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New insights into genome folding by loop extrusion from inducible degron technologies

Abstract

Chromatin folds into dynamic loops that often span hundreds of kilobases and physically wire distant loci together for gene regulation. These loops are continuously created, extended and positioned by structural maintenance of chromosomes (SMC) protein complexes, such as condensin and cohesin, and their regulators, including CTCF, in a highly dynamic process known as loop extrusion. Genetic loss of extrusion factors is lethal, complicating their study. Inducible protein degradation technologies enable the depletion of loop extrusion factors within hours, leading to the rapid reconfiguration of chromatin folding. Here, we review how these technologies have changed our understanding of genome organization, upsetting long-held beliefs on its role in transcription. Finally, we examine recent models that attempt to reconcile observations after chronic versus acute perturbations, and discuss future developments in this rapidly developing field of research.

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Fig. 1: Basic features of chromosome organization.
Fig. 2: Cohesin-mediated loop extrusion.
Fig. 3: Inducible degron technologies.
Fig. 4: Experimental strategies with inducible degron systems.
Fig. 5: Time-delayed effects of promoter–enhancer communication.

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Acknowledgements

The authors are grateful to L. Braccioli and R. Shah for feedback on the manuscript. E.d.W. is supported by a European Research Council (ERC) Consolidator grant FuncDis3D (865459) and is part of Oncode which is partly financed by the Dutch Cancer Society. E.P.N. is supported by National Institutes of Health (NIH) grant 1R35GM142792-01.

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Glossary

CTCF

An 11 zinc finger DNA and RNA-binding protein able to block the extrusion of cohesin in part through its amino-terminal domain that interacts with the STAG and RAD21 cohesin subunits, thereby shielding it from WAPL-mediated release.

Topologically associating domains

(TADs). Genomic regions that show preferential self-interaction and are physically insulated from their neighbours by the binding of CTCF at boundaries. Self-interaction is mediated by the cohesin complex.

Super-enhancers

Multi-kilobase stretches of regulatory DNA that exhibit unusually strong occupancy of transcription factors and co-factors.

Polycomb

A family of chromatin proteins that assemble into the (generally) repressive complexes Polycomb repressive complex 1 (PRC1) and PRC2, which maintain epigenetic silencing of developmental genes.

Cohesive cohesin

A pool of cohesin complex that mediates sister chromatin cohesion, which depends on structural maintenance of chromosomes 3 (SMC3) acetylation, PDS5 and SORORIN binding. Cohesive cohesin is thought to be distinct from extrusive cohesin as it contains PDS5 (and not NIPBL).

Phase separation

A process through which polymer chains (or segments of a polymer chain) spontaneously de-mix and segregate through the formation of immiscible phases.

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de Wit, E., Nora, E.P. New insights into genome folding by loop extrusion from inducible degron technologies. Nat Rev Genet (2022). https://doi.org/10.1038/s41576-022-00530-4

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