Issue 45, 2009
From the journal:

Physical Chemistry Chemical Physics

Mesoscale simulations of two nucleosome-repeat length oligonucleosomes†

Tamar Schlick*a  and  Ognjen Perišića  

* Corresponding authors

a Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York
E-mail: schlick@nyu.edu
Fax: 212-995-4152
Tel: 212-998-3116

Abstract

The compaction of chromatin, accessed through coarse-grained modeling and simulation, reveals different folding patterns as a function of the nucleosome repeat length (NRL), the presence of the linker histone, and the ionic strength. Our results indicate that the linker histone has negligible influence on short NRL fibers, whereas for longer NRL fibers it works like, and in tandem with, concentrated positive counterions to condense the chromatin fiber. Longer NRL fibers also exhibit structural heterogeneity, with solenoid-like conformations viable in addition to irregular zigzags. These features of chromatin and associated internucleosomal patterns presented here help interpret structural dependencies of the chromatin fiber on internal and external factors. In particular, we suggest that longer-NRL are more advantageous for packing and achieving various levels of fiber compaction throughout the cell cycle.

Graphical abstract: Mesoscale simulations of two nucleosome-repeat length oligonucleosomes

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Article information

DOI
https://doi.org/10.1039/B918629H
Article type
Paper
Submitted
08 Sep 2009
Accepted
02 Oct 2009
First published
20 Oct 2009

Phys. Chem. Chem. Phys., 2009,11, 10729-10737

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Mesoscale simulations of two nucleosome-repeat length oligonucleosomes

T. Schlick and O. Perišić, Phys. Chem. Chem. Phys., 2009, 11, 10729 DOI: 10.1039/B918629H

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