Uncovering de-novo recombination events in H2-A and H2-E MHC Class II genes in wild mice (Mus musculus domesticus)

The MHC Class I and Class II loci mediate adaptive immunity in vertebrates and belong to one of the most polymorphic regions in the genome. Allele estimates for some genes are in the millions. In fact, the large number of alleles present in populations has made providing an evolutionary model that fully accounts for this exceptional diversity rather challenging. We argue for the reservoir model proposed for human MHC diversity. The reservoir model states that large pools of rare MHC allele variants are continuously generated by neutral mutational mechanisms. As these new variants can become important in the defense against newly-emerging pathogens, the reservoir model complements the selection-based models to fully account for the extensive diversity. In this study, we utilized sperm-typing approaches to uncover de-novo recombination events in H2-A and H2-E MHC Class II genes from several wild mice (Mus musculus domesticus). Further, we used the Primer ID barcoding strategy virtually identical to Jabara et al. (2011). We recovered 117 recombinant molecules across all samples. Forty-one percent of the recombinant template sequences represented CO events and fifty-nine percent represented NCO events. Data strongly supports the reservoir model of MHC diversity by meiotic recombination. Further, we also explore the influence of t-haplotype on recombination rates and whether recombination occurs in a PRDM9 dependent or independent fashion. However, due to inflation of template sequences due to extensive resampling, we are unable to provide conclusive results. Finally, we discuss possible experimental design improvements to the Primer ID barcoding strategy