T cell receptor V alpha gene segment with alternate splicing in the junctional region

The locus encoding mouse TCR-alpha chain includes approximately 100 V alpha gene segments that can be organized in about 20 structural subfamilies. Southern blot analysis of a T cell line derived from the BALB/c strain, M5T, has indicated that both alpha loci were rearranged, as assessed by the deletion of the delta locus, and that the V alpha gene segment involved in one of the rearrangements did not belong to any of the V alpha subfamilies already described. Transcripts of TCR-alpha chains from the M5T line were cloned after cDNA synthesis and anchored-polymerase chain reaction, revealing a V alpha gene segment of an as yet unidentified subfamily, V alpha 5T. Molecular cloning of germ-line V alpha 5T gene segments has shown that this subfamily contained two members, one of them being a pseudogene. The two members were located to each extremity of the alpha locus associated with a member of the V alpha 13 and V alpha BWB subfamilies. Analysis of transcripts bearing the V alpha 5T gene segment in the M5T line as well as in thymocytes has revealed that J alpha are frequently absent. This is due to an alternate donor splice site generated at the V alpha 5T-J alpha junction that leads to a splicing from the end of V alpha 5T to C alpha instead of the J alpha to C alpha conventional splicing. The impact of J alpha spliced-out transcripts on the allelic exclusion process is discussed.