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Genome Biol. 2013 Dec 27;14(12):R147. doi: 10.1186/gb-2013-14-12-r147.

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


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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