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Series GSE138543 Query DataSets for GSE138543
Status Public on Mar 22, 2021
Title Suppression of liquid-liquid phase separation by 1,6-hexanediol partially compromises the 3D genome organization in living cells
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Liquid-liquid phase separation (LLPS) contributes to the spatial and functional segregation of molecular processes within the cell nucleus. However, the role played by LLPS in chromatin folding in living cells remains unclear. Here, using stochastic optical reconstruction microscopy (STORM) and Hi-C techniques, we studied the effects of 1,6-hexanediol (1,6-HD)- mediated LLPS disruption/modulation on higher-order chromatin organization in living cells. We found that 1,6-HD treatment caused the enlargement of nucleosome clutches and their more uniform distribution in the nuclear space. At a megabase-scale, chromatin underwent moderate but irreversible perturbations that resulted in the partial mixing of A and B compartments. The removal of 1,6-HD from the culture medium did not allow chromatin to acquire initial configurations, and resulted in more compact repressed chromatin than in untreated cells. 1,6-HD treatment also weakened enhancer-promoter interactions and TAD insulation but did not considerably affect CTCF-dependent loops. Our results suggest that 1,6-HD-sensitive LLPS plays a limited role in chromatin spatial organization by constraining its folding patterns and facilitating compartmentalization at different levels.
Overall design This submission contains the following experiments on untreated (Control and Control_T), 1,6-hexanediol treated (Hex5), Tween-20 treated (Tween), 1,6-hexanediol treated + recovery (Recovery) and Tween-20 treated + recovery (Recovery_T) HeLa cells: 2 biological replicates of Hi-C in Control, Control_T, Hex5, Tween, Recovery and Recovery_T cells, 2 biological replicates of CTCF ChIP-seq in Control, Hex5 and Recovery cells.
Contributor(s) Magnitov MD, Razin SV
Citation(s) 33836078
Submission date Oct 07, 2019
Last update date Nov 22, 2023
Contact name Mikhail Magnitov
Organization name The Netherlands Cancer Institute
Street address Plesmanlaan 121
City Amsterdam
ZIP/Postal code 1066CX
Country Netherlands
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (22)
GSM4112807 HiC_Control_rep1
GSM4112808 HiC_Control_rep2
GSM4112809 HiC_Hex5_rep1
BioProject PRJNA576273
SRA SRP224676

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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
GSE138543_ChIPseq_CTCF_peaks.Control.bed.gz 202.0 Kb (ftp)(http) BED
GSE138543_ChIPseq_CTCF_peaks.Hex5.bed.gz 204.3 Kb (ftp)(http) BED
GSE138543_ChIPseq_CTCF_peaks.Recovery.bed.gz 212.1 Kb (ftp)(http) BED 214.8 Mb (ftp)(http) BW 215.6 Mb (ftp)(http) BW 220.5 Mb (ftp)(http) BW 216.6 Mb (ftp)(http) BW 295.8 Mb (ftp)(http) BW 297.5 Mb (ftp)(http) BW
GSE138543_Control.mcool 831.4 Mb (ftp)(http) MCOOL
GSE138543_Hex5.mcool 866.6 Mb (ftp)(http) MCOOL
GSE138543_Recovery.mcool 1.3 Gb (ftp)(http) MCOOL
GSE138543_Recovery_T.mcool 307.3 Mb (ftp)(http) MCOOL
GSE138543_Tween.mcool 342.1 Mb (ftp)(http) MCOOL
GSE138543_compartment_signal.100kb.txt.gz 1.4 Mb (ftp)(http) TXT
GSE138543_loops.Control.bedpe.gz 169.0 Kb (ftp)(http) BEDPE
GSE138543_loops.Hex5.bedpe.gz 142.9 Kb (ftp)(http) BEDPE
GSE138543_loops.Recovery.bedpe.gz 338.3 Kb (ftp)(http) BEDPE
GSE138543_tads.Control.bed.gz 24.6 Kb (ftp)(http) BED
GSE138543_tads.Hex5.bed.gz 23.2 Kb (ftp)(http) BED
GSE138543_tads.Recovery.bed.gz 24.9 Kb (ftp)(http) BED
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