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
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
369-376Informations 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