Genomic 3D compartments emerge from unfolding mitotic chromosomes.
Chromosome decondensation
Hi-C
Nuclear structure
Polymer simulation
Journal
Chromosoma
ISSN: 1432-0886
Titre abrégé: Chromosoma
Pays: Austria
ID NLM: 2985138R
Informations de publication
Date de publication:
03 2019
03 2019
Historique:
received:
14
06
2018
accepted:
07
10
2018
revised:
04
10
2018
pubmed:
26
10
2018
medline:
9
8
2019
entrez:
26
10
2018
Statut:
ppublish
Résumé
The 3D organisation of the genome in interphase cells is not a randomly folded polymer. Rather, experiments show that chromosomes arrange into a network of 3D compartments that correlate with biological processes, such as transcription, chromatin modifications and protein binding. However, these compartments do not exist during cell division when the DNA is condensed, and it is unclear how and when they emerge. In this paper, we focus on the early stages after cell division as the chromosomes start to decondense. We use a simple polymer model to understand the types of 3D structures that emerge from local unfolding of a compact initial state. From simulations, we recover 3D compartments, such as TADs and A/B compartments that are consistently detected in chromosome capture experiments across cell types and organisms. This suggests that the large-scale 3D organisation is a result of an inflation process.
Identifiants
pubmed: 30357462
doi: 10.1007/s00412-018-0684-7
pii: 10.1007/s00412-018-0684-7
pmc: PMC6394678
doi:
Substances chimiques
DNA
9007-49-2
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Pagination
15-20Références
Chromosome Res. 2011 Jan;19(1):37-51
pubmed: 21274616
Science. 2009 Oct 9;326(5950):289-93
pubmed: 19815776
Nat Rev Mol Cell Biol. 2016 Dec;17(12):771-782
pubmed: 27826147
Nat Rev Genet. 2013 Jun;14(6):390-403
pubmed: 23657480
Semin Cancer Biol. 2013 Apr;23(2):90-8
pubmed: 23376421
Cell. 2017 Apr 6;169(2):216-228.e19
pubmed: 28388407
Nat Cell Biol. 2007 Jul;9(7):822-31
pubmed: 17558394
Nature. 2009 Nov 5;462(7269):58-64
pubmed: 19890323
J Cell Biol. 1998 Mar 9;140(5):975-89
pubmed: 9490713
Proc Natl Acad Sci U S A. 2010 Feb 2;107(5):2025-30
pubmed: 20080699
Nucleic Acids Res. 2017 Sep 29;45(17):e152
pubmed: 28973466
Int Rev Cell Mol Biol. 2014;307:275-349
pubmed: 24380598
Curr Opin Cell Biol. 2016 Jun;40:15-22
pubmed: 26895139
Genome Biol. 2009;10(4):R37
pubmed: 19374771
Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16173-8
pubmed: 22988072
Curr Opin Cell Biol. 2006 Dec;18(6):632-8
pubmed: 17046228
Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):E6456-65
pubmed: 26499245
Nat Rev Genet. 2001 Apr;2(4):292-301
pubmed: 11283701
Nature. 2012 Apr 11;485(7398):381-5
pubmed: 22495304
Proc Natl Acad Sci U S A. 1995 Mar 28;92(7):2710-4
pubmed: 7708711
Nat Rev Mol Cell Biol. 2004 Apr;5(4):296-304
pubmed: 15071554
Genes Dev. 2007 Dec 1;21(23):3027-43
pubmed: 18056419
Nat Struct Mol Biol. 2007 Nov;14(11):1049-55
pubmed: 17984967
Nature. 2012 Apr 11;485(7398):376-80
pubmed: 22495300
Mol Syst Biol. 2015 Dec 23;11(12):852
pubmed: 26700852
Science. 2013 Nov 22;342(6161):948-53
pubmed: 24200812