The disequilibrium of nucleosomes distribution along chromosomes plays a functional and evolutionarily role in regulating gene expression

Handle URI:
http://hdl.handle.net/10754/325293
Title:
The disequilibrium of nucleosomes distribution along chromosomes plays a functional and evolutionarily role in regulating gene expression
Authors:
Cui, Peng; Lin, Qiang; Zhang, Lingfang; Ding, Feng ( 0000-0001-8237-4062 ) ; Xin, Chengqi; Zhang, Daoyong; Sun, Fanglin; Hu, Songnian; Yu, Jun
Abstract:
To further understand the relationship between nucleosome-space occupancy (NO) and global transcriptional activity in mammals, we acquired a set of genome-wide nucleosome distribution and transcriptome data from the mouse cerebrum and testis based on ChIP (H3)-seq and RNA-seq, respectively. We identified a nearly consistent NO patterns among three mouse tissues-cerebrum, testis, and ESCs-and found, through clustering analysis for transcriptional activation, that the NO variations among chromosomes are closely associated with distinct expression levels between house-keeping (HK) genes and tissue-specific (TS) genes. Both TS and HK genes form clusters albeit the obvious majority. This feature implies that NO patterns, i.e. nucleosome binding and clustering, are coupled with gene clustering that may be functionally and evolutionarily conserved in regulating gene expression among different cell types. © 2011 Cui et al.
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
Cui P, Lin Q, Zhang L, Ding F, Xin C, et al. (2011) The Disequilibrium of Nucleosomes Distribution along Chromosomes Plays a Functional and Evolutionarily Role in Regulating Gene Expression. PLoS ONE 6: e23219. doi:10.1371/journal.pone.0023219.
Publisher:
Public Library of Science
Journal:
PLoS ONE
Issue Date:
19-Aug-2011
DOI:
10.1371/journal.pone.0023219
PubMed ID:
21886783
PubMed Central ID:
PMC3158759
Type:
Article
ISSN:
19326203
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorCui, Pengen
dc.contributor.authorLin, Qiangen
dc.contributor.authorZhang, Lingfangen
dc.contributor.authorDing, Fengen
dc.contributor.authorXin, Chengqien
dc.contributor.authorZhang, Daoyongen
dc.contributor.authorSun, Fanglinen
dc.contributor.authorHu, Songnianen
dc.contributor.authorYu, Junen
dc.date.accessioned2014-08-27T09:45:23Z-
dc.date.available2014-08-27T09:45:23Z-
dc.date.issued2011-08-19en
dc.identifier.citationCui P, Lin Q, Zhang L, Ding F, Xin C, et al. (2011) The Disequilibrium of Nucleosomes Distribution along Chromosomes Plays a Functional and Evolutionarily Role in Regulating Gene Expression. PLoS ONE 6: e23219. doi:10.1371/journal.pone.0023219.en
dc.identifier.issn19326203en
dc.identifier.pmid21886783en
dc.identifier.doi10.1371/journal.pone.0023219en
dc.identifier.urihttp://hdl.handle.net/10754/325293en
dc.description.abstractTo further understand the relationship between nucleosome-space occupancy (NO) and global transcriptional activity in mammals, we acquired a set of genome-wide nucleosome distribution and transcriptome data from the mouse cerebrum and testis based on ChIP (H3)-seq and RNA-seq, respectively. We identified a nearly consistent NO patterns among three mouse tissues-cerebrum, testis, and ESCs-and found, through clustering analysis for transcriptional activation, that the NO variations among chromosomes are closely associated with distinct expression levels between house-keeping (HK) genes and tissue-specific (TS) genes. Both TS and HK genes form clusters albeit the obvious majority. This feature implies that NO patterns, i.e. nucleosome binding and clustering, are coupled with gene clustering that may be functionally and evolutionarily conserved in regulating gene expression among different cell types. © 2011 Cui et al.en
dc.language.isoenen
dc.publisherPublic Library of Scienceen
dc.rightsCui et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en
dc.rightsArchived with thanks to PLoS ONEen
dc.subjecttranscriptomeen
dc.subjectanimal tissueen
dc.subjectcell functionen
dc.subjectcontrolled studyen
dc.subjectgene clusteren
dc.subjectgene expression regulationen
dc.subjectgene linkage disequilibriumen
dc.subjectgene mappingen
dc.subjectgenetic conservationen
dc.subjecthousekeeping geneen
dc.subjectmouseen
dc.subjectnucleosomeen
dc.subjectphenotypic variationen
dc.subjecttissue specificityen
dc.subjecttranscription initiationen
dc.subjecttranscription regulationen
dc.subjectantibody specificityen
dc.subjectBagg albino mouseen
dc.subjectcluster analysisen
dc.subjectessential geneen
dc.subjectgene expression regulationen
dc.subjectgenetic transcriptionen
dc.subjectgeneticsen
dc.subjectmetabolismen
dc.subjectmolecular evolutionen
dc.subjectMammaliaen
dc.subjectCluster Analysisen
dc.subjectEvolution, Molecularen
dc.subjectGene Expression Regulationen
dc.subjectGenes, Essentialen
dc.subjectMiceen
dc.subjectMice, Inbred BALB Cen
dc.subjectNucleosomesen
dc.subjectOrgan Specificityen
dc.subjectTranscription, Geneticen
dc.titleThe disequilibrium of nucleosomes distribution along chromosomes plays a functional and evolutionarily role in regulating gene expressionen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalPLoS ONEen
dc.identifier.pmcidPMC3158759en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionThe CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, Chinaen
dc.contributor.institutionInstitute of Epigenetics and Cancer Research, School of Medicine, Tsinghua University, Beijing, Chinaen
dc.contributor.institutionGraduate School of the Chinese Academy of Sciences, Beijing, Chinaen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorCui, Pengen
kaust.authorDing, Fengen

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