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Series GSE92407 Query DataSets for GSE92407
Status Public on Apr 30, 2019
Title Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency. (ChIP-seq)
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The mechanisms underlying enhancer activation and the extent to which enhancer-promoter rewiring contributes to spatiotemporal gene expression are not well understood. Using integrative and time resolved analyses we show that the extensive transcriptome and epigenome resetting during the conversion between ‘serum-’ and ‘2i’-states of mouse embryonic stem cells (ESCs) takes place with minimal enhancer-promoter rewiring that becomes more evident in primed-state pluripotency. Instead, differential gene expression is strongly linked to enhancer activation via H3K27ac. Conditional depletion of TFs and allele-specific enhancer analysis reveals an essential role for Esrrb in H3K27-acetylation and activation of 2i-specific enhancers. Restoration of a polymorphic ESRRB motif using CRISPR/Cas9 in a hybrid ESC-line, restores ESRRB binding and enhancer H3K27ac in an allele-specific manner but has no effect on chromatin interactions. Our study shows that enhancer activation in serum- and 2i-ESCs is largely driven by TF-binding and epigenetic marking in a hardwired network of chromatin interactions.
Overall design ChIP-seq analysis of H3K27ac, ESRRB, GFP, CTCF, YY1, SMC1 in E14- or F1-ESCs cultured in 2i, serum or EpiLSC medium. ChIP-seq analysis for H3K27ac in Tamoxifen inducible Nr5a2 or Esrrb- KO ESCs.
Citation(s) 31036938
Submission date Dec 14, 2016
Last update date May 15, 2019
Contact name Hendrik G Stunnenberg
Organization name Radboud University
Street address Geert Grooteplein 30
City Nijmegen
ZIP/Postal code 6525GA
Country Netherlands
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (61)
GSM2429210 H3K27ac_serum_Rep1
GSM2429211 H3K27ac_2i8h_Rep1
GSM2429212 H3K27ac_2iDay1_Rep1
This SubSeries is part of SuperSeries:
GSE92412 Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency.
BioProject PRJNA357480
SRA SRP095132

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Supplementary file Size Download File type/resource
GSE92407_RAW.tar 8.8 Gb (http)(custom) TAR (of BEDGRAPH, BIGWIG, BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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