Fig. 7. Working models illustrating CTCF as a key factor converging long-range loop extrusion and diffusion to enable diverse Vκ recombination.

(a) Roles of the CTCF N-terminus in Igκ recombination. In wild-type cells, CTCF establishes loop barriers that facilitate diffusion, promoting Jκ joining with proximal Vκs in both deletional and inversional orientations. The most critical barriers are likely the Cer and Sis elements, which prevent direct Jκ-to-Vκ extrusion and promote short-range diffusion. For simplicity, only the deletional joining is illustrated for proximal Vκ region (I, II). Additionally, CTCF is important for cohesin processivity, which supports middle and distal Vκ joining (III, IV). In CTCF-Nm cells, CTCF cannot form effective loop barriers, resulting in Vκ joining occurring mainly through linear loop extrusion, which favors deletional joining (V) and suppresses inversional joining (VI). Furthermore, frequent removal of cohesin by WAPL compromises middle and distal Vκ joining (VII). Panel VIII shows enlarged views illustrating how the CTCF N-terminus enables the Cer and Sis elements to function as polar barriers blocking extrusion from the Vκ and Jκ regions, respectively, thereby enforcing diffusion. This function is disrupted by the CTCF-Nm mutation, resulting in direct Vκ-to-Jκ extrusion. (b) Illustration showing that WAPL depletion in CTCF-Nm cells facilitates long-range direct Jκ-to-Vκ loop extrusion, rescuing distal deletional (I) but not inversional (II) Vκ joining. (c) Illustration showing that the dCas9-SunTag blockade targeted to the Vκ-Jκ intergenic region functions as a loop extrusion barrier, rescuing Vκ recombination in both deletional (I) and inversional (II) orientations across the locus.