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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 ke...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053927/ https://www.ncbi.nlm.nih.gov/pubmed/24373287 http://dx.doi.org/10.1186/gb-2013-14-12-r147 |
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author | Serandour, Aurelien A Brown, Gordon D Cohen, Joshua D Carroll, Jason S |
author_facet | Serandour, Aurelien A Brown, Gordon D Cohen, Joshua D Carroll, Jason S |
author_sort | Serandour, Aurelien A |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4053927 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-40539272014-06-12 Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties Serandour, Aurelien A Brown, Gordon D Cohen, Joshua D Carroll, Jason S Genome Biol Method 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. BioMed Central 2013 2013-12-27 /pmc/articles/PMC4053927/ /pubmed/24373287 http://dx.doi.org/10.1186/gb-2013-14-12-r147 Text en Copyright © 2013 Serandour et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Method Serandour, Aurelien A Brown, Gordon D Cohen, Joshua D Carroll, Jason S Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties |
title | Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties |
title_full | Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties |
title_fullStr | Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties |
title_full_unstemmed | Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties |
title_short | Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties |
title_sort | development of an illumina-based chip-exonuclease method provides insight into foxa1-dna binding properties |
topic | Method |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053927/ https://www.ncbi.nlm.nih.gov/pubmed/24373287 http://dx.doi.org/10.1186/gb-2013-14-12-r147 |
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