Topological interactions between ring polymers: Implications for chromatin loops

The Journal of Chemical Physics
Manfred Bohn, Dieter W Heermann

Abstract

Chromatin looping is a major epigenetic regulatory mechanism in higher eukaryotes. Besides its role in transcriptional regulation, chromatin loops have been proposed to play a pivotal role in the segregation of entire chromosomes. The detailed topological and entropic forces between loops still remain elusive. Here, we quantitatively determine the potential of mean force between the centers of mass of two ring polymers, i.e., loops. We find that the transition from a linear to a ring polymer induces a strong increase in the entropic repulsion between these two polymers. On top, topological interactions such as the noncatenation constraint further reduce the number of accessible conformations of close-by ring polymers by about 50%, resulting in an additional effective repulsion. Furthermore, the transition from linear to ring polymers displays changes in the conformational and structural properties of the system. In fact, ring polymers adopt a markedly more ordered and aligned state than linear ones. The forces and accompanying changes in shape and alignment between ring polymers suggest an important regulatory function of such a topology in biopolymers. We conjecture that dynamic loop formation in chromatin might act as a versa...Continue Reading

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Citations

Dec 6, 2012·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Songling Li, Dieter W Heermann
Jan 20, 2011·PloS One·Manfred Bohn, Dieter W Heermann
Jan 5, 2012·PloS One·Yang Zhang, Dieter W Heermann
Sep 15, 2011·The Journal of Chemical Physics·Maxim DolgushevAlexander Blumen
Nov 21, 2012·The Journal of Chemical Physics·Daniele CoslovichAngel J Moreno
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Oct 3, 2014·The Journal of Chemical Physics·Marta Montes-SaraleguiGerhard Kahl
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Apr 8, 2011·Current Opinion in Cell Biology·Dieter W Heermann
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Jun 3, 2017·Development, Growth & Differentiation·Takeshi Sugawara, Akatsuki Kimura
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Aug 2, 2014·ACS Macro Letters·Mohammed Zakaria SlimaniAngel J Moreno

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