Biogenesis and function of retrotransposon-derived circular DNA

ABSTRACT Retrotransposons are highly enriched in animal genome. Their activation can rewrite the host genetic information and fundamentally impact host biology. While developmental activation of retrotransposons can bring hosts benefits, such as against virus infection, uncontrolled activation promotes diseases or potentially drives aging. Despite their abundance and fundamental impacts on host physiology and pathology, the study of retrotransposons remains an underexplored area of biomedical research. Using new tools and biological systems developed by my team, in the long-term, we aim to characterize the retrotransposon replication cycle and explore the impact of their activation to the hosts under physiological and pathological conditions. Upon activation, retrotransposons use their mRNA as templates to synthesize double-stranded DNA for making new insertions in the host genome. While the reverse transcriptase encoded by them can synthesize the 1st- strand DNA, how the 2nd-strand DNA is generated remains largely unknown. Our recent studies on both Drosophila and mouse retrotransposons indicated that they hijack the alternative end-joining (alt-EJ) DNA repair process from the hosts for a circularization step to synthesize their 2nd-strand DNA. Strikingly, we found that only 10% of replicated retrotransposon DNA achieve new insertions, while 90% exist as extrachromosomal circular DNA (eccDNA). These results lead us to propose that alt-EJ plays a conserved function for retrotransposon DNA replication by driving a circularization step, and that this step dominantly manufactures retrotransposon eccDNA to impact on host biology. To test these hypotheses, we aim to characterize how alt-EJ mediates the circularization step for retrotransposon DNA replication (Aim 1), to investigate how retrotransposon eccDNA can generate genomic variation by integrating into the host genome (Aim 2), and to explore whether human retrotransposons also hijack alt-EJ pathway for eccDNA biogenesis (Aim 3). Collectively, our proposed research will broadly impact the field by identifying new mechanisms to understand the replication process of the most abundant genomic elements. Meanwhile, our work will elucidate how retrotransposon eccDNA could impact host genome by creating genomic variations. As such, our work will provide a new perspective to understand the process and consequence of retrotransposon life cycle.