Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties.
Published version
Peer-reviewed
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Authors
Serandour, Aurelien A
Brown, Gordon D
Cohen, Joshua D
Carroll, Jason S
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.
Description
Keywords
Animals, Binding Sites, Cell Line, Tumor, Chromatin Immunoprecipitation, DNA, Hepatocyte Nuclear Factor 3-alpha, Humans, Liver, MCF-7 Cells, Mice
Journal Title
Genome Biol
Conference Name
Journal ISSN
1474-760X
1474-760X
1474-760X
Volume Title
14
Publisher
Springer Science and Business Media LLC