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Series GSE77670 Query DataSets for GSE77670
Status Public on Apr 08, 2016
Title Pioneer transcription factor FoxA maintains an accessible nucleosome configuration at enhancers for tissue-specific gene activation [ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Nuclear DNA is wrapped around core histones to form nucleosomes, which constrains how transcription factors bind to gene regulatory sequences. Pioneer transcription factors have the special ability to bind target DNA on nucleosomes and initiate gene regulatory events, often leading to a local opening of chromatin. Yet the nucleosomal configuration of such open chromatin and the basis for chromatin opening is unclear. Here we combine low and high levels of MNase digestion along with core histone ChIP-seq to assess the presence of nucleosomes at enhancers and promoters in mouse liver. We find that the pioneer factor FoxA displaces linker histone H1, thereby keeping enhancer nucleosomes accessible in chromatin and helping other transcription factors bind. MNase-accessible nucleosomes, bound by transcription factors, are retained substantially more at liver-specific enhancers than promoters and tissue-ubiquitous enhancers. Thus, nucleosomes are not exclusively repressive to gene regulation when they are retained with, and exposed by, pioneer factors.
Overall design This study assesses genome-wide binding of the transcription factors FoxA3, HNF4a, and CEBPb along with linker histone H1 in WT mice and in FoxAflox;Alfp-Cre mutant mice lacking both FoxA1 and FoxA2. ChIP-seq signal is adjusted by input to account for local sonication efficiency biases. All ChIPs and the input were assessed using two biological replicates in each genetic background.
Contributor(s) Iwafuchi-Doi M, Donahue G, Kakumanu A, Watts JA, Mahony S, Pugh BF, Lee D, Kaestner KH, Zaret KS
Citation(s) 27058788
Submission date Feb 08, 2016
Last update date May 15, 2019
Contact name Gregory Donahue
Organization name The University of Pennsylvania
Department Cell & Developmental Biology
Lab Zaret Lab
Street address 3400 Civic Center Blvd, Bldg 421
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (10)
GSM2055883 FoxA3 ChIP-seq in WT Mice
GSM2055884 FoxA3 ChIP-seq in FoxAflox;Alfp-Cre Mice
GSM2055885 CEBPb ChIP-seq in WT Mice
This SubSeries is part of SuperSeries:
GSE57559 Hypersensitive Nucleosomes in Chromatin Are Intrinsic to the Structure of Active, Tissue-Specific Enhancers
BioProject PRJNA311179
SRA SRP069766

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Supplementary file Size Download File type/resource
GSE77670_RAW.tar 4.9 Gb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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