NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE92412 Query DataSets for GSE92412
Status Public on Apr 30, 2019
Title Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency.
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
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.

This SuperSeries is composed of the SubSeries listed below.
 
Overall design Refer to individual Series
 
Citation(s) 31036938
Submission date Dec 14, 2016
Last update date May 15, 2019
Contact name Hendrik G Stunnenberg
E-mail(s) h.stunnenberg@ncmls.ru.nl
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 (194)
GSM2429110 RNAseq_2i_Rep1
GSM2429111 RNAseq_2i_Rep2
GSM2429112 RNAseq_2i_Day1_Rep1
This SuperSeries is composed of the following SubSeries:
GSE92403 Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency. (RNA-seq)
GSE92407 Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency. (ChIP-seq)
GSE92411 Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency. (ATAC-seq)
Relations
BioProject PRJNA357492

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
GSE92412_RAW.tar 12.2 Gb (http)(custom) TAR (of BEDGRAPH, BIGWIG, BW)
SRA Run SelectorHelp

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