Leveraging natural and directed evolution to dissect the functional consequences of sequence variation in human L1 retrotransposons

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PROJECT SUMMARY Transposable elements have generated the majority of the sequence in the human genome, and all of human biology has evolved in the ever-present DNA, RNA, and protein made by these self-replicating pieces of selfish DNA. The replication of transposable elements constitutes a major source of new mutations in humans which drive genome instability and a variety of genetic diseases. Our group previously discovered the rapid evolution of several restriction factors of Long Interspersed Element-1 (L1), the endogenous retroelements most active in humans. This pattern of evolution suggests that L1s have evolved to evade these restriction factors, driving rapid host evolution to keep pace. However, it is unknown how sequence variation in L1s impacts their ability to evade and replicate in the presence of host restriction factors. We are specifically interested in understanding – have transposable elements evolved to evade the defense mechanisms of the human genome? What are the mechanisms of transposable element evasion? What are the consequences to human health of evasive transposable elements replicating at times and places they are normally repressed? To answer these questions, our lab employs non-traditional combinations of approaches including retrospective analyses of genomes to understand what has happened and prospective experiments to ask what could happen. We propose to leverage the lab’s recently generated, diverse panel of more than 130 young human L1s to search for variation in the ability of L1s to replicate in the presence of otherwise effective host restriction factors. This variation could indicate adaptation of an L1 to evade host restriction or adaptation of the host to restrict evasive L1s. In addition to this retrospective analysis of evolutionary history, we propose to ‘speed up’ evolution by building an in vitro evolution system to select for L1s that evade a defined restriction factor. Comparison of these historical and prospective evolutionary approaches will help us decode the selective pressures that drove L1 and human evolution. This research will address a fascinating basic science question about the mechanisms of L1 evolution in the face of the host innate immune system with impact on our understanding of sporadic autoimmune diseases without a clear genetic contribution. Our lab combines a dedication to mentorship and scientific outreach with effort to build a communicative and accommodating space to enable creative, daring science. Our diverse and experienced team of scientists integrates expertise in comparative genomics, genome evolution, L1 biology, in vitro evolution, and protein evolution and function to bring an evolution-driven approach to the proposed projects. With our record of pushing conceptual and technical boundaries to bring new understanding to the fields of protein evolution and restriction factor biology, our team is uniquely poised to bring about a new understanding of L1 evolution and biology with implications for genome evolution and numerous disease states with clear L1 involvement. (30 lines)