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Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties

Aurelien A Serandour, Gordon D Brown, Joshua D Cohen and Jason S Carroll*

Author Affiliations

Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK

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Genome Biology 2013, 14:R147  doi:10.1186/gb-2013-14-12-r147

Published: 27 December 2013

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.