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

## TL;DR

The CTCF protein helps organize the genome to enable diverse antibody production by controlling chromatin structure during gene rearrangement.

## Contribution

CTCF is shown to couple loop extrusion and diffusion mechanisms to regulate Igκ locus recombination.

## Key findings

- CTCF's N-terminus stabilizes cohesin and promotes long-range loop extrusion.
- CTCF forms loop barriers that enable chromatin diffusion for inversional Vκ joining.
- Defects in inversional joining are rescued by dCas9-blockade mimicking CTCF barriers.

## Abstract

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 locus 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.

Coordinated gene segment rearrangement across a long genomic distance is essential for antibody gene production, but how this is regulated at the chromatin level is still unclear. Here the authors show that an architectural protein, CTCF, modulates both chromatin loop extrusion and diffusion to enforce diverse Vκ gene segment utilization for a diverse Igκ repertoire.