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.