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Abstract

All animals begin their life from a single initial cell. A cascade of cellular transitions and proliferation events during embryonic development eventually gives rise to tissues and organs. Their functionality is highly dependent on the composition of cellular machines - proteins. Since majority of cells contain same genetic material, the regulation of how this material is used, in other words how genes are expressed, results in a specific protein composition in cells that is critical for their individual function and thereby the proper development of metazoan organisms. During my doctoral studies, I have focused my research efforts on understanding how gene expression is regulated by enhancers, non-coding elements that regulate spatiotemporal gene expression, thus acting as the decisive ‘controllers’ in the establishment of cellular identity during development. My interests revolve around two key topics in enhancer biology: How do specific transcription factors modulate enhancer activity, and what is their role in the formation of tissues such as mesoderm? What is the topological organization of enhancer-to-promoter interactions during development, and how do they relate to other regulatory features, such as the chromatin state? address these questions, I collaborated with experimentalists within the Furlong lab on three projects, each using embryonic development in Drosophila melanogaster as a model system: 1. Characterization of the recruitment of the repressive Polycomb complex (PhoRC) in a specific cell type during development; 2. Dissecting properties of enhancer to promoter interactions in two spatial (whole- embryo and mesoderm), and temporal (3-4h and 6-8h of development) contexts in the largest 4C-seq study up to date; 3. A description of more global chromatin topology, using high-resolution Hi-C data. Using extensive statistical analyses, I found that a significant portion of PhoRC binding sites overlap with mesodermal developmental enhancers, have strong association with other Polycomb proteins, and cause repression of both enhancer and gene activity. The topological studies revealed that these enhancers tend to form a vast amount of long-range interactions, even within the compact Drosophila genome. These interactions remain largely unchanged, even though the embryo undergoes severe morphological transitions from multipotency to cellular specification during these stages, and correlate with the occupancy of paused RNA Polymerase II. Taken together, these results have provided important new insights into how enhancer function, from the recruitment of transcription factors and their role in embryonic development, to the deciphering of the topological organization of chromatin in three-dimensional nuclear space.