CTCF N-terminal Domain Regulates Clustered Protocadherin Gene Expression by Enhancing Cohesin Processivity [ChIP-seq]

CTCF structures 3D genome folding by anchoring or forestalling cohesin loop extrusion, but the exact mechanism remains obscure. Here, using clustered protocadherins (cPcdh) as model genes, we report that CTCF stabilizes or facilitates cohesin loop extrusion by enhancing its processivity. Specifically, we show that, compared with the Pcdh alpha and gamma clusters, the Pcdh beta cluster is greatly affected upon CTCFY226A/F228A mutation in the N-terminal domain. Given the long-range distance of the Pcdh beta cluster from the distal enhancer, this finding has interesting implications in CTCF regulation of cohesin processivity along the linear chromatin during DNA loop extrusion. In particular, the effect on cohesin processivity upon CTCFY226A/F228A mutation is conspicuously similar to that of WAPL overexpression, demonstrating that, contrary to the general view of blocking or forestalling cohesin, CTCF actually enhances or facilitates cohesin loop extrusion. Here, through CRISPR editing of the YDF motif - the key cohesin interacting moiety - of the CTCF N-terminal domain (NTD) in N2a cells in vitro and in mice in vivo, in conjunction with RNA-seq, ChIP-seq, 4C, and Hi-C analyses, we found that members of the Pcdh beta cluster are highly susceptible to the perturbed cohesin processivity owing to their distal genomic arrangement relative to the downstream super-enhancer region. Our data broaden the molecular logic that generates Pcdh isoform diversity required for neural circuit assembly via a unique 3D genome organization. Please note that each processed data generated from both replicates is linked to the corresponding rep1 sample records.