GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE71947 Query DataSets for GSE71947
Status Public on May 30, 2018
Title Pioneer transcription factor FoxA maintains an open nucleosome configuration for tissue-specific gene activation [MNase-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 status of such open chromatin, e.g., at active enhancers, is not clear. Here we develop a combination of 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 liver-specific enhancers retain preferentially MNase-accessible nucleosomes, with factors bound, substantially more than ubiquitous enhancers. Furthermore, the pioneer factor FoxA2 is required to keep enhancer nucleosomes accessible in chromatin at active liver genes. Thus, nucleosomes are not exclusively repressive to gene regulation when they are retained with, and exposed by, pioneer factors.
Overall design This experiment includes two technical replicates (F1, F2) of two biological replicates each, examining high and low concentration MNase-seq digestions of adult mouse liver chromatin, either in WT mice or in mice with a deletion of FoxA1 and FoxA2, size-selecting libraries with full nucleosomes or at the sub-nucleosomal size distribution. It does not include sub-nucleosomal sequencing runs for high MNase-seq digestion.
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 Aug 11, 2015
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 (24)
GSM1847793 Mutant.High.Whole.Rep1.F1
GSM1847794 WT.High.Whole.Rep1.F1
GSM1847795 Mutant.High.Whole.Rep2.F1
This SubSeries is part of SuperSeries:
GSE57559 Hypersensitive Nucleosomes in Chromatin Are Intrinsic to the Structure of Active, Tissue-Specific Enhancers
BioProject PRJNA292552
SRA SRP062277

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource 153.1 Mb (ftp)(http) BW 143.7 Mb (ftp)(http) BW 560.7 Mb (ftp)(http) BW 599.4 Mb (ftp)(http) BW 268.7 Mb (ftp)(http) BW 270.1 Mb (ftp)(http) BW 362.3 Mb (ftp)(http) BW 379.0 Mb (ftp)(http) BW 595.2 Mb (ftp)(http) BW 622.2 Mb (ftp)(http) BW 220.2 Mb (ftp)(http) BW 261.2 Mb (ftp)(http) BW 296.8 Mb (ftp)(http) BW 343.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap