Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites.

ABSTRACT:

Motivation

Histone acetylation (HAc) is associated with open chromatin, and HAc has been shown to facilitate transcription factor (TF) binding in mammalian cells. In the innate immune system context, epigenetic studies strongly implicate HAc in the transcriptional response of activated macrophages. We hypothesized that using data from large-scale sequencing of a HAc chromatin immunoprecipitation assay (ChIP-Seq) would improve the performance of computational prediction of binding locations of TFs mediating the response to a signaling event, namely, macrophage activation.

Results

We tested this hypothesis using a multi-evidence approach for predicting binding sites. As a training/test dataset, we used ChIP-Seq-derived TF binding site locations for five TFs in activated murine

SUBMITTER: Ramsey SA 

PROVIDER: S-EPMC2922897 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature