Tcrd Rearrangement Redirects a Processive Tcra Recombination Program to Expand the Tcra Repertoire

Abstract

Adaptive immunity depends on diverse T cell receptor repertoires generated by variable, diversity, and joining (V[D]J) recombination. Here, we define the principles by which combinatorial diversity is generated in the murine Tcra repertoire. Tcra and Tcrd gene segments share the Tcra-Tcrd locus, with interspersed V_α and V_δ segments undergoing V_δ-D_δ-J_δ rearrangement in CD4^-CD8^- thymocytes and then multiple rounds of V_α-J_α rearrangement in CD4⁺CD8⁺ thymocytes. We document stepwise, highly coordinated proximal-to-distal progressions of V_α and J_α use on individual Tcra alleles, limiting combinatorial diversity. This behavior is supported by an extended chromatin conformation in CD4⁺CD8⁺ thymocytes, with only nearby V_α and J_α segments contacting each other. Tcrd rearrangements can use distal V_δ segments due to a contracted Tcra-Tcrd conformation in CD4^-CD8^- thymocytes. These rearrangements expand the Tcra repertoire by truncating the V_α array to permit otherwise disfavored V_α-J_α combinations. Therefore, recombination events at two developmental stages with distinct chromatin conformations synergize to promote Tcra repertoire diversity.