Statistical inference reveals the role of length, GC content, and local sequence 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 TCRβ 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,

SUBMITTER: Russell ML 

PROVIDER: S-EPMC10212571 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature