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

Area of Science:

• Genomics
• Molecular Biology
• Immunology

Background:

• Dynamic genome folding is essential for V(D)J recombination at the immunoglobulin kappa (Igκ) locus.
• Chromatin loop extrusion and diffusion are key mechanisms for Igκ locus folding, but their coordination is not well understood.

Purpose of the Study:

• To elucidate the role of CTCF in coordinating loop extrusion and diffusion during Igκ V-J rearrangement.
• To understand how CTCF facilitates recombination in both deletional and inversional orientations across long genomic distances.

Main Methods:

• Investigated CTCF's role in Igκ V-J rearrangement using B cells with CTCF N-terminal deficiency.
• Utilized WAPL depletion and dCas9-blockade to assess the functions of CTCF in genome folding and recombination.

Main Results:

• CTCF couples loop extrusion and diffusion for Igκ V-J recombination, promoting both deletional and inversional joining.
• The CTCF N-terminus stabilizes cohesin for long-range loop extrusion and forms barriers for chromatin diffusion.
• Defects in inversional Vκ joining in CTCF-deficient cells are rescued by dCas9-blockade, not WAPL depletion.

Conclusions:

• CTCF is a key regulator coordinating genome folding mechanisms, including cohesin stabilization and extrusion barrier formation.
• CTCF's dual roles ensure efficient V(D)J recombination and the generation of a diverse Igκ repertoire.