V(D)J recombination is a developmentally regulated process by which germline variable (V), diversity (D) and joining (J) gene segments are assembled to provide T and B lymphocytes highly diverse antigen-specific receptor repertoires.

Despite the longstanding correlation between transcription and V(D)J recombination, it is unknown whether transcription can direct recombinase targeting. Here, we have analyzed the functional role of transcription in recombination through the generation of a transcription terminator and its introduction in the murine Tcra locus. Targeted introduction of the terminator downstream of Jα56 effectively blocked transcription initiated at upstream promoters, and suppressed Vα to Jα recombination and chromatin remodeling at downstream Jα segments. The transcriptional blockade also derepressed cryptic Jα promoters. Our results reveal two key roles for transcription in Tcra locus regulation. Transcription increases recombination of Jα segments located within several kilobases of a promoter, and prevents activation of downstream promoters through transcriptional interference. These influences promote an ordered progression of Tcra locus recombination events and selection of a robust Tcra repertoire.

Noncoding transcription of the eukaryotic genome is widespread but its functional significance is largely unknown. The TEA promoter in the murine Tcra locus generates transcripts that extend across the 65 kb Jα array. Here, we have analyzed the significance of noncoding TEA transcription in the regulation of the Tcra locus through the targeted introduction of the transcription terminator downstream of TEA. We demonstrate that noncoding transcription driven by this promoter can instruct both positively and negatively the activity of downstream Jα promoters, and can similarly instruct Jα chromatin structure and recombination events. TEA transcription activates promoters associated with relatively proximal Jα segments and stimulates acetylation and methylation of histones and accessibility in this region. In contrast, at more distal locations TEA transcription inhibits promoter activity through transcriptional interference and suppresses both histone acetylation and methylation, and accessibility. In combination these effects target initial Vα to Jα recombination events to TEA-proximal Jα segments and promote the ordered usage of the Jα array. The ability of TEA transcription to coordinate the activity of multiple downstream promoters maximizes the biological potential of the Jα array and diversifies the Tcra repertoire.