Junctional sequences of fetal T cell receptor β chains have few N regions

Abstract

T cell receptors (TCRs) and immunoglobulins (Igs) derive a large fraction of their repertoire from diversity generated at the junctions of the V, D, and J coding segments. This diversity is derived both from the random deletion of nucleotides from the ends of coding regions and from the subsequent addition of nontemplated N region nucleotides. While the vast majority of TCRs and Igs from adult mice have N regions, <5% of both TCR-γ/δ and Ig from fetal and neonatal mice have N regions. This study analyzed the ontogeny of junctional diversity of TCR-α/β. Genomic DNA or Cβ-primed cDNA was prepared from thymocytes of mice at varying stages in ontogeny, and the rearranged Vβ8 or Vβ5 sequences were amplified by polymerase chain reactions. Sequencing of the Vβ-Dβ-Jβ junctions showed few N regions early in ontogeny, although the fraction of sequences with N regions exceeded that previously reported for Ig and for TCR-γ/δ N regions were found in 13% of Vβ junctional sequences from day 18-19 fetal thymocytes, 33% of sequences from newborn thymocytes, 76% of sequences from day 4 postnatal thymocytes, and 88% of sequences from 5-wk-old thymocytes. In addition, nonrandom usage of the Dβ and Jβ segments was observed in both fetal and adult TCR sequences. While the usage of each of the six Jβ2 segments was different, the same pattern of usage was seen regardless of whether Dβ1 or Dβ2 was used, suggesting that a factor controlling the rate of usage of each J segment is intrinsic to the J gene itself. Since TCRs derive so much of their diversity from N regions, the relative paucity of N regions in fetal α/β T cells would create a fetal TCR-α/β repertoire that would be quite different from, and smaller than, the adult repertoire. The lack of N regions might be predicted to limit the range of affinities of TCR-MHC + peptide interactions, which may have important consequences for positive and negative selection of fetal and newborn T cells.