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Series GSE98119 Query DataSets for GSE98119
Status Public on May 01, 2018
Title The energetics and physiological impact of cohesin extrusion
Organisms Homo sapiens; Mus musculus
Experiment type Other
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Cohesin extrusion is thought to play a central role in establishing the architecture of mammalian genomes. However, extrusion has not been visualized in vivo, and thus, its functional impact and energetics are unknown. Using ultra-deep Hi-C, we show that loop domains form by a process that requires cohesin ATPases. Once formed, however, loops and compartments are maintained for hours without energy input. Strikingly, without ATP, we observe the emergence of hundreds of CTCF-independent loops that link regulatory DNA. We also identify architectural "stripes" where a loop anchor interacts with entire domains at high frequency. Stripes often tether super-enhancers to cognate promoters, and in B cells, they facilitate Igh transcription and recombination. Stripe anchors represent major hotspots for topoisomerase-mediated lesions, which promote chromosomal translocations and cancer. In plasmacytomas, stripes can deregulate Igh-translocated oncogenes. We propose that higher organisms have coopted cohesin extrusion to enhance transcription and recombination, with implications for tumor development.
Overall design ChIP-seq, ChIA-PET, insitu Hi-C, 4C, localHiC, ChromRNAseq, and/or RNAseq from mouse stem cells, activated B cells, CH12 cell line, and plasmacytomas
Contributor(s) Vian L, Pekowska A, Rao S, Kieffer-Kwon K, Jung S, Baranello L, Huang S, Dose M, Pruett N, Sanborn A, Canela A, Maman Y, Oksanen A, Resch W, Li X, Lee B, Kovalchuk A, Tang Z, Nelson S, Pierro MD, Cheng R, Machol I, Hilaire BG, Durand N, Shamim M, Stamenova E, Onuchic J, Ruan Y, Nussenzweig A, Levens D, Lieberman-Aiden E, Casellas R
Citation(s) 29706548
Submission date Apr 24, 2017
Last update date Jul 25, 2021
Contact name Seolkyoung Jung
Organization name NIH
Department NIAMS
Lab biodata mining and discovery section
Street address 10 Center Dr
City bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (6)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (352)
GSM2587372 ch12_ZF9to11_ChIAPET
GSM2587373 ch12_wt_ChIAPET
GSM2587375 aB24h_wt_Nipbl_rep1
BioProject PRJNA384026
SRA SRP105082

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
GSE98119_7134_SAd_4C.bedGraph.gz 443.8 Kb (ftp)(http) BEDGRAPH
GSE98119_7134_wt_4C.bedGraph.gz 476.0 Kb (ftp)(http) BEDGRAPH
GSE98119_RAW.tar 397.9 Gb (http)(custom) TAR (of BED, BW, HIC)
GSE98119_Series-level_HIC_readme.txt 1.4 Kb (ftp)(http) TXT
GSE98119_Vian-2018-CH12_cells_CTCFZF9to11_mutant_30.hic 12.8 Gb (ftp)(http) HIC
GSE98119_Vian-2018-CH12_cells_wt_30.hic 15.2 Gb (ftp)(http) HIC
GSE98119_Vian-2018-activated_B_cells_24_hours_WT.hic 3.4 Gb (ftp)(http) HIC
GSE98119_Vian-2018-activated_B_cells_24_hours_WT_30.hic 3.1 Gb (ftp)(http) HIC
GSE98119_Vian-2018-activated_B_cells_24_hours_flavopiridol.hic 14.9 Gb (ftp)(http) HIC
GSE98119_Vian-2018-activated_B_cells_24_hours_flavopiridol_30.hic 14.0 Gb (ftp)(http) HIC
GSE98119_Vian-2018-activated_B_cells_24_hours_oligomycin_30.hic 7.4 Gb (ftp)(http) HIC
GSE98119_Vian-2018-activated_B_cells_30_hours_HU_treated.hic 1.4 Gb (ftp)(http) HIC
GSE98119_Vian-2018-activated_B_cells_30_hours_HU_treated_30.hic 1.3 Gb (ftp)(http) HIC
GSE98119_Vian-2018-activated_B_cells_30_hours_WT.hic 1.2 Gb (ftp)(http) HIC
GSE98119_Vian-2018-activated_B_cells_30_hours_WT_30.hic 1.1 Gb (ftp)(http) HIC 313.6 Mb (ftp)(http) BW 194.0 Mb (ftp)(http) BW 335.8 Mb (ftp)(http) BW 46.5 Mb (ftp)(http) BW 540.2 Mb (ftp)(http) BW 369.1 Mb (ftp)(http) BW
GSE98119_ch12_wt_CTCF_peaks.bed.gz 575.4 Kb (ftp)(http) BED 218.9 Mb (ftp)(http) BW 227.7 Mb (ftp)(http) BW 864.9 Mb (ftp)(http) BW
GSE98119_rBaB_CTCF_peaks.narrowPeak.gz 1.6 Mb (ftp)(http) NARROWPEAK
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Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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