Activity of Endogenous L1 Retrotransposons in Human Embryonal Cells

Recent high throughput studies have led to the discovery of de novo L1 retrotransposition in malignant somatic cells, as well as large numbers of novel insertions, many of which are highly active in cell culture assays. These data suggest that L1 elements are robustly active, undergoing extensive diversification in contemporary human genomes. Despite this there is little direct evidence of endogenous L1 retrotransposition in the human germline or early embryogenesis: data from very rare disease causing insertions is indirect, subject to strong acquisition bias, and is often equivocal with respect to the origin of the insertions. For L1s to be evolutionarily successful they must retrotranspose during early human development or in the germline, in order to transmit copies to the next generation. The purpose of this thesis was to develop sensitive and yet robust methods to screen human embryos and embryonic cell models for de novo full-length endogenous L1 insertions. We developed a new high throughput sequencing technique, which was able to recover single molecule retrotransposition events. Based on this technique we identified 172 candidate novel L1 insertions in a total of three human embryos, represented by whole-genome amplified DNA of individually dissected blastomeres and the remaining blastocyst tissue. 57 of these insertions are potentially genuine de novo endogenous L1 insertions. Moreover, we have identified a candidate germline specific L1 insertion from a healthy adult donor. Therefore, this study has detected candidate de novo L1 retrotransposition events in human embryos and germlines, using an approach that enables complete validation and characterization of the insertions, despite operating at the single molecule and single cell level. We consider this technical innovation will be most significant in the ongoing dissection of how L1, the dominant human transposon, is actively driving the evolution of modern human genomes.