The Mechanism, Regulation and Evolution of V(D)J Recombination

Abstract

During lymphocyte development, diverse primary repertoires of antigen receptors are created by V(D)J recombination. In the first phase of the V(D)J recombination reaction, double-stranded (ds) DNA breaks are generated by the recombinase machinery made up of the lymphocyte lineage-specific proteins recombination-activating gene (RAG) 1 and RAG2 (collectively, RAG), which are aided by the ubiquitously expressed DNA-binding/bending protein, high mobility group box protein 1 (HMGB1). Extensive mechanistic insights into the V(D)J recombination cleavage phase have been obtained from structures of RAG bound to substrate DNA. The second phase of V(D)J recombination, end-processing and end-joining, is carried out by DNA repair proteins of the non-homologous end joining (NHEJ) DNA repair pathway. Various mechanisms are associated with NHEJ diversify V(D)J junctions, while the lymphocyte-specific TdT factor further diversifies junctions via N-region addition. V(D)J recombination is tightly regulated during lymphocyte development. RAG proteins initiate the reaction from their location in recombination centres in various antigen receptor loci. Chromatin loop extrusion then presents RAG with chromatin containing substrate segments embedded within megabase DNA segments. Chromatin loop extrusion facilitates various mechanisms, including transcription, to mediate chromatin accessibility of particular variable region gene segments by increasing their interaction with recombination centre-bound RAG during scanning. The loop extrusion mechanism confines RAG activity to loop domains containing antigen receptor loci, thereby dampening aberrant V(D)J recombinase activity that can promote oncogenic chromosomal translocations. In this chapter, we consider in detail our knowledge of the V(D)J recombination reaction, including the biochemistry of the cleavage reactions, activities and evolution of the RAG proteins and regulation of recombination in the context of chromatin loop extrusion.