Identification of transcription factor binding sites from ChIP-seq data at high resolution.

ABSTRACT:

Motivation

Chromatin immunoprecipitation coupled to next-generation sequencing (ChIP-seq) is widely used to study the in vivo binding sites of transcription factors (TFs) and their regulatory targets. Recent improvements to ChIP-seq, such as increased resolution, promise deeper insights into transcriptional regulation, yet require novel computational tools to fully leverage their advantages.

Results

To this aim, we have developed peakzilla, which can identify closely spaced TF binding sites at high resolution (i.e. resolves individual binding sites even if spaced closely), as we demonstrate using semisynthetic datasets, performing ChIP-seq for the TF Twist in Drosophila embryos with different experimental fragment sizes, and analyzing ChIP-exo datasets. We show that the incr

SUBMITTER: Bardet AF 

PROVIDER: S-EPMC3799470 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature