Transcriptional Bursts in a Nonequilibrium Model for Gene Regulation by Supercoiling.


Journal

Biophysical journal
ISSN: 1542-0086
Titre abrégé: Biophys J
Pays: United States
ID NLM: 0370626

Informations de publication

Date de publication:
23 07 2019
Historique:
received: 22 03 2019
accepted: 11 04 2019
pubmed: 20 5 2019
medline: 12 9 2020
entrez: 20 5 2019
Statut: ppublish

Résumé

We analyze transcriptional bursting within a stochastic nonequilibrium model, which accounts for the coupling between the dynamics of DNA supercoiling and gene transcription. We find a clear signature of bursty transcription when there is a separation between the timescales of transcription initiation and supercoiling dissipation (the latter may either be diffusive or mediated by topological enzymes, such as type I or type II topoisomerases). In multigenic DNA domains, we observe either bursty transcription or transcription waves; the type of behavior can be selected for by controlling gene activity and orientation. In the bursty phase, the statistics of supercoiling fluctuations at the promoter are markedly non-Gaussian.

Identifiants

pubmed: 31103229
pii: S0006-3495(19)30342-X
doi: 10.1016/j.bpj.2019.04.023
pmc: PMC6702136
pii:
doi:

Substances chimiques

DNA, Superhelical 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

369-376

Informations de copyright

Copyright © 2019. Published by Elsevier Inc.

Références

J Mol Biol. 1999 Sep 10;292(1):19-37
pubmed: 10493854
Proc Natl Acad Sci U S A. 1999 Dec 7;96(25):14294-9
pubmed: 10588699
FASEB J. 2000 Feb;14(2):242-54
pubmed: 10657981
Nucleic Acids Res. 2004 Jun 03;32(10):3040-52
pubmed: 15178741
Mol Microbiol. 2005 Jan;55(2):601-10
pubmed: 15659173
Cell. 2005 Dec 16;123(6):1025-36
pubmed: 16360033
Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Aug;76(2 Pt 1):021926
pubmed: 17930084
BMC Genomics. 2008 Feb 27;9:102
pubmed: 18304323
Science. 2008 Apr 4;320(5872):65-8
pubmed: 18388284
PLoS Comput Biol. 2008 Jul 11;4(7):e1000109
pubmed: 18617999
Cell. 2008 Oct 17;135(2):216-26
pubmed: 18957198
Proc Natl Acad Sci U S A. 2009 Feb 24;106(8):2583-8
pubmed: 19196995
PLoS One. 2010 Nov 16;5(11):e15442
pubmed: 21103382
Science. 2011 Apr 22;332(6028):472-4
pubmed: 21415320
Nature. 2011 May 19;473(7347):337-42
pubmed: 21593866
Nucleic Acids Res. 2012 Nov 1;40(20):10432-40
pubmed: 22923519
Science. 2012 Oct 5;338(6103):94-7
pubmed: 22983709
Nat Struct Mol Biol. 2013 Mar;20(3):387-95
pubmed: 23416946
Nat Struct Mol Biol. 2013 Mar;20(3):396-403
pubmed: 23416947
Cell. 2014 Jul 17;158(2):314-326
pubmed: 25036631
PLoS Comput Biol. 2015 Oct 16;11(10):e1004292
pubmed: 26474290
Elife. 2016 Feb 20;5:
pubmed: 26896676
Cell. 2016 Jul 14;166(2):358-368
pubmed: 27293191
Phys Rev Lett. 2016 Jul 1;117(1):018101
pubmed: 27419594
Phys Rev E. 2016 Sep;94(3-1):032133
pubmed: 27739741
Proc Natl Acad Sci U S A. 1987 Oct;84(20):7024-7
pubmed: 2823250
Phys Rev Lett. 2017 Oct 13;119(15):158002
pubmed: 29077467
Nucleic Acids Res. 2018 Jul 6;46(12):5924-5934
pubmed: 29860397
Cell. 1986 Jul 4;46(1):115-22
pubmed: 3459589
Biochemistry. 1981 Nov 24;20(24):6929-48
pubmed: 7317363

Auteurs

Marco Ancona (M)

SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom. Electronic address: mar.ancona92@gmail.com.

Alessandro Bentivoglio (A)

SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom.

Chris A Brackley (CA)

SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom.

Giuseppe Gonnella (G)

Dipartimento di Fisica, INFN, Università degli Studi di Bari Aldo Moro, Sezione di Bari, Bari, Italy.

Davide Marenduzzo (D)

SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom.

Articles similaires

A computational model for bacteriophage ϕX174 gene expression.

Alexis M Hill, Tanvi A Ingle, Claus O Wilke
1.00
Gene Expression Regulation, Viral Promoter Regions, Genetic Bacteriophage phi X 174 Computer Simulation Models, Genetic
Animals Cattle Female Fertility Gene-Environment Interaction
Mycobacterium tuberculosis Animals Guinea Pigs Bacterial Proteins Toxin-Antitoxin Systems

Clr4

Hyun-Soo Kim, Benjamin Roche, Sonali Bhattacharjee et al.
1.00
Schizosaccharomyces pombe Proteins Schizosaccharomyces Heterochromatin Ubiquitination Cell Cycle Proteins

Classifications MeSH