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Series GSE50029 Query DataSets for GSE50029
Status Public on Sep 12, 2013
Title Long-range chromatin contacts reveal a role for the pluripotency and Polycomb networks in genome organization
Organism Mus musculus
Experiment type Other
Summary We mapped long-range chromatin interactions in embryonic stem cells (ESCs), iPSCs, and fibroblasts, and uncovered an ESC-specific genome organization that is gradually re-established during reprogramming. Confirming previous results, we show that open, accessible and closed chromatin character is the primary determinant of long-range chromatin interaction preferences. Importantly, we find that in ESCs, genomic regions extensively occupied by the pluripotency factors Oct4, Sox2, and Nanog preferentially co-localize. Similarly, regions strongly enriched for Polycomb-proteins and H3K27me3 frequently interact, and loss of the Polycomb-protein Eed diminishes these interactions without dramatically changing overall chromosome-conformation. Consistent with a spatial segregation of transcriptional networks in ESCs, Nanog and Polycomb-proteins occupy distinct nuclear spaces. Together, our data reveal that transcriptional networks that govern ESC identity play a role in genome-organization.
Overall design 4C-seq was performed using a variety of baits on range of mouse cell lines, namely, ESCs, reprogrammed iPSCs, partially reprogrammed pre-iPSCs, and differentiated MEFs. Additionally, 4C-seq was performed on a partially overlapping set of baits for a Eed mutant mouse ESC line and a sibling wild-type ESC line.
Contributor(s) Denholtz M, Bonora G, Chronis C, Splinter E, deLaat W, Ernst J, Pellegrini M, Plath K
Citation(s) 24035354
Submission date Aug 20, 2013
Last update date May 15, 2019
Contact name Kathrin Plath
Organization name UCLA
Street address 615 Charles E. Young Drive South
City Los Angeles
ZIP/Postal code 90095
Country USA
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (201)
GSM1212762 EED-/- ESC Hoxa10 replicate 1 read counts
GSM1212763 EED-/- ESC Hoxa10 replicate 2 read counts
GSM1212764 EED-/- ESC Hoxa10 replicate 3 read counts
BioProject PRJNA215840
SRA SRP028930

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Supplementary file Size Download File type/resource
GSE50029_Denholtz_Bonora_-_4C_primer_list_with_reference_to_GEO_data_sets.xlsx 75.0 Kb (ftp)(http) XLSX
GSE50029_RAW.tar 868.1 Mb (http)(custom) TAR (of BEDGRAPH)
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Raw data are available in SRA
Processed data provided as supplementary file

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