Eukaryotic genomes likely contain up to hundreds of thousands of enhancers, but the functional principle of
these important elements is still poorly understood. The Ph.D. project aims at understanding the influence of
the genomic context on the specificity of enhancer – promoter interactions during early Drosophila
embryogenesis. Embryonic development is controlled by the complex regulation of gene expression, which
involves promoters and enhancers. Enhancers can be located either proximal or distal to their target promoter,
sometimes skipping intervening genes. The 3D proximity between promoters and enhancers seems to be
favoured by the spatial configuration of chromatin into Topologically Associating Domains (TADs). This led to
the notion that TADs constitute basic functional domains driving enhancer-promoter interactions. However,
the molecular mechanisms driving the interaction specificity between enhancers and promoters are still largely
unknown. To identify what might control enhancer-promoter specificity, the Twist (the master regulator of
mesoderm formation) locus has been systematically perturbed in Drosophila melanogaster using CRISPR/CAS9
technique. A number of transgenic fly lines have been generated where one of the enhancers of Twist is
located in different locations and/or different orientations and it has been assessed the impact of these
rearrangements during embryogenesis on transcription and chromatin organization using RNA-seq, 4C-seq and
3D DNA FISH. Taken together, these experiments will provide a better understanding of enhancer biology,
chromatin organization and transcription regulation during early Drosophila embryogenesis.
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