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SMC complexes can traverse physical roadblocks bigger than their ring size

Journal Article (2022)
Author(s)

Biswajit Pradhan (TU Delft - BN/Bionanoscience, Kavli institute of nanoscience Delft, TU Delft - BN/Cees Dekker Lab)

Roman Barth (Kavli institute of nanoscience Delft, TU Delft - BN/Cees Dekker Lab)

Eugene Kim (Kavli institute of nanoscience Delft, TU Delft - BN/Cees Dekker Lab, TU Delft - BN/Bionanoscience)

Theo van Laar (Kavli institute of nanoscience Delft, TU Delft - BN/Nynke Dekker Lab)

Wayne Yang (TU Delft - BN/Bionanoscience, TU Delft - BN/Cees Dekker Lab, Kavli institute of nanoscience Delft)

Je Kyung Ryu (Kavli institute of nanoscience Delft, TU Delft - BN/Cees Dekker Lab)

Jaco van der Torre (TU Delft - BN/Cees Dekker Lab, Kavli institute of nanoscience Delft)

Jan Michael Peters (Research Institute of Molecular Pathology, Vienna)

Cees Dekker (Kavli institute of nanoscience Delft, TU Delft - BN/Cees Dekker Lab, TU Delft - BN/Bionanoscience)

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DOI related publication
https://doi.org/10.1016/j.celrep.2022.111491 Final published version
More Info
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Publication Year
2022
Language
English
Related content
Issue number
3
Volume number
41
Article number
111491
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Abstract

Ring-shaped structural maintenance of chromosomes (SMC) complexes like condensin and cohesin extrude loops of DNA. It remains, however, unclear how they can extrude DNA loops in chromatin that is bound with proteins. Here, we use in vitro single-molecule visualization to show that nucleosomes, RNA polymerase, and dCas9 pose virtually no barrier to loop extrusion by yeast condensin. We find that even DNA-bound nanoparticles as large as 200 nm, much bigger than the SMC ring size, also translocate into DNA loops during extrusion by condensin and cohesin. This even occurs for a single-chain version of cohesin in which the ring-forming subunits are covalently linked and cannot open to entrap DNA. The data show that SMC-driven loop extrusion has surprisingly little difficulty in accommodating large roadblocks into the loop. The findings also show that the extruded DNA does not pass through the SMC ring (pseudo)topologically, hence pointing to a nontopological mechanism for DNA loop extrusion.