MCM complexes are barriers that restrict cohesin-mediated loop extrusion

Bart J. H. Dequeker, Matthias J. Scherr, Hugo B. Brandão, Johanna Gassler, Sean Powell, Imre Gaspar, Ilya M. Flyamer, Aleksandar Lalic, Wen Tang, Roman Stocsits, Iain F. Davidson, Jan-Michael Peters, Karl E. Duderstadt (), Leonid A. Mirny () and Kikuë Tachibana ()
Additional contact information
Bart J. H. Dequeker: Vienna BioCenter (VBC)
Matthias J. Scherr: Max Planck Institute of Biochemistry (MPIB)
Hugo B. Brandão: Harvard University
Johanna Gassler: Vienna BioCenter (VBC)
Sean Powell: Vienna BioCenter (VBC)
Imre Gaspar: Max Planck Institute of Biochemistry (MPIB)
Ilya M. Flyamer: University of Edinburgh
Aleksandar Lalic: Max Planck Institute of Biochemistry (MPIB)
Wen Tang: Vienna BioCenter (VBC)
Roman Stocsits: Vienna BioCenter (VBC)
Iain F. Davidson: Vienna BioCenter (VBC)
Jan-Michael Peters: Vienna BioCenter (VBC)
Karl E. Duderstadt: Max Planck Institute of Biochemistry (MPIB)
Leonid A. Mirny: Massachusetts Institute of Technology (MIT)
Kikuë Tachibana: Vienna BioCenter (VBC)

Nature, 2022, vol. 606, issue 7912, 197-203

Abstract: Abstract Eukaryotic genomes are compacted into loops and topologically associating domains (TADs)1–3, which contribute to transcription, recombination and genomic stability4,5. Cohesin extrudes DNA into loops that are thought to lengthen until CTCF boundaries are encountered6–12. Little is known about whether loop extrusion is impeded by DNA-bound machines. Here we show that the minichromosome maintenance (MCM) complex is a barrier that restricts loop extrusion in G1 phase. Single-nucleus Hi-C (high-resolution chromosome conformation capture) of mouse zygotes reveals that MCM loading reduces CTCF-anchored loops and decreases TAD boundary insulation, which suggests that loop extrusion is impeded before reaching CTCF. This effect extends to HCT116 cells, in which MCMs affect the number of CTCF-anchored loops and gene expression. Simulations suggest that MCMs are abundant, randomly positioned and partially permeable barriers. Single-molecule imaging shows that MCMs are physical barriers that frequently constrain cohesin translocation in vitro. Notably, chimeric yeast MCMs that contain a cohesin-interaction motif from human MCM3 induce cohesin pausing, indicating that MCMs are ‘active’ barriers with binding sites. These findings raise the possibility that cohesin can arrive by loop extrusion at MCMs, which determine the genomic sites at which sister chromatid cohesion is established. On the basis of in vivo, in silico and in vitro data, we conclude that distinct loop extrusion barriers shape the three-dimensional genome.

Date: 2022
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DOI: 10.1038/s41586-022-04730-0

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