CCCTC-binding factor (CTCF) and cohesin shape the genome into loops and topologically associating domains (TADs), yet how CTCF dynamics govern cohesin function and TAD regulation remains unclear. Using integrated experimental and computational approaches, we show that individual CTCF-DNA complexes are intrinsically mobile over distances and timescales compatible with cohesin loop extrusion, driven by dynamic rearrangements of zinc-finger (ZF) domains. Genome-wide single-molecule accessibility and sequencing analyses reveal that these dynamics occur in cells. This intrinsic flexibility is modulated by DNA sequence, methylation, and nucleosome positioning, and enables a previously uncharacterized single-stranded DNA-binding state. Through biochemical dissection of cohesin components, we find that PDS5—a negative regulator of loop extrusion—remodels ZF dynamics and imparts exceptional mechanical stability. In doing so, PDS5 may facilitate CTCF-cohesin interaction and help explain how they synergize to reinforce and regulate TAD boundaries. Our findings identify transcription-factor conformational dynamics as a fundamental regulatory property that can transform local, base-pair-level motions into chromosome-scale rearrangements.
Rudnizky et al. (Sun,) studied this question.