title: Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties.
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.
authors.forename: Aurelien A
authors.initials: AA
authors.lastname: Serandour
authors.forename: Gordon D
authors.initials: GD
authors.lastname: Brown
authors.forename: Joshua D
authors.initials: JD
authors.lastname: Cohen
authors.forename: Jason S
authors.initials: JS
authors.lastname: Carroll
mesh_terms: D000818:Animals; D001665:Binding Sites; D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004247:DNA / Q000378:metabolism*; D051541:Hepatocyte Nuclear Factor 3-alpha / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D008099:Liver / Q000378:metabolism; D061986:MCF-7 Cells; D051379:Mice
chemical_list: C496499:FOXA1 protein, human; C496500:Foxa1 protein, mouse; D051541:Hepatocyte Nuclear Factor 3-alpha; D004247:DNA