Genome-wide identification of autosomal genes with allelic imbalance of chromatin state

In mammals, monoallelic gene expression can result from X-chromosome inactivation, genomic imprinting, and random monoallelic expression (RMAE). Epigenetic regulation of RMAE is not fully understood. Here we analyze allelic imbalance in chromatin state of autosomal genes using ChIP-seq in a clonal c...

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Autores: Savol, Andrej J., Wang, Peggy I., Jeon, Yesu, Colognori, David, Yildirim, Eda, Pinter, Stefan F., Payer, Bernhard, Lee, Jeannie T., Sadreyev, Ruslan Ilyasovich
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2017
País:España
Institución:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/35149
Acceso en línea:http://hdl.handle.net/10230/35149
http://dx.doi.org/10.1371/journal.pone.0182568
Access Level:acceso abierto
Palabra clave:Gene expression
Chromatin
Histones
Inbred strains
DNA transcription
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spelling Genome-wide identification of autosomal genes with allelic imbalance of chromatin stateSavol, Andrej J.Wang, Peggy I.Jeon, YesuColognori, DavidYildirim, EdaPinter, Stefan F.Payer, BernhardLee, Jeannie T.Sadreyev, Ruslan IlyasovichGene expressionChromatinHistonesInbred strainsDNA transcriptionIn mammals, monoallelic gene expression can result from X-chromosome inactivation, genomic imprinting, and random monoallelic expression (RMAE). Epigenetic regulation of RMAE is not fully understood. Here we analyze allelic imbalance in chromatin state of autosomal genes using ChIP-seq in a clonal cell line. We identify approximately 3.7% of autosomal genes that show significant differences between chromatin states of two alleles. Allelic regulation is represented among several functional gene categories including histones, chromatin modifiers, and multiple early developmental regulators. Most cases of allelic skew are produced by quantitative differences between two allelic chromatic states that belong to the same gross type (active, silent, or bivalent). Combinations of allelic states of different types are possible but less frequent. When different chromatin marks are skewed on the same gene, their skew is coordinated as a result of quantitative relationships between these marks on each individual allele. Finally, combination of allele-specific densities of chromatin marks is a quantitative predictor of allelic skew in gene expression.Public Library of Science (PLoS)201820182017info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/35149http://dx.doi.org/10.1371/journal.pone.0182568reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésPLoS One. 2017 Aug 10;12(8):e0182568© 2017 Savol et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/351492026-06-12T07:21:37Z
dc.title.none.fl_str_mv Genome-wide identification of autosomal genes with allelic imbalance of chromatin state
title Genome-wide identification of autosomal genes with allelic imbalance of chromatin state
spellingShingle Genome-wide identification of autosomal genes with allelic imbalance of chromatin state
Savol, Andrej J.
Gene expression
Chromatin
Histones
Inbred strains
DNA transcription
title_short Genome-wide identification of autosomal genes with allelic imbalance of chromatin state
title_full Genome-wide identification of autosomal genes with allelic imbalance of chromatin state
title_fullStr Genome-wide identification of autosomal genes with allelic imbalance of chromatin state
title_full_unstemmed Genome-wide identification of autosomal genes with allelic imbalance of chromatin state
title_sort Genome-wide identification of autosomal genes with allelic imbalance of chromatin state
dc.creator.none.fl_str_mv Savol, Andrej J.
Wang, Peggy I.
Jeon, Yesu
Colognori, David
Yildirim, Eda
Pinter, Stefan F.
Payer, Bernhard
Lee, Jeannie T.
Sadreyev, Ruslan Ilyasovich
author Savol, Andrej J.
author_facet Savol, Andrej J.
Wang, Peggy I.
Jeon, Yesu
Colognori, David
Yildirim, Eda
Pinter, Stefan F.
Payer, Bernhard
Lee, Jeannie T.
Sadreyev, Ruslan Ilyasovich
author_role author
author2 Wang, Peggy I.
Jeon, Yesu
Colognori, David
Yildirim, Eda
Pinter, Stefan F.
Payer, Bernhard
Lee, Jeannie T.
Sadreyev, Ruslan Ilyasovich
author2_role author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Gene expression
Chromatin
Histones
Inbred strains
DNA transcription
topic Gene expression
Chromatin
Histones
Inbred strains
DNA transcription
description In mammals, monoallelic gene expression can result from X-chromosome inactivation, genomic imprinting, and random monoallelic expression (RMAE). Epigenetic regulation of RMAE is not fully understood. Here we analyze allelic imbalance in chromatin state of autosomal genes using ChIP-seq in a clonal cell line. We identify approximately 3.7% of autosomal genes that show significant differences between chromatin states of two alleles. Allelic regulation is represented among several functional gene categories including histones, chromatin modifiers, and multiple early developmental regulators. Most cases of allelic skew are produced by quantitative differences between two allelic chromatic states that belong to the same gross type (active, silent, or bivalent). Combinations of allelic states of different types are possible but less frequent. When different chromatin marks are skewed on the same gene, their skew is coordinated as a result of quantitative relationships between these marks on each individual allele. Finally, combination of allele-specific densities of chromatin marks is a quantitative predictor of allelic skew in gene expression.
publishDate 2017
dc.date.none.fl_str_mv 2017
2018
2018
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/35149
http://dx.doi.org/10.1371/journal.pone.0182568
url http://hdl.handle.net/10230/35149
http://dx.doi.org/10.1371/journal.pone.0182568
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv PLoS One. 2017 Aug 10;12(8):e0182568
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Public Library of Science (PLoS)
publisher.none.fl_str_mv Public Library of Science (PLoS)
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
repository.mail.fl_str_mv
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