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Series GSE37275 Query DataSets for GSE37275
Status Public on Jul 24, 2013
Title The pluripotent genome in three dimensions is shaped around pluripotency factors
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary It is becoming increasingly clear that the shape of the genome importantly influences transcription regulation. Pluripotent stem cells (PSCs) such as embryonic stem cells (ESCs) were recently shown to organize their chromosomes into topological domains that are largely invariant between cell types. Here, we applied 4C technology and combined ChIP-seq with Hi-C data to demonstrate that inactive chromatin is unusually disorganized in PSC nuclei. We show that gene promoters engage in contacts between topological domains in a largely tissue-independent manner while enhancers have a more tissue-restricted interaction profile. Most strikingly, genomic clusters of pluripotency factor binding sites find each other very efficiently, in a manner that is strictly PSC-specific, dependent on the presence of Oct4 and Nanog protein and inducible upon artificial recruitment of Nanog to a selected chromosomal site. We conclude that pluripotent stem cells have a unique higher-order genome structure shaped by pluripotency factors. We speculate that this interactome enhances the robustness of the pluripotent state.
Overall design 4C-seq was performed on a range of viewpoints in pluripotent (2x ESC, iPSC) and differentiated (neural precursor cells and astrocytes) cell lines.
Contributor(s) de Wit E, Bouwman B, Klous P, Splinter E, Welling M, Geijsen N, de Laat W, Zhu Y, Verstegen M, Nora E, Heard E, Festuccia N, Chambers I, Krijger P, Poot R
Citation(s) 23883933
Submission date Apr 13, 2012
Last update date May 15, 2019
Contact name Elzo de Wit
Phone +31 30 2121 800
Organization name Hubrecht Institute
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584 CT
Country Netherlands
Platforms (3)
GPL9185 Illumina Genome Analyzer (Mus musculus)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (50)
GSM915349 AB_part_AC_E14
GSM915350 AB_part_ESC_129_Cast
GSM915351 AB_part_ESC_E14
BioProject PRJNA159171
SRA SRP012213

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Supplementary file Size Download File type/resource
GSE37275_RAW.tar 17.5 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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