Development of an Illumina-based ChIP-exonuclease Method Provides Insight into FoxA1-DNA Binding Properties

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2013 Dec 31

PMID 24373287

Citations 51

Authors

Aurelien A Serandour

Gordon D Brown

Joshua D Cohen

Jason S Carroll

Affiliations

Soon will be listed here.

Abstract

ChIP-exonuclease (ChIP-exo) is a modified ChIP-seq approach for high resolution mapping of transcription factor DNA sites. We describe an Illumina-based ChIP-exo method which provides a global improvement of the data quality of estrogen receptor (ER) ChIP and insights into the motif structure for key ER-associated factors. ChIP-exo of the ER pioneer factor FoxA1 identifies protected DNA with a predictable 8 bp overhang from the Forkhead motif, which we term mesas. We show that mesas occur in multiple cellular contexts and exist as single or overlapping motifs. Our Illumina-based ChIP-exo provides high resolution mapping of transcription factor binding sites.

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