Chromatin boundary permeability is controlled by CTCF conformational ensembles.

Area of Science:

• Molecular Biology
• Genomics
• Biophysics

Background:

• CCCTC-binding transcription factor (CTCF) and cohesin complex are crucial for genome architecture, forming loops and topologically associating domains (TADs).
• The precise mechanisms linking CTCF's dynamic behavior to its role as a cohesin barrier remain incompletely understood.

Purpose of the Study:

• To investigate the intrinsic dynamics of CTCF-DNA complexes and their role in genome organization.
• To elucidate how CTCF's molecular flexibility influences cohesin-mediated loop extrusion and TAD boundary formation.

Main Methods:

• Integrated experimental (single-molecule accessibility and sequencing) and computational approaches.
• Biochemical dissection of cohesin components, including the PDS5 protein.

Main Results:

• Individual CTCF-DNA complexes exhibit intrinsic mobility, facilitating cohesin capture during loop extrusion.
• CTCF dynamics are modulated by DNA sequence, methylation, and nucleosomes, enabling a single-stranded DNA binding state.
• PDS5 remodels CTCF dynamics, enhancing its mechanical stability on DNA and regulating loop extrusion.

Conclusions:

• The conformational dynamics of CTCF are a fundamental regulatory property linking molecular motions to large-scale genome organization.
• CTCF's intrinsic flexibility provides a kinetic mechanism for establishing and regulating TAD boundaries.