39043639 PMCID: PMC11266658 DOI: 10.1038/s41467-024-50419-5] [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: 08/22/2023] [Accepted: 07/04/2024] [Indexed: 07/25/2024]  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
Sahoo S, Kadam S, Padinhateeri R, Kumar PBS. Nonequilibrium switching of segmental states can influence compaction of chromatin. SOFT MATTER 2024;20:4621-4632. [PMID: 38819321 DOI: 10.1039/d4sm00274a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
8
Ayyamperumal P, Naik HC, Naskar AJ, Bammidi LS, Gayen S. Epigenomic states contribute to coordinated allelic transcriptional bursting in iPSC reprogramming. Life Sci Alliance 2024;7:e202302337. [PMID: 38320809 PMCID: PMC10847334 DOI: 10.26508/lsa.202302337] [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: 08/24/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024]  Open
9
Bai G, Dhillon N, Felton C, Meissner B, Saint-John B, Shelansky R, Meyerson E, Hrabeta-Robinson E, Hodjat B, Boeger H, Brooks AN. Probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585815. [PMID: 38562899 PMCID: PMC10983977 DOI: 10.1101/2024.03.20.585815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
10
Chanou A, Weiβ M, Holler K, Sajid A, Straub T, Krietsch J, Sanchi A, Ummethum H, Lee CSK, Kruse E, Trauner M, Werner M, Lalonde M, Lopes M, Scialdone A, Hamperl S. Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency. Nucleic Acids Res 2023;51:12303-12324. [PMID: 37956271 PMCID: PMC10711542 DOI: 10.1093/nar/gkad1022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 10/12/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023]  Open
11
Wu R, Zhou B, Wang W, Liu F. Regulatory Mechanisms for Transcriptional Bursting Revealed by an Event-Based Model. RESEARCH (WASHINGTON, D.C.) 2023;6:0253. [PMID: 39290237 PMCID: PMC11407585 DOI: 10.34133/research.0253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/01/2023] [Indexed: 09/19/2024]
12
Quantifying how promoter-associated nucleosomes regulate transcriptional bursting. Nat Struct Mol Biol 2023;30:577-578. [PMID: 37130986 DOI: 10.1038/s41594-023-00982-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
13
Brouwer I, Kerklingh E, van Leeuwen F, Lenstra TL. Dynamic epistasis analysis reveals how chromatin remodeling regulates transcriptional bursting. Nat Struct Mol Biol 2023;30:692-702. [PMID: 37127821 DOI: 10.1038/s41594-023-00981-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/30/2023] [Indexed: 05/03/2023]
14
Sheu KM, Guru AA, Hoffmann A. Quantifying stimulus-response specificity to probe the functional state of macrophages. Cell Syst 2023;14:180-195.e5. [PMID: 36657439 PMCID: PMC10023480 DOI: 10.1016/j.cels.2022.12.012] [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: 06/01/2022] [Revised: 10/05/2022] [Accepted: 12/22/2022] [Indexed: 01/19/2023]
15
Levinsohn J, Li S, Ha E, Susztak K. Combing Genome-Wide Association Studies and Single-Cell Analysis to Elucidate the Mechanisms of Kidney Disease: Proceedings of the Henry Shavelle Professorship. GLOMERULAR DISEASES 2023;3:258-265. [PMID: 38033715 PMCID: PMC10686632 DOI: 10.1159/000534678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/13/2023] [Indexed: 12/02/2023]
16
Halder K, Chaudhuri A, Abdin MZ, Majee M, Datta A. Chromatin-Based Transcriptional Reprogramming in Plants under Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2022;11:1449. [PMID: 35684223 PMCID: PMC9182740 DOI: 10.3390/plants11111449] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 06/15/2023]
17
Huertas J, Woods EJ, Collepardo-Guevara R. Multiscale modelling of chromatin organisation: Resolving nucleosomes at near-atomistic resolution inside genes. Curr Opin Cell Biol 2022;75:102067. [DOI: 10.1016/j.ceb.2022.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/24/2022] [Accepted: 02/04/2022] [Indexed: 12/15/2022]
18
Boeger H. Kinetic Proofreading. Annu Rev Biochem 2022;91:423-447. [PMID: 35363508 DOI: 10.1146/annurev-biochem-040320-103630] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
19
Merkl PE, Schächner C, Pilsl M, Schwank K, Hergert K, Längst G, Milkereit P, Griesenbeck J, Tschochner H. Analysis of Yeast RNAP I Transcription of Nucleosomal Templates In Vitro. Methods Mol Biol 2022;2533:39-59. [PMID: 35796981 PMCID: PMC9761914 DOI: 10.1007/978-1-0716-2501-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
20
Xiong K, Gerstein M, Masel J. Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate pulses. Genetics 2021;219:6358726. [PMID: 34740240 DOI: 10.1093/genetics/iyab140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 08/17/2021] [Indexed: 01/02/2023]  Open
21
Van Dyke K, Lutz S, Mekonnen G, Myers CL, Albert FW. Trans-acting genetic variation affects the expression of adjacent genes. Genetics 2021;217:6126816. [PMID: 33789351 DOI: 10.1093/genetics/iyaa051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/16/2020] [Indexed: 11/13/2022]  Open
22
Garbuzov FE, Gursky VV. Nonequilibrium model of short-range repression in gene transcription regulation. Phys Rev E 2021;104:014407. [PMID: 34412298 DOI: 10.1103/physreve.104.014407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 06/24/2021] [Indexed: 11/07/2022]
23
Chanou A, Hamperl S. Single-Molecule Techniques to Study Chromatin. Front Cell Dev Biol 2021;9:699771. [PMID: 34291054 PMCID: PMC8287188 DOI: 10.3389/fcell.2021.699771] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 05/26/2021] [Indexed: 12/14/2022]  Open
24
Farr SE, Woods EJ, Joseph JA, Garaizar A, Collepardo-Guevara R. Nucleosome plasticity is a critical element of chromatin liquid-liquid phase separation and multivalent nucleosome interactions. Nat Commun 2021;12:2883. [PMID: 34001913 PMCID: PMC8129070 DOI: 10.1038/s41467-021-23090-3] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/23/2021] [Indexed: 12/19/2022]  Open
25
Crooijmans ME, Delzenne TO, Hensen T, Darehei M, de Winde JH, van Heusden GPH. Cell-to-cell heterogeneity of phosphate gene expression in yeast is controlled by alternative transcription, 14-3-3 and Spl2. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021;1864:194714. [PMID: 33971368 DOI: 10.1016/j.bbagrm.2021.194714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 11/25/2022]
26
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
27
Wolff MR, Schmid A, Korber P, Gerland U. Effective dynamics of nucleosome configurations at the yeast PHO5 promoter. eLife 2021;10:58394. [PMID: 33666171 PMCID: PMC8004102 DOI: 10.7554/elife.58394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 03/04/2021] [Indexed: 12/11/2022]  Open
28
Multifaceted Chromatin Structure and Transcription Changes in Plant Stress Response. Int J Mol Sci 2021;22:ijms22042013. [PMID: 33670556 PMCID: PMC7922328 DOI: 10.3390/ijms22042013] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 01/06/2023]  Open
29
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
30
Wong F, Gunawardena J. Gene Regulation in and out of Equilibrium. Annu Rev Biophys 2020;49:199-226. [PMID: 32375018 DOI: 10.1146/annurev-biophys-121219-081542] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
31
Vasdekis AE, Singh A. Microbial metabolic noise. WIREs Mech Dis 2020;13:e1512. [PMID: 33225608 DOI: 10.1002/wsbm.1512] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 09/23/2020] [Accepted: 10/26/2020] [Indexed: 11/06/2022]
32
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
33
Sullivan KM, Susztak K. Unravelling the complex genetics of common kidney diseases: from variants to mechanisms. Nat Rev Nephrol 2020;16:628-640. [PMID: 32514149 PMCID: PMC8014547 DOI: 10.1038/s41581-020-0298-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2020] [Indexed: 12/20/2022]
34
Zeitlinger J. Seven myths of how transcription factors read the cis-regulatory code. CURRENT OPINION IN SYSTEMS BIOLOGY 2020;23:22-31. [PMID: 33134611 PMCID: PMC7592701 DOI: 10.1016/j.coisb.2020.08.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
35
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
36
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]
37
Llorà-Batlle O, Tintó-Font E, Cortés A. Transcriptional variation in malaria parasites: why and how. Brief Funct Genomics 2020;18:329-341. [PMID: 31114839 DOI: 10.1093/bfgp/elz009] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/04/2019] [Accepted: 04/10/2019] [Indexed: 12/24/2022]  Open
38
Rodrigo G. Ab initio scaling laws between noise and mean of gene expression. Phys Rev E 2020;100:032415. [PMID: 31640034 DOI: 10.1103/physreve.100.032415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Indexed: 12/17/2022]
39
Nucleosomal proofreading of activator-promoter interactions. Proc Natl Acad Sci U S A 2020;117:2456-2461. [PMID: 31964832 DOI: 10.1073/pnas.1911188117] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
40
Xu H, Liu JJ, Liu Z, Li Y, Jin YS, Zhang J. Synchronization of stochastic expressions drives the clustering of functionally related genes. SCIENCE ADVANCES 2019;5:eaax6525. [PMID: 31633028 PMCID: PMC6785257 DOI: 10.1126/sciadv.aax6525] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/10/2019] [Indexed: 05/18/2023]
41
Smirnov E, Hornáček M, Vacík T, Cmarko D, Raška I. Discontinuous transcription. Nucleus 2019;9:149-160. [PMID: 29285985 PMCID: PMC5973254 DOI: 10.1080/19491034.2017.1419112] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]  Open
42
Sun M, Zhang J. Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells. PLoS Genet 2019;15:e1008389. [PMID: 31525198 PMCID: PMC6762216 DOI: 10.1371/journal.pgen.1008389] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/26/2019] [Accepted: 08/28/2019] [Indexed: 12/31/2022]  Open
43
Feed-forward regulation adaptively evolves via dynamics rather than topology when there is intrinsic noise. Nat Commun 2019;10:2418. [PMID: 31160574 PMCID: PMC6546794 DOI: 10.1038/s41467-019-10388-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 05/09/2019] [Indexed: 12/17/2022]  Open
44
Donovan BT, Huynh A, Ball DA, Patel HP, Poirier MG, Larson DR, Ferguson ML, Lenstra TL. Live-cell imaging reveals the interplay between transcription factors, nucleosomes, and bursting. EMBO J 2019;38:embj.2018100809. [PMID: 31101674 DOI: 10.15252/embj.2018100809] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 04/12/2019] [Accepted: 04/25/2019] [Indexed: 12/19/2022]  Open
45
de Jong TV, Moshkin YM, Guryev V. Gene expression variability: the other dimension in transcriptome analysis. Physiol Genomics 2019;51:145-158. [DOI: 10.1152/physiolgenomics.00128.2018] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
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Nikopoulou C, Parekh S, Tessarz P. Ageing and sources of transcriptional heterogeneity. Biol Chem 2019;400:867-878. [DOI: 10.1515/hsz-2018-0449] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/27/2019] [Indexed: 12/14/2022]
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Bernheim-Groswasser A, Gov NS, Safran SA, Tzlil S. Living Matter: Mesoscopic Active Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018;30:e1707028. [PMID: 30256463 DOI: 10.1002/adma.201707028] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/27/2018] [Indexed: 06/08/2023]
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Pichon X, Lagha M, Mueller F, Bertrand E. A Growing Toolbox to Image Gene Expression in Single Cells: Sensitive Approaches for Demanding Challenges. Mol Cell 2018;71:468-480. [DOI: 10.1016/j.molcel.2018.07.022] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/21/2022]
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Nicolas D, Zoller B, Suter DM, Naef F. Modulation of transcriptional burst frequency by histone acetylation. Proc Natl Acad Sci U S A 2018;115:7153-7158. [PMID: 29915087 PMCID: PMC6142243 DOI: 10.1073/pnas.1722330115] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
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Bameta T, Das D, Padinhateeri R. Coupling of replisome movement with nucleosome dynamics can contribute to the parent-daughter information transfer. Nucleic Acids Res 2018;46:4991-5000. [PMID: 29850895 PMCID: PMC6007630 DOI: 10.1093/nar/gky207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 03/09/2018] [Indexed: 01/09/2023]  Open
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