Identification of Gene Conversion Events in Horse IGHV Suggests Preferential Hotspots for Diversification

The humoral immune response relies on a diverse antibody repertoire, which is generated through V(D)J recombination in B lymphocytes. This repertoire is then expanded further by processes such as somatic hypermutation, gene conversion and class-switch recombination, which are primarily mediated by activation-induced cytidine deaminase (AID). Gene conversion is the main generator of diversity in immunoglobulin heavy chains (IGHVs) in species such as chickens and rabbits, but it has not been widely studied. As the equine IGHV repertoire is limited to just three functional genes, we examined gene conversion events in the horse's IGHV repertoire to determine its role in diversifying the equine antibody response. Gene conversion events were identified using a modified version of BrepConvert to improve the output resolution. These events were found in 6.9% of immunoglobulin sequences. The results showed that most gene conversion events occurred at the beginning of framework region 1 (FR1) and in the complementarity-determining region (CDR) 2, suggesting a preferential region. The most frequently used pseudogenes were IGHV4-35, IGHV4-53, and IGHV4-38, whereas the functional genes with the highest number of gene conversion events were IGHV4-21, IGHV4-22, and IGHV4-29. We also identified a potential role of non-B DNA conformations, flanking regions, and ZNF707 in the occurrence of gene conversion events. These findings suggest that gene conversion events significantly contribute to the diversity of the equine antibody repertoire by targeting specific regions within IGHV.