Cutting Edge: Proper Orientation of CTCF Sites in Cer Is Required for Normal J{kappa}-Distal and J{kappa}-Proximal V{kappa} Gene Usage [CUTTING EDGE]

Ig locus contraction and V gene usage are controlled by Cer, a cis-acting sequence in the V–J intervening region. This effect is attributed to two CTCF-binding sites within Cer that are oriented toward the V gene region. However, the importance of Cer CTCF orientation in regulating VJ rearrangement is unknown. We used CRISPR/Cas9 editing to delete and invert Cer in murine Abl pro–B cell lines. This revealed that Cer orientation is critical because clones with either an inverted or deleted Cer element show skewing toward J-proximal V gene usage. However, only Cer deletion increased J-proximal V germline transcription, suggesting an insulating function of Cer. Lastly, circularized chromosome conformation capture interaction data show that Cer CTCF orientation regulates long-range interactions with inversion clones displaying fewer interactions with regions in the middle and distal parts of the V locus and more interactions to downstream regions compared with wild-type or deletion clones.

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