CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning.

Abstract

RAG endonuclease initiates antibody heavy chain variable region exon assembly from V, D, and J segments within a chromosomal V(D)J recombination center (RC) by cleaving between paired gene segments and flanking recombination signal sequences (RSSs). The IGCR1 control region promotes DJ_H intermediate formation by isolating Ds, J_Hs, and RCs from upstream V_Hs in a chromatin loop anchored by CTCF-binding elements (CBEs). How V_Hs access the DJ_HRC for V_H to DJ_H rearrangement was unknown. We report that CBEs immediately downstream of frequently rearranged V_H-RSSs increase recombination potential of their associated V_H far beyond that provided by RSSs alone. This CBE activity becomes particularly striking upon IGCR1 inactivation, which allows RAG, likely via loop extrusion, to linearly scan chromatin far upstream. V_H-associated CBEs stabilize interactions of D-proximal V_Hs first encountered by the DJ_HRC during linear RAG scanning and thereby promote dominant rearrangement of these V_Hs by an unanticipated chromatin accessibility-enhancing CBE function.