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Series GSE197231 Query DataSets for GSE197231
Status Public on Feb 27, 2022
Title Cohesin and CTCF control chromosomal contact dynamics in living cells [Hi-C]
Organism Mus musculus
Experiment type Other
Summary Mammalian chromosomes are partitioned into topologically associating domains (TADs) by the loop-extrusion activity of cohesin that is blocked at specific DNA sites bound by CTCF. Chromosome structure inside TADs is highly variable in single cells, yet little is known about its temporal dynamics, how it influences the rates and durations of chromosomal contacts, and how it depends on CTCF and cohesin. To address these questions we combine two quantitative live-cell imaging strategies that minimize locus-specific confounding effects. We show that loop extrusion by cohesin globally reduces the mobility of the chromatin fiber in living cells, while also increasing the rates of formation and durations of contacts between sequences inside the same TAD. Quantitative analysis of high-resolution microscopy data reveals that contacts assemble and disassemble frequently in the course of the cell cycle, and become substantially more frequent and longer in the presence of convergent CTCF sites. Comparison with polymer modeling additionally reveals that cohesin-mediated CTCF loops last around 10 minutes on average. Our data support the notion that chromosome structure within TADs is highly dynamic and provide a quantitative framework for understanding the principles that link chromosome structure to biological function.
 
Overall design We performed Hi-C experiment for 3 conditions: WT, 90min af Rad21 degradation and 240min of Rad21 degradation. There are 2 aims. 1. Choose induction time : 90 or 240 min. The changes at 90 similar to 240 so we proceed with 90 min. 2. Check that after Rad21 degradation CTCF loopes on the contact map are gone, which holds true.
 
Contributor(s) Mach P, Kos P, Zhan Y, Cramard J, Gaudin S, T√ľnnermann J, Eglinger J, Zuin J, Kryzhanovska M, Smallwood S, Gelman L, Marchi E, Nora EP, Tiana G, Giorgetti L
Citation(s) 36471076
Submission date Feb 22, 2022
Last update date Jun 01, 2024
Contact name Luca Giorgetti
Organization name Friedrich Miescher Institute for Biomedical Research
Street address Fabrikstrasse 24
City Basel
ZIP/Postal code 4056
Country Switzerland
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (3)
GSM5911352 HiC WT
GSM5911353 HiC auxin treatment 90 min
GSM5911354 HiC auxin treatment 240 min
This SubSeries is part of SuperSeries:
GSE197238 Cohesin and CTCF control chromosomal contact dynamics in living cells
Relations
BioProject PRJNA809402

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Supplementary file Size Download File type/resource
GSE197231_RAW.tar 737.2 Mb (http)(custom) TAR (of COOL)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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