Understanding the evolutionary origins of genome structural novelty in mouse

During evolution, each lineage follows its own independent path of accumulating genome variation. Variation exists at both sequence and structural level - the latter representing dramatic changes in the organisation of the genome. This structural variation is encompassed by the term chromosomal rearrangements (CRs). It can take many forms such as inversions, translocations, fissions or fusions. Chromosomal rearrangements can have profound consequences both for fertility at the individual level and for inter-individual reproductive compatibility. Understanding how CRs arise and spread within the population is thus pivotal to understanding multiple areas of reproductive and evolutionary biology, from individual fertility through to speciation. Formation of CRs can be described by the Integrative Breakage Model - generation of CRs requires the formation of double-strand breaks (DSBs) during gamete production, followed by rejoining of loci that are physically adjacent within the nucleus. In this thesis, I address this element by studying the genetic, and epigenetic contexts of DSBs occurring in spermatogenesis, in combination with the 3D organisation of chromatin in male germ cells and show that this explains the locations of evolutionary breakpoint regions throughout rodent evolution. Once CRs are formed, selective dynamics will subsequently determine whether they go to fixation or not. An understudied aspect of this is the potential for "drive", in which genetic or epigenetic factors bias the meiotic process and lead to non-Mendelian inheritance of CRs from heterozygous carriers. In this thesis, I address this element by investigating the genetic and epigenetic effects at play in male mice heterozygous for a Robertsonian chromosome fusion reported to show non-Mendelian inheritance.

Key findings:

• EBRs are associated with DSBs formed during spermiogenesis and not with meiotic DSBs.

• Spermatid DSBs are associated with specific chromatin state changes during spermatogenesis, and with predicted non-B DNA structures that may regulate DNA tension during sperm head compaction.

• In the Rb6.16 fusion model I identified a range of non-synonymous gene variants linked to the fusion breakpoint, which may explain the reported transmission skewing.

• Unexpectedly, I found no evidence for chromatin silencing in the vicinity of the Robertsonian breakpoint(s), indicating that Robertsonian fusions may be regulated differently to other structural variants during spermatogenesis.