Transcriptomics

Dataset Information

0

Transcription profiling by array of human CD4 positive cells after activation with antiCD3/28 beads


ABSTRACT: The positioning of nucleosomes with respect to DNA plays an important role in regulating transcription. However, nucleosome mapping has been performed for only limited genomic regions in humans. We have generated genome-wide maps of nucleosome positions in both resting and activated human CD4+ T cells by direct sequencing of nucleosome ends using the Solexa high-throughput sequencing technique. Corresponding ChIP-Seq data are available in NCBI's Short Read Archive at ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/SRA000234/; We find that nucleosome phasing relative to the transcription start sites (TSSs) is directly correlated to RNA polymerase II binding. Furthermore, the first nucleosome downstream of TSSs exhibits differential positioning in active and silent genes. TCR signaling induces extensive nucleosome reorganization in promoters and enhancers to allow transcriptional activation or repression. Our results suggest that H2A.Z-containing and modified nucleosomes are preferentially lost from the -1 nucleosome position. Our data provide a comprehensive view of the nucleosome landscape and its dynamic regulation in the human genome. This microarray dataset is the gene expression data from resting and activated CD4+ T cells. We used this data to look at nucleosome positioning, Pol II and a few chromatin modifications at genes that are silent and activated in both resting and activated T cells as well as genes that are induced or repressed with T cell activation. Experiment Overall Design: Gene expression data from resting (M0 and T0) and activated (M18 and T18) T cells.

INSTRUMENT(S): 418 [Affymetrix]

ORGANISM(S): Homo sapiens  

SUBMITTER: Dustin E. Schones  

PROVIDER: E-GEOD-10437 | ArrayExpress | 2008-04-08

SECONDARY ACCESSION(S): GSE10437PRJNA108097

REPOSITORIES: GEO, ArrayExpress

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Publications

Dynamic regulation of nucleosome positioning in the human genome.

Schones Dustin E DE   Cui Kairong K   Cuddapah Suresh S   Roh Tae-Young TY   Barski Artem A   Wang Zhibin Z   Wei Gang G   Zhao Keji K  

Cell 20080301 5


The positioning of nucleosomes with respect to DNA plays an important role in regulating transcription. However, nucleosome mapping has been performed for only limited genomic regions in humans. We have generated genome-wide maps of nucleosome positions in both resting and activated human CD4+ T cells by direct sequencing of nucleosome ends using the Solexa high-throughput sequencing technique. We find that nucleosome phasing relative to the transcription start sites is directly correlated to RN  ...[more]

Publication: 1/2

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