Abstract
In the nucleus of eukaryotic cells, the DNA molecule, that carries genetic infor-mation, associates with proteins such as histones to form chromatin. Over the pastdecade, techniques known as "chromosome conformation capture" have revealedthat chromatin is hierarchically organised into physical domains called Topologi-cally Associating Domains (TADs). TADs play a critical role in gene regulation byfacilitating physical interactions between genes and their regulatory elements suchas enhancers, promoters, and insulators. However, the molecular mechanisms andfactors involved in the formation of these structures during embryonic development,as well as their influence on gene activation and repression in differentiated tissues,remain poorly understood.In this study, we investigated the role of certain factors in establishing interac-tions between genes and their regulatory elements to better understand their im-pact on transcriptional regulation in Drosophila. To do this, we used bioinformaticapproaches and an advanced microscopy technique (Hi-M). These innovative toolsallowed us to highlight the importance of Class I insulator proteins in mediatingthese interactions during embryonic development in Drosophila. We were able toshow that interactions between regions bound by Class I insulator proteins are rare,mainly observed in pairs, and that their formation precedes the emergence of TADsduring the nuclear cycle 14. Subsequently, our research focused on the role of in-teractions between genes and their regulatory elements in differentiated tissues inmammals. To this end, we produced Hi-M data and developed a novel machine-learning tool to decompose chromatin structure into fundamental units, which wetermed "Chromatin Folding Motifs" (CFMs). This allowed us to show that a set ofCFMs is essential for explaining the structure of a given locus. As a result, we wereable to show that the three-dimensional architecture varies not only between tis-sues, but also between different cell-types by adjusting the proportion of the CFMs.Finally, we showed that 3D architecture is affected during the onset of diseases suchas type II diabetes. Collectively, these studies aim to open new perspectives forunderstanding the mechanisms involved in 3D genome organisation.