current
TCPA: For many genes cis-acting elements located hundreds of kilobases away from the promoter region provide critical regulatory information, as exemplified by the dramatic consequences of mutations of such elements in humans. The 3D folding of the genome plays an essential role in regulating the communication between distant elements, and therefore contributes to the robustness and specificity of the transcriptional programs that control cell fate and function. Therefore understanding the molecular basis of the processes that organize the 3D arrangement of the genome and how they impact enhancer-promoter interactions resulting in specific gene expression levels will be of particular importance. Here we propose to identify cis-acting elements and chromatin features that physically organize the 3D conformation of genomic loci in order to fine-tune gene expression. For this purpose, we will develop a cross-disciplinary approach using advanced chromosomal engineering tools, live-imaging with high spatial and temporal resolution as well as computational modeling. We will generate high-resolution Hi-C maps of genomic regions in a large collection of mouse strains carrying local chromosomal rearrangements impacting defined genomic loci or mutations in key regulators of chromatin conformation. We will use these large, coherent datasets to improve predictive models of chromatin folding, and identify regions and elements orchestrating the specific conformations adopted by a locus. We will develop and perform live-cell imaging of enhancer-promoter interactions in different contexts, and use biophysical modelling of this process to identify the connections between structural dynamics and gene expression changes. Altogether, these detailed, functional analyses should provide novel insights into the molecular mechanisms that guide the 3D folding of the genome in different structures and their role in determining gene expression. We will conduct most of our studies in vivo, in the biological context where these different structures modulate enhancer-promoter interactions to control gene expression and cellular phenotypes. Consequently, our data will directly provide insights into the molecular and physiological consequences associated with altered 3D organization observed in human patients at the corresponding loci. Furthermore, we expect that our improved models of chromatin folding and enhancer-promoter communication will allow to better interpret current 3D maps and will open the way to better evaluate the consequences of structural variants that could be identified in human patients.