N-nucleotide additions by Terminal deoxynucleotidyl Transferase do not protect against deletion of the D segment during VDJ recombination in T-cell receptors

Abstract

T-cell receptor (TCR) diversity is fundamental to the immune system's ability to recognise foreign antigens. TCRs are put together in a semi-stochastic process called V(D)J recombination, where the α-chain consists of a variable (V) and junction (J) gene segment, and the β-chain consists of a V, diversity (D), and J gene segment. During V(D)J-recombination one segment of each of these genes are recombined, with deletions by exonucleases and non template nucleotide additions by a protein called Terminal deoxynucleotidyl Transferase (TdT) occurring at the junctions of these segments. Prior research has shown that some abundant β chain sequences lack the D segment. We test their hypothesis that the absence of TdT may cause the deletion of the D segment. By comparing sequences of TdT knock-out and wild-type mice, we find that abundant β-chain sequences often have no D segment, but see no significant increase in the TdT knock-out group, suggesting that TdT does not protect against the deletion of the D segment. Additionally, our analyses revealed that V and J gene segment usage differs significantly between TdT knock-out and wild-type sequences, and that almost 60% of abundant wild-type sequences used either the TRBV1 or TRBV16 gene segment.