Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties.
Serandour, Aurelien A
Brown, Gordon D
Cohen, Joshua D
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Serandour, A. A., Brown, G. D., Cohen, J. D., & Carroll, J. (2013). Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties.. Genome biology, 14 (12), R147. https://doi.org/10.1186/gb-2013-14-12-r147
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.
Liver, Cell Line, Tumor, Animals, Humans, Mice, DNA, Chromatin Immunoprecipitation, Binding Sites, Hepatocyte Nuclear Factor 3-alpha, MCF-7 Cells
External DOI: https://doi.org/10.1186/gb-2013-14-12-r147
This record's URL: https://www.repository.cam.ac.uk/handle/1810/292233
Attribution 4.0 International
Licence URL: https://creativecommons.org/licenses/by/4.0/