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Series GSE72164 Query DataSets for GSE72164
Status Public on Dec 07, 2015
Title Dynamic reorganization of extremely long-range promoter-promoter interactions between two states of pluripotency
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Serum-to-2i interconversion of mouse Embryonic Stem Cells (mESCs) is a valuable in vitro model for early embryonic development. To assess whether 3D chromatin organization changes during this transition, we established Capture Hi-C with target-sequence enrichment of DNase I hypersensitive sites. We detected extremely long-range intra- and inter-chromosomal interactions between a small subset of H3K27me3 marked bivalent promoters involving the Hox clusters in serum grown cells. Notably, these promoter-mediated interactions are not present in 2i ground-state pluripotent mESCs but appear upon further development into primed-like serum mESCs. Reverting serum mESCs to ground-state 2i mESCs removes these promoter-promoter interactions in a spatiotemporal manner. H3K27me3, which is largely absent at bivalent promoters in ground-state 2i mESCs, is necessary but not sufficient to establish these interactions, as confirmed by Capture Hi-C on Eed-/- serum mESCs. Our results implicate H3K27me3 and PRC2 as critical players in chromatin alteration during priming of ESCs for differentiation.

Overall design To study dynamics in chromatin architecture and to characterize long-range interaction, we performed Hi-C using DpnII as the restriction enzyme, potentially reaching a genome-wide coverage at a less than 1Kb resolution. We subsequently performed enrichment of interaction by a target capture similar to the exome sequencing approach. We enriched for DNaseI hyper-sensitive sites (DHS’s) in chromatin from mESCs. Probes were designed against the union of all DHS’s of Serum and 2i mESCs. Capture Hi-C reveals Extremely Long-Range Interactions (ELRI) in Serum but not in 2i ESCs. We observed H3K27me3 as a prominent characteristic, but not exclusive feature of ELRI loci in Serum mESCs. To further elucidate the involvement of constituents of PRC1 and PRC2 in ELRI, we performed ChIP-seq experiment on Suz12 and Ring1B during serum-to-2i transition. In addition, RNA-seq was performed to compare the expression levels of genes.
Contributor(s) Joshi O, Wang SY, Atlasi Y, Peng T, Saeed S, Handoko L, Kuznetsova T
Citation(s) 26637943
Submission date Aug 18, 2015
Last update date May 15, 2019
Contact name Shuang-Yin Wang
Organization name RIMLS
Department Molecular Biology
Street address Geert Grooteplein 28
City Nijmegen
ZIP/Postal code 6525GA
Country Netherlands
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (76)
GSM1856416 CHi-C_mESCs_serum_BR1
GSM1856417 CHi-C_mESCs_serum_BR2
GSM1856418 CHi-C_mESCs_2i_BR1
BioProject PRJNA293238
SRA SRP062574

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
GSE72164_Hi-C_Merged_interactions_intervals.txt.gz 193.8 Mb (ftp)(http) TXT
GSE72164_RAW.tar 21.5 Gb (http)(custom) TAR (of BEDGRAPH, BEDPE, BW, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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