Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations.

Cytosine methylation is one of the most important epigenetic marks that regulate the process of gene expression. Here, we have examined the effect of epigenetic DNA methylation on nucleosomal stability using molecular dynamics simulations and elastic deformation models. We found that methylation of...

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Autores principales:	Guillem Portella, Federica Battistini, Modesto Orozco
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/029f6b54fbd841eaafacdc02fb87eabd
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spelling	oai:doaj.org-article:029f6b54fbd841eaafacdc02fb87eabd2021-11-18T05:53:21ZUnderstanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations.1553-734X1553-735810.1371/journal.pcbi.1003354https://doaj.org/article/029f6b54fbd841eaafacdc02fb87eabd2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24278005/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Cytosine methylation is one of the most important epigenetic marks that regulate the process of gene expression. Here, we have examined the effect of epigenetic DNA methylation on nucleosomal stability using molecular dynamics simulations and elastic deformation models. We found that methylation of CpG steps destabilizes nucleosomes, especially when these are placed in sites where the DNA minor groove faces the histone core. The larger stiffness of methylated CpG steps is a crucial factor behind the decrease in nucleosome stability. Methylation changes the positioning and phasing of the nucleosomal DNA, altering the accessibility of DNA to regulatory proteins, and accordingly gene functionality. Our theoretical calculations highlight a simple physical-based explanation on the foundations of epigenetic signaling.Guillem PortellaFederica BattistiniModesto OrozcoPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 9, Iss 11, p e1003354 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Guillem Portella Federica Battistini Modesto Orozco Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations.
description	Cytosine methylation is one of the most important epigenetic marks that regulate the process of gene expression. Here, we have examined the effect of epigenetic DNA methylation on nucleosomal stability using molecular dynamics simulations and elastic deformation models. We found that methylation of CpG steps destabilizes nucleosomes, especially when these are placed in sites where the DNA minor groove faces the histone core. The larger stiffness of methylated CpG steps is a crucial factor behind the decrease in nucleosome stability. Methylation changes the positioning and phasing of the nucleosomal DNA, altering the accessibility of DNA to regulatory proteins, and accordingly gene functionality. Our theoretical calculations highlight a simple physical-based explanation on the foundations of epigenetic signaling.
format	article
author	Guillem Portella Federica Battistini Modesto Orozco
author_facet	Guillem Portella Federica Battistini Modesto Orozco
author_sort	Guillem Portella
title	Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations.
title_short	Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations.
title_full	Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations.
title_fullStr	Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations.
title_full_unstemmed	Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations.
title_sort	understanding the connection between epigenetic dna methylation and nucleosome positioning from computer simulations.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/029f6b54fbd841eaafacdc02fb87eabd
work_keys_str_mv	AT guillemportella understandingtheconnectionbetweenepigeneticdnamethylationandnucleosomepositioningfromcomputersimulations AT federicabattistini understandingtheconnectionbetweenepigeneticdnamethylationandnucleosomepositioningfromcomputersimulations AT modestoorozco understandingtheconnectionbetweenepigeneticdnamethylationandnucleosomepositioningfromcomputersimulations
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Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations.

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