Immunoglobulin heavy (IgH) and light (IgL) chain variable region exons are assembled from V, D and J segments by V(D)J recombination, which is initiated by RAG1/RAG2 endonuclease (RAG) that introduces DNA double-stranded breaks (DSBs) between a pair of V, D, and J coding segments and flanking recombination signal sequences (RSSs). IgH V(D)J recombination is ordered, with D-JH joining occurring before appendage of a VH to a DJH intermediate in pro-B cells. In pre-B cells, a single-step VL-to-JL recombination event is invoked at IgL loci, with Ig kappa rearrangement usually preceding that of Ig lambda. The mechanisms of Ig V(D)J recombination, especially long-range VH-to-DJH and Vkappa-to-Jkappa recombination are still not fully understood. Recently, our work showed CTCF-binding elements (CBEs) immediately downstream of frequently rearranged VH-RSSs increase recombination potential of their associated VH far beyond that provided by RSS alone. This CBE activity becomes particularly striking upon the inactivation of IgH IGCR1 control element, which promotes DJH intermediate formation by insulting Ds, JHs, and recombination center (RC) from upstream VHs in a CBE-anchored chromatin loop. By developing and applying 3C-HTGTS, a new high-throughput chromosome conformation capture method that shows great advantages over classical 4C-seq in sensitivity and specificity, we found VH-associated CBEs promotes interaction with the RC. Based on these, we proposed a RAG chromatin scanning model for V(D)J recombination, in which VH CBEs stabilize interactions of D-proximal VHs first encountered by the DJH RC during linear RAG scanning on chromatin and thereby promote dominant rearrangement of these VHs by an unanticipated chromatin accessibility-enhancing CBE function. However, it is still not known if such chromatin scanning also happens on other antigen receptor loci and what the underlying mechanism is. Here, we will show our new findings on the roles of RAG chromatin scanning in Vkappa-to-Jkappa recombination at Ig kappa locus by multiple comprehensive approaches. Moreover, we will also discuss our most updated understanding of the mechanisms underlying RAG chromatin scanning using a novel and sophisticated approach. The potent mutagenic and oncogenic effects of aberrant RAG chromatin scanning at RAG “off-target” sites genome-wide will be also discussed.

Citation Format: Zhaoqing Ba, Suvi Jain, Jiazhi Hu, Frederick Alt. Elucidating the mechanisms that underpin RAG chromatin scanning in V(D)J recombination at antigen receptor gene loci [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B099.