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 bar..., , # CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igk repertoire

Dataset DOI: [10.5061/dryad.2z34tmq0n](https://doi.org/10.5061/dryad.2z34tmq0n)

## Description of the data and file structure

This data was collected with the Attune Cytpix Flow Cytometer. In short, Rosa26-OsTIR1 and untreated and 1 uM 5-Ph-IAA treated Wapl-AID2 v-Abl pro-B cells were collected at indicated time points and cell cycle stages, spun down, PBS washed once, and resuspended in PBS with 2.5% FBS prior for flow cytometry analysis.

### Files and variables

#### File: flow_cytometry_raw_data.zip

**Description:** This .zip file contains the wild type and experimental .fcs files at the indicated time points during 5-Ph-IAA treatment and the subsequent G1 arrest of samples as previously described in the data description. Each file within the zip file is named according to the genotype, treatment, or non-treatment with 5-Ph-IAA, and timepoint of experiment, including the final G1 arrested ...,