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Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1

ABSTRACT: By analysis of ChIP-exo of FOXA1 in LNCaP, we find that an astonishing genome-wide "well-positioned" configuration prevalently occurs between FOXA1 motif and the dyad of nucleosome. Here we performed ChIP-seq data of eight chromatin remodelers and found a higher occupancy of these remodelers on these well-positioned FOXA1 motif sites. Together, our results support a positional-nucleosome-oriented accessing model, in which FOXA1 can examine each underlying DNA nucleotide and be able to sense all potential motifs regardless if they face inward or outward to histone octamers along the DNA helix axis. We have performed ChIP-seq of eight chromatin remodeler factors.

ORGANISM(S): Homo sapiens

SUBMITTER: Zhenqing Ye

PROVIDER: E-GEOD-72690 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1.

Ye Zhenqing Z Chen Zhong Z Sunkel Benjamin B Frietze Seth S Huang Tim H-M TH Wang Qianben Q Jin Victor X VX

Nucleic acids research 20160725 16

The compaction of nucleosomal structures creates a barrier for DNA-binding transcription factors (TFs) to access their cognate cis-regulatory elements. Pioneer factors (PFs) such as FOXA1 are able to directly access these cis-targets within compact chromatin. However, how these PFs interplay with nucleosomes remains to be elucidated, and is critical for us to understand the underlying mechanism of gene regulation. Here, we have conducted a computational analysis on a strand-specific paired-end C ...[more]

PMID: 27458208

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