Illuminating the dynamics of transcription and chromatin at the exit from mitosis

In spite of intense investigations, it remains unclear whether and how the interaction between promoters and distant enhancers has an instructive role in transcription. I will tackle this question by tracking the spatial and temporal dynamics of gene regulatory sequences alongside nascent transcription during the critical biological event that is the mitosis-to-interphase transition in live cells. During mitosis, chromatin undergoes a massive reorganization, resulting in the loss of long-range interactions, the displacement of transcription factors, and a global reduction in transcription. The re-establishment of interphase gene expression programs is essential for the maintenance (or a chance for the change) of cell identity; however, the molecular mechanism of such re-establishment is an unsolved biological problem. Previous studies, largely relying on fixed cells and next-generation sequencing technologies, have not captured the dynamic nature of these events. I will use state-of-the-art genome engineering and live imaging technologies in proliferating mouse embryonic stem cells to simultaneously monitor the movement of regulatory sequences and the re-initiation of transcription at key pluripotency genes at the exit from mitosis, as well as test the role of mitotically-retained transcription factors. This project, termed DynaMitE, will address the burning question of how genome folding influences transcription within a physiological context of transcription re-activation, and will uncover mechanistic insights into the restoration of interphase gene expression with unparalleled temporal resolution in single cells.Importantly, by achieving the objectives of DynaMitE within the host laboratory, I will complement my expertise in genomics and developmental biology with advanced skills in cutting edge microscopy, image analysis and a biophysical lens on gene regulation, shaping the profile of the future group leader I aspire to be.