MCM complexes are barriers that restrict cohesin-mediated loop extrusion.

Area of Science:

• Genomics
• Molecular Biology
• Cell Biology

Background:

• Eukaryotic genomes are organized into loops and topologically associating domains (TADs), crucial for gene regulation and genomic stability.
• Cohesin is known to extrude DNA into loops, typically stopping at CTCF boundaries.
• The role of DNA-bound machines, like the MCM complex, in impeding loop extrusion remains largely unknown.

Purpose of the Study:

• To investigate whether DNA-bound machines, specifically the minichromosome maintenance (MCM) complex, act as barriers to cohesin-mediated loop extrusion.
• To understand the impact of MCM complexes on the formation of CTCF-anchored loops and TAD boundary insulation.
• To elucidate the mechanism by which MCM complexes influence three-dimensional genome organization and sister chromatid cohesion.

Main Methods:

• Single-nucleus Hi-C (high-resolution chromosome conformation capture) in mouse zygotes and HCT116 cells.
• Computational simulations to model MCM complex behavior as barriers.
• Single-molecule imaging to observe MCM-cohesin interactions in vitro.
• Creation of chimeric yeast MCMs with human cohesin-interaction motifs.

Main Results:

• MCM complex loading reduces CTCF-anchored loops and decreases TAD boundary insulation in G1 phase.
• MCMs act as physical barriers that constrain cohesin translocation, both in silico and in vitro.
• Chimeric MCMs with specific motifs induce cohesin pausing, indicating MCMs are active barriers.
• MCMs influence the number of CTCF-anchored loops and gene expression in HCT116 cells.

Conclusions:

• The minichromosome maintenance (MCM) complex functions as a barrier that restricts cohesin-mediated loop extrusion before CTCF sites.
• MCM complexes are identified as active barriers that influence the establishment of sister chromatid cohesion.
• Distinct loop extrusion barriers, including MCM complexes, play a critical role in shaping the three-dimensional genome organization.