Chromatin Compaction Multiscale Modeling: A Complex Synergy Between Theory, Simulation, and Experiment

Frontiers in Molecular Biosciences
Artemi BendandiWalter Rocchia

Abstract

Understanding the mechanisms that trigger chromatin compaction, its patterns, and the factors they depend on, is a fundamental and still open question in Biology. Chromatin compacts and reinforces DNA and is a stable but dynamic structure, to make DNA accessible to proteins. In recent years, computational advances have provided larger amounts of data and have made large-scale simulations more viable. Experimental techniques for the extraction and reconstitution of chromatin fibers have improved, reinvigorating theoretical and experimental interest in the topic and stimulating debate on points previously considered as certainties regarding chromatin. A great assortment of approaches has emerged, from all-atom single-nucleosome or oligonucleosome simulations to various degrees of coarse graining, to polymer models, to fractal-like structures and purely topological models. Different fiber-start patterns have been studied in theory and experiment, as well as different linker DNA lengths. DNA is a highly charged macromolecule, making ionic and electrostatic interactions extremely important for chromatin topology and dynamics. Indeed, the repercussions of varying ionic concentration have been extensively examined at the computational...Continue Reading

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Citations

Feb 25, 2021·Physical Chemistry Chemical Physics : PCCP·Konstantin Röder
Mar 10, 2021·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·S W BotchwayM Yusuf
Nov 23, 2020·Journal of Molecular Biology·Daniël P Melters, Yamini Dalal
Mar 30, 2021·NAR Genomics and Bioinformatics·Julen Mendieta-EstebanMarc A Marti-Renom
Apr 6, 2021·Current Opinion in Plant Biology·Célia Baroux
May 7, 2021·Nature Reviews. Molecular Cell Biology·Ivana Jerkovic, Giacomo Cavalli
Aug 24, 2021·Nature Computational Science·Tamar Schlick, Stephanie Portillo-Ledesma
Jul 10, 2021·The Journal of Chemical Physics·Xingcheng LinBin Zhang

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Methods Mentioned

BETA
Hi-C
Atomic Force Microscopy
X-ray
AFM
FCS
NMR
Fluorescence
optical microscopy
super-resolution microscopy
fluorescence microscopy

Software Mentioned

SAXS
DelPhi
NanoShaper
MC
VMD
STORM
Hi

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