Unveiling the murine t-haplotype’s extent and emergence of diversity in MHC class II genes

Genes of the major histocompatibility complex locus that present pathogen peptides to T-Lymphocytes are among the most polymorphic genes in mammals. Within the major histocompatibility complex diversity is under positive selection and new alleles are generated by point mutations and recombination events. In some house mice (Mus musculus) however the major histocompatibility complex (called H-2) is part of the t-haplotype, a meiotic driver located on Chromosome 17 carried by 10 to 40 percent of the natural population. Meiotic drivers are selfish chromosomal arrangements defined by the deviation of Mendelian ratio of inheritance, meaning that they are over-proportionally transmitted to offspring. As such purifying selection on meiotic drivers is reduced and deleterious mutations can accumulate although outside of lethal alleles few non-synonymous mutations are observed. Additionally meiotic drivers often show strong linkage disequilibrium which is the result of reduced recombination between the wildtype chromo ome and the chromosome carrying the genetic driver often caused by structural variations between chromosomes such as inversions. In this thesis, the physical extent of the t-haplotype inversions is resolved using optical mapping at higher resolution than ever done before. Evidence for a fifth inversion in the t-haplotype of Mus musculus domesticus was found. Also the allelic diversity of the MHC class II gene H2Aa in t-haplotype individuals of the subspecies Mus musculus musculus and Mus musculus domesticus was described based on sanger sequenced exons. The degree of diversity found here indicates that recombination between the t-haplotype and the wildtype might play an important role in diversifying this H2Aa exon. Lastly, to uncover de novo meiotic recombination events within the H2Aa gene and the Prdm9 ZnF Array, which determines the placement of meiotic hotspots, Nanopore Sequencing was implemented. To identify the original template of sequenced amplicons the Primer ID as presented by Jabara et al., 2011 as included in the Primers for amplifying gene regions to be sequenced. However due to low coverage with Primer IDs no definite de novo recombination events could be defined, leaving the use of Primer IDs in Nanopore Sequencing up to discussion