UNRAVELING HUMAN T-CELL RECEPTOR JUNCTIONAL REGION SEQUENCES

Careful analysis of functional V delta 2-J delta 1 and V gamma 9-J gam ma 1.2 rearrangements of peripheral T-lymphocytes showed high frequenc ies of leucine and valine at a fixed position in the V delta 2-J delta 1 junctional regions. This phenomenon remained unnoticed in the numer ous published junctional regions for over several years. Because compa rable preferential motifs might also occur in junctional regions of ot her T-cell populations in health and disease, more precise analysis of junctional region diversity is needed. For this reason we describe ge neral guidelines for identification of the various elements in TcR jun ctional regions: D-gene-derived nucleotides (in case of TcR-beta and T cR-delta genes), P-region nucleotides, N-region nucleotides, and delet ion of nucleotides by trimming of the rearranged gene segments. In add ition, we summarized the known genomic germline sequences of rearrangi ng TcR gene segments, which are necessary for proper application of th e general guidelines. Subsequent analysis of the majority of published TcR junctional regions, allowed us to determine the composition and a verage insertion and deletion of nucleotides in genomic junctional reg ions. Because the protein junctional region instead of the genomic jun ctional region determines the actual specificity of TcR chains, the am ino acid composition of the protein junctional regions of different ty pes of TcR gene rearrangements was determined. This revealed some unex pected characteristics, such as the virtual absence of cysteine in all functional TcR junctional regions and increased or decreased frequenc ies of particular amino acid residues in specific TcR junctional regio ns. Application of the guidelines in combination with the summarized T cR germline sequences may contribute to uniformity in the analysis of junctional regions and may lead to important information concerning Tc R specificity.