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

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(H)s, and RCs from upstream V(H)s in a chromatin loop anchored by CTCF-binding elements (CBEs). How V(H)s access the DJ(H)RC 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(H)s first encountered by the DJ(H)RC during linear RAG scanning and thereby promote dominant rearrangement of these V(H)s by an unanticipated chromatin accessibility-enhancing CBE function.