Statistical inference reveals the role of length, breathing, and nucleotide identity in V(D)J nucleotide trimming

Abstract To appropriately defend against a wide array of pathogens, humans somatically generate highly diverse repertoires of B cell and T cell receptors (BCRs and TCRs) through a random process called V(D)J recombination. Receptor diversity is achieved during this process through both the combinatorial assembly of V(D)J-genes and the junctional deletion and insertion of nucleotides. While the Artemis protein is often regarded as the main nuclease involved in V(D)J recombination, the exact mechanism of nucleotide trimming is not understood. Using a previously-published TCR β repertoire sequencing data set, we have designed a flexible probabilistic model of nucleotide trimming that allows us to explore various mechanistically-interpretable sequence-level features. We show that local sequence context and the capacity for sequence-breathing, together, can most accurately predict the trimming probabilities of a given V-gene sequence. This model suggests that double-stranded DNA needs to be able to “breathe” for trimming to occur, and provides evidence of a sequence motif that appears to get preferentially trimmed, independent of breathing. Further, we find that the inferred mechanistic coefficients from this model provide accurate prediction for V- and J-gene sequences from other adaptive immune receptor loci. These results refine our understanding of how the Artemis nuclease may function to trim nucleotides during V(D)J recombination and provide another step towards understanding how V(D)J recombination generates diverse receptors and supports a powerful, unique immune response in healthy humans.