Encounter times of chromatin loci influenced by polymer decondensation
Name
PhysRevE.97.032417.pdf
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366.24 KB
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Adobe PDF
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Author(s)
Holcman, D.
Amitai, Assaf
Date Issued
March 2018
Journal
Physical Review E
Publisher
American Physical Society
Citation
Amitai, A. and D. Holcman. "Encounter times of chromatin loci influenced by polymer decondensation." Physical Review E 97, 3 (March 2018): 032417 © 2018 American Physical Society
Version
Final published version
Abstract
The time for a DNA sequence to find its homologous counterpart depends on a long random search inside the cell nucleus. Using polymer models, we compute here the mean first encounter time (MFET) between two sites located on two different polymer chains and confined locally by potential wells. We find that reducing tethering forces acting on the polymers results in local decondensation, and numerical simulations of the polymer model show that these changes are associated with a reduction of the MFET by several orders of magnitude. We derive here new asymptotic formula for the MFET, confirmed by Brownian simulations. We conclude from the present modeling approach that the fast search for homology is mediated by a local chromatin decondensation due to the release of multiple chromatin tethering forces. The present scenario could explain how the homologous recombination pathway for double-stranded DNA repair is controlled by its random search step.
MIT Department
Institute for Medical Engineering and Science
Massachusetts Institute of Technology. Department of Chemical Engineering
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Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.
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DOI of Published Version
https://doi.org/10.1103/PhysRevE.97.032417
