Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging

Animal genomes are folded into loops and topologically associating domains (TADs) by CTCF and loop-extruding cohesins, but the live dynamics of loop formation and stability remain unknown. Here, we directly visualized chromatin looping at the TAD in mouse embryonic stem cells using super-resolution...

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Published inScience (American Association for the Advancement of Science) Vol. 376; no. 6592; pp. 496 - 501
Main Authors Gabriele, Michele, Brandão, Hugo B, Grosse-Holz, Simon, Jha, Asmita, Dailey, Gina M, Cattoglio, Claudia, Hsieh, Tsung-Han S, Mirny, Leonid, Zechner, Christoph, Hansen, Anders S
Format Journal Article
LanguageEnglish
Published United States The American Association for the Advancement of Science 29.04.2022
Subjects
Animals
Bayes Theorem
Bayesian analysis
CCCTC-Binding Factor
Cell Cycle Proteins - metabolism
Cells (biology)
Chromatin
Chromosomal Proteins, Non-Histone - metabolism
Cohesin
Cohesins
Domains
Gene expression
Genomes
Mathematical models
Mice
Static models
Statistical inference
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Summary:Animal genomes are folded into loops and topologically associating domains (TADs) by CTCF and loop-extruding cohesins, but the live dynamics of loop formation and stability remain unknown. Here, we directly visualized chromatin looping at the TAD in mouse embryonic stem cells using super-resolution live-cell imaging and quantified looping dynamics by Bayesian inference. Unexpectedly, the loop was both rare and dynamic, with a looped fraction of approximately 3 to 6.5% and a median loop lifetime of approximately 10 to 30 minutes. Our results establish that the TAD is highly dynamic, and about 92% of the time, cohesin-extruded loops exist within the TAD without bridging both CTCF boundaries. This suggests that single CTCF boundaries, rather than the fully CTCF-CTCF looped state, may be the primary regulators of functional interactions.
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Author contributions: ASH conceived and initiated the project. HBB, MG, SGH, LM, CZ, ASH designed the project. ASH performed genome-editing and generated the cell lines. GMD cloned plasmids. MG, AJ, CC, and ASH characterized and validated the cell lines. THSH performed Micro-C. CC performed ChIP-Seq. MG, AJ, and HBB optimized imaging experiments with input from ASH. MG and AJ collected the imaging data. MG and AJ performed control experiments and characterized the AID cell lines. HBB developed image processing pipeline, the CNN, and analyzed the imaging data with input from ASH, SGH, MG, and AJ. HBB performed polymer simulations with input from SGH and LM. MG, AJ, HBB, and ASH annotated trajectory data. SGH and CZ designed BILD with input from HBB, LM, and ASH. SGH developed and benchmarked BILD, applied BILD to trajectory data, and developed MSD analysis with input from HBB, LM, ASH, and CZ. HBB and SGH analyzed polymer simulations. ASH, LM, and CZ supervised the project. HBB, MG, SGH, AJ, and ASH drafted the manuscript and figures. All authors edited the manuscript and figures.
present address: Illumina Inc.; San Diego, CA 92122, USA
These authors contributed equally to this work and may list their own name first.
ISSN:0036-8075
1095-9203
1095-9203
DOI:10.1126/science.abn6583