Abstract
The genome of eukaryotic cells exhibits a highly hierarchical three-dimensional organisation. Among these levels of compartmentalisation, topologically associating domains (TADs) are regions rich in chromatin interactions and are involved in gene regulation. These domains must remain intact to maintain the physical proximity between gene regulatory elements such as enhancers and promoters, which is essential for precise gene expression. Disruption of enhancer-promoter communication can lead to aberrant gene expression, contributing to diseases including cancers and genetic disorders. Thus, the enhancer-promoter interaction is critical for sustaining normal cellular functions and for responding to developmental and environmental cues. The initial objective of my thesis project is to study the complex mechanisms underlying enhancer promoter interactions, chromatin conformation, and gene expression profiles in different cell types. To address these questions, the two studies presented in this manuscript were conducted on two different types of biological samples: the pupal leg and the adult brains of Drosophila melanogaster. Part of my thesis project focused on the development and application of Hi-M (an imaging technique that reconstructs chromatin conformation at the single-cell level) to study the regulation of gene expression by enhancerpromoter interactions. The results chapter of this manuscript is divided into a secondary project and a primary project. Both studies examine the role of chromatin structure in gene expression regulation within different tissues of Drosophila melanogaster. In the study by Denaud et al. (2024), we explore how a loop between two Polycomb response elements (PRE), located at the dac gene, influences enhancer-promoter interactions and transcription. We demonstrated that the PRE loop at the dac locus acts as a structural element that restricts and specifies communication between enhancers and promoters, shedding light on the complex regulatory mechanisms involved in gene expression control. On the other hand, my primary project explores the link between genome conformation and gene expression in the adult Drosophila brain. During my thesis, I developed tools to detect genome conformation and identify enhancer-promoter interactions specific to different types of neurons in the adult Drosophila brain. I focused particularly on studying the chromatin conformation of genomic regions that include genes involved in memory formation. By examining enhancer-promoter interactions and the chromatin folding patterns in Kenyon cells, my work complements the results of Denaud et al. (2024) by providing insights into the broader regulatory networks involved in a differentiated tissue. The exploration of differential enhancer-promoter interactions and the study of chromatin conformation that we conducted should contribute to a better understanding of how chromatin conformation, such as the PRE loop located at the dac locus, can be involved in the expression of certain genes in complex tissues. In conclusion, the research article by Denaud et al. (2024) and my primary project collectively contribute to a better understanding of the regulatory mechanisms mediated by chromatin structures in gene expression control. With this work, we hope that our studies will provide valuable information to the scientific community, although further investigations into the molecular processes are needed to explain the role of chromatin conformation in complex mechanisms such as gene expression or memory formation in Drosophila.