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Epigenetic control and impact of mammalian retrotransposons in pluripotent genomes

Final Report Summary - EPIPLURIRETRO (Epigenetic control and impact of mammalian retrotransposons in pluripotent genomes)

Although more than half of the human genome has been generated by the activity of Transposable Elements (TEs), and sporadically new TE insertions can be mutagenic, it is remarkable that our genome continue to expand in size due to the activity of TEs. In humans, only TEs from the “copy and paste” class, termed retrotransposons, continue to be active. These elements move using a copy and paste replicative mechanism, increasing the size of our genome overtime, and are known as LINE and SINEs, depending on their size. Long elements (LINE-1 or L1) are autonomous TEs in our genome, which are also responsible to mobilize short elements (SINEs as Alu elements). In humans, most heritable new L1 insertions seem to occur during early embryogenesis, which implies that our pluripotent genome is the substrate for new L1 insertions. Despite their abundance, we know very little about their regulation and impact.
EPIPLURIRETRO aimed to learn more on the regulation and impact of new L1 insertions in pluripotent genomes. Our research has revealed the presence of an active battle between LINEs and our pluripotent genome, and we have characterized a new pathway that sense new L1 insertions and epigenetically silence the new L1, to avoid further rounds of mobilization. Using a combination of genomic, genetic and biochemical methods, we have analysed how this L1-silencing works, which reveal a bi-modal recognition system to silence L1 insertions: initiation and maintenance. Furthermore, we have identified new genes that specifically control L1 expression in our pluripotent cells, which in essence form part of the ongoing battle between active LINE-1s and our heritable genome.
Beside the characterization of the L1-silencing pathway in pluripotent cells, within EPIPLURIRETRO we have dissected whether epigenetic modifications linked to new L1 insertions can have a phenotypic impact in cells carrying new silenced L1 insertions. To do that, we have developed new systems to study the mobilization of LINE-1s in cultured cells, allowing generating tag and untagged L1 insertions using DNA recombination. Notably, the untagged new L1 insertions are very similar to endogenous L1 insertions, which has allowed us to infer the phenotypic impact of epigenetic alterations induced by the new L1 insertion in the insertion site of pluripotent cells. Using chromatin immunoprecipitation (ChIP) and other molecular methods, we have demonstrated that, occasionally, a new L1 insertion can be mutagenic because the epigenetic modifications induced by the new L1 insertion in pluripotent cells can spread to the flanking genome of the cell with the new L1 insertion. Thus, these data revealed that new L1 insertions in pluripotent cells could act as epimutagens, which is a new concept in human biology.