The disequilibrium of nucleosomes distribution along chromosomes plays a functional and evolutionarily role in regulating gene expression
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KAUST DepartmentComputational Bioscience Research Center (CBRC)
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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.
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.
PublisherPublic Library of Science (PLoS)
PubMed Central IDPMC3158759
- A novel mechanism of epigenetic regulation: nucleosome-space occupancy.
- Authors: Cui P, Zhang L, Lin Q, Ding F, Xin C, Fang X, Hu S, Yu J
- Issue date: 2010 Jan 1
- Evolution of nucleosome occupancy: conservation of global properties and divergence of gene-specific patterns.
- Authors: Tsui K, Dubuis S, Gebbia M, Morse RH, Barkai N, Tirosh I, Nislow C
- Issue date: 2011 Nov
- Identification and analysis of house-keeping and tissue-specific genes based on RNA-seq data sets across 15 mouse tissues.
- Authors: Zeng J, Liu S, Zhao Y, Tan X, Aljohi HA, Liu W, Hu S
- Issue date: 2016 Jan 15
- Insights into distinct regulatory modes of nucleosome positioning.
- Authors: Dai Z, Dai X, Xiang Q, Feng J, Deng Y, Wang J
- Issue date: 2009 Dec 14
- Genome-wide transcriptome mapping analysis identifies organ-specific gene expression patterns along human chromosomes.
- Authors: Yamashita T, Honda M, Takatori H, Nishino R, Hoshino N, Kaneko S
- Issue date: 2004 Nov
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