DNA break and repair in programmed DNA elimination

Genome integrity is important for organisms as major changes to the genome are often associated with disease. However, some organisms undergo a physiological process of DNA loss known as programmed DNA elimination (PDE). In metazoans, PDE often occurs during early embryogenesis in all pre-somatic cells, generating a reduced somatic genome. However, the molecular mechanisms of PDE are not well understood. Among metazoans, PDE has been primarily studied in nematodes and recent findings suggest that it is widespread across the nematode clade. In nematodes, PDE results in DNA double-strand breaks (DSBs) that reproducibly fragment the genome. These breaks are healed with neotelomere addition, creating new chromosome ends. The best studied metazoan with PDE is the human and pig parasitic nematode, Ascaris, which is a robust biochemical model. More recently, Oscheius tipulae, a free-living nematode closely related to the model organism Caenorhabditis elegans, was discovered to undergo PDE, providing the first genetically tractable model to study DNA elimination in a metazoan. Using the strengths of each model we can decipher new insights into PDE and compare the mechanisms between phylogenetically diverse nematodes. Specifically, this work addresses when and where DSBs occur in the genome, how DSBs are processed before healing, and describe neotelomere addition at DSBs. We compare the DSB and healing processes in Ascaris and O. tipulae, describing the characteristics of motif-dependent and motif-independent PDE processes. In addition, we adapted a technique to specifically isolate eliminated DNA in Ascaris. This sample preparation allowed us to identify concerted DSBs occur during Ascaris PDE. Furthermore, the positions with the highest break frequency led to the identification of a motif potentially involved in regulating Ascaris PDE.