Chromatin Loop Extrusion and Chromatin Unknotting.

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Version: Final published version
License: CC BY 4.0
Serval ID
serval:BIB_381D19E8C38F
Type
Article: article from journal or magazin.
Collection
Publications
Title
Chromatin Loop Extrusion and Chromatin Unknotting.
Journal
Polymers
Author(s)
Racko D., Benedetti F., Goundaroulis D., Stasiak A.
ISSN
2073-4360 (Electronic)
ISSN-L
2073-4360
Publication state
Published
Issued date
11/10/2018
Peer-reviewed
Oui
Volume
10
Number
10
Pages
1126
Language
english
Notes
Publication types: Journal Article
Publication Status: epublish
Abstract
It has been a puzzle how decondensed interphase chromosomes remain essentially unknotted. The natural expectation is that in the presence of type II DNA topoisomerases that permit passages of double-stranded DNA regions through each other, all chromosomes should reach the state of topological equilibrium. The topological equilibrium in highly crowded interphase chromosomes forming chromosome territories would result in formation of highly knotted chromatin fibres. However, Chromosome Conformation Capture (3C) methods revealed that the decay of contact probabilities with the genomic distance in interphase chromosomes is practically the same as in the crumpled globule state that is formed when long polymers condense without formation of any knots. To remove knots from highly crowded chromatin, one would need an active process that should not only provide the energy to move the system from the state of topological equilibrium but also guide topoisomerase-mediated passages in such a way that knots would be efficiently unknotted instead of making the knots even more complex. We perform coarse-grained molecular dynamics simulations of the process of chromatin loop extrusion involving knotted and catenated chromatin fibres to check whether chromatin loop extrusion may be involved in active unknotting of chromatin fibres. Our simulations show that the process of chromatin loop extrusion is ideally suited to actively unknot, decatenate and demix chromatin fibres in interphase chromosomes.
Keywords
DNA knots, DNA topoisomerases, biopolymers, chromatin, chromatin loop extrusion, chromosomes, cohesin
Pubmed
Web of science
Open Access
Yes
Create date
19/11/2018 18:01
Last modification date
26/10/2019 5:09
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