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.