Studying genomic and transcriptomic profile of MEF, MEF transdifferentiated into iDA cells and MEF transdifferentiated in presence of LINE1 inhibitor Lamivudine 3TC.

Recent reports showed that LINE1(L1) repetitive elements are expressed in a tissue specific manner and significantly coincide with major regulatory elements like enhancers and promoters. Further, it was recently reported that full-lenght L1 are expressed in iPSC and an engineered L1 can retrotraspose much better in iPSC than in somatic cells. We hypothesized that retrotrasposition activity may play a fundamental role for efficient somatic cell reprogramming allowing the switch to a de novo imposed gene expression program. The transdifferentiation of embryo fibroblasts (MEF) into induced dopaminergic neurons (iDA), by the overexpression of three neural transcription factors (Nurr1, Lmx1a, Ascl1), represents a suitable model for studying the involvement of LINE1 in cell fate decision. To characterize the function of L1 elements, we challenged the retrotransposition reaction by Lamivudine treatment during the entire transdifferentiation process. This experiments showed a strongly reduced reprograming efficiency of treated cells compared to the control, directly attributable to the L1 retrotransposition impairment.To verify that new L1 insertions in the genome are targetted to “hot” loci relevant for the tissue specific transcriptional regulation we performed experiments of Whole Genome Sequencing and de novo assembly. Genomic data were integrated with Total RNA deep sequencing to control how L1 retrotransposition affect the global genome landscape.