Genomics

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Chromatin Poises miRNA- and Protein-coding Genes for Expression


ABSTRACT: Chromatin modifications have been implicated in regulation of gene expression. While association of certain modifications with expressed or silent genes has been established, it remains unclear how changes in chromatin environment relate to changes in gene expression. In this report, we used ChIP-Seq to analyze the genome-wide changes in chromatin modifications during activation of total human CD4+ T cells by T cell receptor (TCR) signaling. Surprisingly, we found that the chromatin modification patterns at many induced and silenced genes are relatively stable during the short-term activation of resting T cells. Active chromatin modifications were already in place for a majority of inducible protein-coding genes even while the genes were silent in resting cells. Similarly, genes that were silenced upon T cell activation retained positive chromatin modifications even after being silenced. To investigate if these observations are also valid for miRNA-coding genes, we systematically identified promoters for known miRNA genes using epigenetic marks and profiled their expression patterns using deep sequencing. We found that chromatin modifications can poise miRNA-coding genes as well. Our data suggest that miRNA- and protein-coding genes share similar mechanisms of regulation by chromatin modifications, which poise inducible genes for activation in response to environmental stimuli. Keyword(s): Epigenetics Examination of several chromatin modifications in human CD4+ T cells

ORGANISM(S): Homo sapiens  

SUBMITTER: Keji Zhao   Suresh Cuddapah  Raja Jothi  Artem Barski 

PROVIDER: E-GEOD-16657 | ArrayExpress | 2009-08-10

SECONDARY ACCESSION(S): SRP001361GSE16657PRJNA116249

REPOSITORIES: GEO, ArrayExpress, ENA

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Chromatin poises miRNA- and protein-coding genes for expression.

Barski Artem A   Jothi Raja R   Cuddapah Suresh S   Cui Kairong K   Roh Tae-Young TY   Schones Dustin E DE   Zhao Keji K  

Genome research 20090827 10


Chromatin modifications have been implicated in the regulation of gene expression. While association of certain modifications with expressed or silent genes has been established, it remains unclear how changes in chromatin environment relate to changes in gene expression. In this article, we used ChIP-seq (chromatin immunoprecipitation with massively parallel sequencing) to analyze the genome-wide changes in chromatin modifications during activation of total human CD4(+) T cells by T-cell recept  ...[more]

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