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Series GSE116255 Query DataSets for GSE116255
Status Public on Jul 26, 2019
Title Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2 [ATAC-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Pioneer transcription factors (PTF) can recognize their binding sites on nucleosomal DNA and trigger chromatin opening for recruitment of other non-pioneer transcription factors. However, critical properties of PTFs are still poorly understood, such as how can these transcription factors selectively recognize cell type-specific binding sites and under which conditions can they initiate chromatin remodelling. Here we show that early endoderm binding sites of the paradigm PTF Foxa2 are epigenetically primed by low levels of active chromatin modifications in embryonic stem cells (ESC). Priming of these binding sites is supported by preferential recruitment of Foxa2 to endoderm binding sites compared to lineage-inappropriate binding sites, when ectopically expressed in ESCs. We further show that binding of Foxa2 is required for chromatin opening during endoderm differentiation. However, increased chromatin accessibility was only detected on binding sites which are synergistically bound with other endoderm transcription factors. Thus, our data suggest that binding site selection of PTFs is directed by the chromatin environment and that chromatin opening requires collaboration of PTFs with additional transcription factors.
Overall design Chromatin accessibility analysis in ES, mesendoderm and endoderm cells;control and Foxa2 KO ES or endoderm cells; control and Foxa2-overexpressing ES cells; Foxa2 and Gata4 overexpressing ES cells.
Contributor(s) Cernilogar FM, Schotta G
Citation(s) 31350899, 34168324
Submission date Jun 25, 2018
Last update date Aug 17, 2021
Contact name Filippo M. Cernilogar
Organization name LMU Munich
Department Biomedical Center
Street address Grosshaderner Strasse 9
City Planegg-Martinsried
ZIP/Postal code 82152
Country Germany
Platforms (1)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (18)
GSM3223234 ATAC.d2.FVFn.r1
GSM3223235 ATAC.d2.FVFn.r2
GSM3223236 ATAC.d2.FVFp.r1
This SubSeries is part of SuperSeries:
GSE116262 Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2
BioProject PRJNA477871
SRA SRP151317

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Supplementary file Size Download File type/resource
GSE116255_RAW.tar 4.4 Gb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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