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Two CTCF motifs impede cohesin-mediated DNA loop extrusion.

Roman Barth1, Richard Janissen1, Laura Muras1

  • 1Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft 2629HZ, the Netherlands.

Molecular Cell
|December 5, 2025
PubMed
Summary
This summary is machine-generated.

Human cohesin extrudes DNA into loops, but how it stalls at CTCF is unclear. Researchers found two CTCF motifs, YDF and KTYQR, that hinder DNA loop extrusion (LE) through distinct mechanisms, revealing how CTCF regulates genome structure.

Keywords:
AlphaFoldCTCFDNA loop extrusionchromosome organizationcohesinmagnetic tweezerssingle-molecule fluorescence

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • Human cohesin mediates DNA loop extrusion (LE), a fundamental process in genome organization.
  • Cohesin stalling at the CCCTC-binding factor (CTCF) is crucial for genome positioning but the underlying mechanism remains elusive.
  • The N-terminal region (NTR) of CTCF is implicated in stalling cohesin's DNA loop extrusion activity.

Purpose of the Study:

  • To elucidate the molecular mechanism by which CTCF's N-terminal region (NTR) stalls cohesin-mediated DNA loop extrusion (LE).
  • To identify specific amino acid motifs within the CTCF NTR responsible for hindering cohesin's extrusion activity.

Main Methods:

  • Employed single-molecule assays to directly monitor DNA loop extrusion (LE) dynamics.
  • Utilized fragments of the CTCF N-terminal region (NTR) containing specific amino acid motifs (YDF, KTYQR) to probe interactions with cohesin.
  • Assessed the impact of these motifs on cohesin's LE step cycles and directionality.

Main Results:

  • Identified two critical amino acid motifs in CTCF's NTR: YDF and KTYQR, which impede cohesin's DNA loop extrusion (LE).
  • The KTYQR motif completely abolished cohesin's LE activity.
  • The YDF motif hindered the completion of LE step cycles and induced unidirectional extrusion by enhancing STAG1-DNA binding.

Conclusions:

  • Two distinct motifs within CTCF's NTR, YDF and KTYQR, stall cohesin-mediated DNA loop extrusion (LE) through different yet synergistic mechanisms.
  • These findings reveal how CTCF utilizes specific motifs to modulate cohesin's activity, thereby shaping and regulating genome architecture.
  • Highlights the complex interplay between CTCF and cohesin in establishing higher-order chromatin structures.