Transcriptomics

Dataset Information

3

Genome-wide analysis reveals determinants of redundant and specific binding within a transcription factor family


ABSTRACT: A central question in transcription factor biology is how a specific member of a transcription factor family occupies a promoter in vivo, when all family members bind the same consensus site in vitro. To uncover the mechanisms regulating DNA binding specificity within transcription factor families, we have used the techniques of chromatin immunoprecipitation coupled with genome-wide microarray analysis to query the occupancy of three members of the ETS transcription factor family in a human T-cell line. Unexpectedly, redundant occupancy was frequently detected while specific occupancy was less likely. An unbiased bioinformatics approach correlated redundant binding with consensus ETS binding sequences near transcription start sites, whereas specific binding sites diverged dramatically from the consensus, were coupled with a site for a cooperative binding partner, and were found further from transcription start sites. The specific and redundant DNA binding modes illustrate the regulation of transcription factor specificity in vivo and suggest two distinct roles for members of the ETS transcription factor family. Keywords: ChIP-chip Chromatin IP from uninduced asynchronous Jurkat T cells, or HT29 colon cells using antibodies to three ETS transcription factors (ETS1, ELF1, and GABPa) or the transcription factors RUNX1 or E2F4. IP and whole input DNAs are amplified (WGA2 kit sigma) and labeled and compared by promoter microarrays (Agilent). Each experiment requires 2 microarrays to cover the genome. Proximal promoter arrays assay 1kb surrounding transcription start sites, extended promoter arrays assay 7kb surrounding transcription start sites. Each microarray is performed as two biological replicates with the exception of ETS1 in HT29 proximal promoter array which were done once, and ETS1 in Jurkat proximal promoter array which was done three times.

ORGANISM(S): Homo sapiens  

SUBMITTER: Peter Hollenhorst   Atul A Shah  Peter C Hollenhorst  Barbara J Graves 

PROVIDER: E-GEOD-7449 | ArrayExpress | 2007-07-27

SECONDARY ACCESSION(S): GSE7449PRJNA100225

REPOSITORIES: GEO, ArrayExpress

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Publications

Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family.

Hollenhorst Peter C PC   Shah Atul A AA   Hopkins Christopher C   Graves Barbara J BJ  

Genes & development 20070724 15


The conservation of in vitro DNA-binding properties within families of transcription factors presents a challenge for achieving in vivo specificity. To uncover the mechanisms regulating specificity within the ETS gene family, we have used chromatin immunoprecipitation coupled with genome-wide promoter microarrays to query the occupancy of three ETS proteins in a human T-cell line. Unexpectedly, redundant occupancy was frequently detected, while specific occupancy was less likely. Redundant bindi  ...[more]

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