Cell-type specificity of ChIP-predicted transcription factor binding sites.

ABSTRACT:

Background

Context-dependent transcription factor (TF) binding is one reason for differences in gene expression patterns between different cellular states. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identifies genome-wide TF binding sites for one particular context-the cells used in the experiment. But can such ChIP-seq data predict TF binding in other cellular contexts and is it possible to distinguish context-dependent from ubiquitous TF binding?

Results

We compared ChIP-seq data on TF binding for multiple TFs in two different cell types and found that on average only a third of ChIP-seq peak regions are common to both cell types. Expectedly, common peaks occur more frequently in certain genomic contexts, such as CpG-rich promoters, whe

SUBMITTER: Handstad T 

PROVIDER: S-EPMC3574057 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature