Nucleotide Sequence Analysis of 77.7 kb of the Human V[beta] T-Cell Receptor Gene Locus: Direct Primer-Walking Using Cosmid Template DNAs

Abstract

The nucleotide sequence of 77.7 kb from the human T-cell receptor [beta]-chain locus was determined directly from three overlapping cosmid clones using the primer-walking approach. Computer-aided analyses of this sequence reveal the presence of at least 11 genic regions that are closely related to the human T-cell receptor [beta] variable region (TCRBV) gene family. These include five germline sequences that have previously been determined, V[beta]21.2, V[beta]8.1, V[beta]8.2, V[beta]8.3, and V[beta]16, and four whose sequences have partially been determined at the mRNA level, V[beta]6, V[beta]23, V[beta]12.2, V[beta]24. The two remaining V[beta] Tcr-related sequences have eluded discovery by cDNA and RT-PCR cloning and genomic blot hybridization methods. These two V[beta] Tcr-related genes lack >75% nucleotide sequence identity with any other V[beta] Tcr gene member and therefore, by convention, are referred to as new subfamily members V[beta]25 and V[beta]26. This lack of shared identity with other subfamily members explains why they were not detected by hybridization. The promoter regions of these V[beta] Tcr genes contain the conserved Tcr decamer element located between 80 and 110 bp 5' of the translation start site, generally near a putative TATAA promoter element. Our sequence analysis also reveals that a 3.3-kb duplication unit was involved in the recombination event that produced the closely related V[beta]8.1 and 8.2 gene subfamily members. This sequenced region of the V[beta] locus contains an average number of repetitive DNA elements (21 Alu, three L1, three MER, and three retrovirus-related elements).