Genome-wide chromatin remodeling identified at GC-rich long nucleosome-free regions.

To gain deeper insights into principles of cell biology, it is essential to understand how cells reorganize their genomes by chromatin remodeling. We analyzed chromatin remodeling on next generation sequencing data from resting and activated T cells to determine a whole-genome chromatin remodeling l...

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Autores principales:	Karin Schwarzbauer, Ulrich Bodenhofer, Sepp Hochreiter
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/da26f7430e43405f8252ab39e4bb14ad
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spelling	oai:doaj.org-article:da26f7430e43405f8252ab39e4bb14ad2021-11-18T08:10:00ZGenome-wide chromatin remodeling identified at GC-rich long nucleosome-free regions.1932-620310.1371/journal.pone.0047924https://doaj.org/article/da26f7430e43405f8252ab39e4bb14ad2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23144837/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203To gain deeper insights into principles of cell biology, it is essential to understand how cells reorganize their genomes by chromatin remodeling. We analyzed chromatin remodeling on next generation sequencing data from resting and activated T cells to determine a whole-genome chromatin remodeling landscape. We consider chromatin remodeling in terms of nucleosome repositioning which can be observed most robustly in long nucleosome-free regions (LNFRs) that are occupied by nucleosomes in another cell state. We found that LNFR sequences are either AT-rich or GC-rich, where nucleosome repositioning was observed much more prominently in GC-rich LNFRs - a considerable proportion of them outside promoter regions. Using support vector machines with string kernels, we identified a GC-rich DNA sequence pattern indicating loci of nucleosome repositioning in resting T cells. This pattern appears to be also typical for CpG islands. We found out that nucleosome repositioning in GC-rich LNFRs is indeed associated with CpG islands and with binding sites of the CpG-island-binding ZF-CXXC proteins KDM2A and CFP1. That this association occurs prominently inside and also prominently outside of promoter regions hints at a mechanism governing nucleosome repositioning that acts on a whole-genome scale.Karin SchwarzbauerUlrich BodenhoferSepp HochreiterPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 11, p e47924 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Karin Schwarzbauer Ulrich Bodenhofer Sepp Hochreiter Genome-wide chromatin remodeling identified at GC-rich long nucleosome-free regions.
description	To gain deeper insights into principles of cell biology, it is essential to understand how cells reorganize their genomes by chromatin remodeling. We analyzed chromatin remodeling on next generation sequencing data from resting and activated T cells to determine a whole-genome chromatin remodeling landscape. We consider chromatin remodeling in terms of nucleosome repositioning which can be observed most robustly in long nucleosome-free regions (LNFRs) that are occupied by nucleosomes in another cell state. We found that LNFR sequences are either AT-rich or GC-rich, where nucleosome repositioning was observed much more prominently in GC-rich LNFRs - a considerable proportion of them outside promoter regions. Using support vector machines with string kernels, we identified a GC-rich DNA sequence pattern indicating loci of nucleosome repositioning in resting T cells. This pattern appears to be also typical for CpG islands. We found out that nucleosome repositioning in GC-rich LNFRs is indeed associated with CpG islands and with binding sites of the CpG-island-binding ZF-CXXC proteins KDM2A and CFP1. That this association occurs prominently inside and also prominently outside of promoter regions hints at a mechanism governing nucleosome repositioning that acts on a whole-genome scale.
format	article
author	Karin Schwarzbauer Ulrich Bodenhofer Sepp Hochreiter
author_facet	Karin Schwarzbauer Ulrich Bodenhofer Sepp Hochreiter
author_sort	Karin Schwarzbauer
title	Genome-wide chromatin remodeling identified at GC-rich long nucleosome-free regions.
title_short	Genome-wide chromatin remodeling identified at GC-rich long nucleosome-free regions.
title_full	Genome-wide chromatin remodeling identified at GC-rich long nucleosome-free regions.
title_fullStr	Genome-wide chromatin remodeling identified at GC-rich long nucleosome-free regions.
title_full_unstemmed	Genome-wide chromatin remodeling identified at GC-rich long nucleosome-free regions.
title_sort	genome-wide chromatin remodeling identified at gc-rich long nucleosome-free regions.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/da26f7430e43405f8252ab39e4bb14ad
work_keys_str_mv	AT karinschwarzbauer genomewidechromatinremodelingidentifiedatgcrichlongnucleosomefreeregions AT ulrichbodenhofer genomewidechromatinremodelingidentifiedatgcrichlongnucleosomefreeregions AT sepphochreiter genomewidechromatinremodelingidentifiedatgcrichlongnucleosomefreeregions
_version_	1718422139966586880

Genome-wide chromatin remodeling identified at GC-rich long nucleosome-free regions.

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