CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igk repertoire

Dynamic genome folding is important for V(D)J recombination at the
immunoglobulin kappa (Igκ) locus, which recombines Jκ and Vκ gene segments
across a 3.2 Mb region in both deletional and inversional orientations.
Chromatin loop extrusion and diffusion are considered two key mechanisms
underlying Igκ folding, but how they coordinate remains unclear.
Here we show that CTCF is a key regulator coupling loop extrusion and
diffusion during Igκ V-J rearrangement, promoting recombination in both
orientations across long genomic distances. Mechanistically, the CTCF
N-terminus promotes long-range loop extrusion that facilitates distal Vκ
usage by stabilizing cohesin against WAPL release, and also forms loop
barriers enabling chromatin diffusion for inversional Vκ joining. In CTCF
N-terminal-deficient B cells, defects in inversional Vκ joining are not
restored by WAPL depletion but are instead largely rescued by a
dCas9-blockade targeted to the Vκ-Jκ intergenic region, mimicking the CTCF
barrier. Our findings thus highlight how CTCF coordinates distinct
genome-folding mechanisms through its dual roles in cohesin stabilization
and extrusion barrier formation to ensure the generation of a
diverse Igκ repertoire.