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Series GSE213501 Query DataSets for GSE213501
Status Public on Dec 31, 2023
Title Enhancer Cis Elements Instruct Promoter-Enhancer Interaction, Promoter-Enhancer Insulation and Compartmental Segregation
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Enhancers harbor instructions encoded for the interactions between cis-elements and transcription factors to orchestrate lineage specific gene programs. Here we developed a modified method for chromosome conformation capture (3C), named MID Hi-C, to reveal how in mouse embryonic stem cells differential cooperation of enhancers and the chromatin remodeler BAF, as instructed by the underlying transcription factor motifs, modulate enhancer-promoter communication. We show that BAF-dependent enhancers permit genomic interactions beyond enhancer boundaries. BAF-dependent enhancers do not dictate genomic interactions within enhancer-promoter loop domains but rather act to instruct remote enhancer-promoter communication. In contrast, BAF-independent enhancers interact with promoter regions within tightly insulated enhancer-promoter loop domains that are marked by promoter and enhancer boundary elements. In addition, enhancer activeness modulated by BAF enforces compartment segregation. Based on these observations, we propose that enhancer cis elements instruct with great precision BAF-induced enhancer-promoter communication and compartmental segregation.
Overall design We benchmarked the qualities of MID Hi-C data against published in situ Hi-C and Micro-C data on mouse embryonic stem cells (mESCs). Then, using ATAC-seq and our newly-developed MID Hi-C, we investigated changes in chromatin accessibilities and chromatin interactions during BRG1 degradation in mESCs.
Contributor(s) Lu H, Pham PD, Han H, Zhou JJ, Wang W, Cho KW, Murre C
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Sep 16, 2022
Last update date Jan 01, 2024
Contact name Hanbin Lu
Organization name UCSD
Lab Murre Lab
Street address 9500 Gilman Drive, NSB 5108
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (30)
GSM6588190 ATAC_Brg1FV_mESC_0h
GSM6588191 ATAC_Brg1FV_mESC_3h
GSM6588192 ATAC_Brg1FV_mESC_6h
BioProject PRJNA881254

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE213501_ATAC_Brg1FV_mESC_0h_combined.hic 1.6 Gb (ftp)(http) HIC
GSE213501_ATAC_Brg1FV_mESC_0h_combined.hic.mcool 977.1 Mb (ftp)(http) MCOOL
GSE213501_ATAC_Brg1FV_mESC_24h_combined.hic 1.5 Gb (ftp)(http) HIC
GSE213501_ATAC_Brg1FV_mESC_24h_combined.hic.mcool 894.0 Mb (ftp)(http) MCOOL
GSE213501_ATAC_Brg1FV_mESC_3h_combined.hic 1.6 Gb (ftp)(http) HIC
GSE213501_ATAC_Brg1FV_mESC_3h_combined.hic.mcool 943.6 Mb (ftp)(http) MCOOL
GSE213501_ATAC_Brg1FV_mESC_6h_combined.hic 1.6 Gb (ftp)(http) HIC
GSE213501_ATAC_Brg1FV_mESC_6h_combined.hic.mcool 912.2 Mb (ftp)(http) MCOOL
GSE213501_MIDHiC_WT_mESC_combined.hic 5.8 Gb (ftp)(http) HIC
GSE213501_MIDHiC_WT_mESC_combined.hic.mcool 4.3 Gb (ftp)(http) MCOOL
GSE213501_MIDHiChIP_H3K27ac_WT_mESC_combined.hic 855.2 Mb (ftp)(http) HIC
GSE213501_MIDHiChIP_H3K27ac_WT_mESC_combined.hic.mcool 747.5 Mb (ftp)(http) MCOOL
GSE213501_MIDHiChIP_cohesin_WT_mESC_combined.hic 739.0 Mb (ftp)(http) HIC
GSE213501_MIDHiChIP_cohesin_WT_mESC_combined.hic.mcool 675.1 Mb (ftp)(http) MCOOL
GSE213501_RAW.tar 425.8 Mb (http)(custom) TAR (of BIGWIG)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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