Yes / Mammalian genomes contain several dozens of large (>0.5 Mbp) lineage-specific gene loci harbouring functionally related genes. However, spatial chromatin folding, organization of the enhancer-promoter networks and their relevance to Topologically Associating Domains (TADs) in these loci remain poorly understood. TADs are principle units of the genome folding and represents the DNA regions within which DNA interacts more frequently and less frequently across the TAD boundary. Here, we used Chromatin Conformation Capture Carbon Copy (5C) technology to characterize spatial chromatin interaction network in the 3.1 Mb Epidermal Differentiation Complex (EDC) locus harbouring 61 functionally related genes that show lineage-specific activation during terminal keratinocyte differentiation in the epidermis. 5C data validated by 3D-FISH demonstrate that the EDC locus is organized into several TADs showing distinct lineage-specific chromatin interaction networks based on their transcription activity and the gene-rich or gene-poor status. Correlation of the 5C results with genome-wide studies for enhancer-specific histone modifications (H3K4me1 and H3K27ac) revealed that the majority of spatial chromatin interactions that involves the gene-rich TADs at the EDC locus in keratinocytes include both intra- and inter-TAD interaction networks, connecting gene promoters and enhancers. Compared to thymocytes in which the EDC locus is mostly transcriptionally inactive, these interactions were found to be keratinocyte-specific. In keratinocytes, the promoter-enhancer anchoring regions in the gene-rich transcriptionally active TADs are enriched for the binding of chromatin architectural proteins CTCF, Rad21 and chromatin remodeler Brg1. In contrast to gene-rich TADs, gene-poor TADs show preferential spatial contacts with each other, do not contain active enhancers and show decreased binding of CTCF, Rad21 and Brg1 in keratinocytes. Thus, spatial interactions between gene promoters and enhancers at the multi-TAD EDC locus in skin epithelial cells are cell type-specific and involve extensive contacts within TADs as well as between different gene-rich TADs, forming the framework for lineage-specific transcription. / This study was supported by the grants 5R01AR064580 and 1RO1AR071727 to VAB, TKS and AAS, as well as by the grants from MRC (MR/ M010015/1) and BBSRC (BB/K010050/1) to VAB.

Chromatin ist ein Makromolekül, dessen Genregulation innerhalb des räumlich eingeschränkten Zellkerns organisiert werden muss. Die Genomorganisation ist eng mit Genaktivierung und Genrepression verknüpft. In den vergangenen Jahren wurde gezeigt, dass die DNA hierarchisch organisiert ist. Die Faltung läuft in aufeinander folgenden Schritten ab, wobei jede Organisationsebene sowohl zur räumlichen Komprimierung, als auch zur Genregulation beiträgt. In dieser Dissertation wurden mit Hilfe von hochauflösender Mikroskopie verschiedene Ebenen der 3D Chromatinorganisation auf Einzelzell-Basis untersucht. Auf der kleinsten Organisationsebene wurde die Struktur zweier, nebeneinander liegender topologischer Domänen (TADs) am Sox9-Lokus erforscht. Mit Hilfe von Fluoreszenz in situ Hybridisierung (FISH) in 3D Zellen, sowie Cryoschnitten in embryonalen Stammzellen von Mäusen konnten Interaktionen zwischen den benachbarten TADs festgestellt werden. FISH in Zellen mit genomischen Duplikationen, zeigte das Entstehen von zwei unterschiedlichen, durch die Duplikation entstandenen, Konformationen. Unter Verwendung von FISH wurden long-range Kontakte, die zuvor mit GAM entdeckt wurden, untersucht und es zeigte sich, dass sie häufig zwischen TADs die regulatorischen Domänen enthalten auftreten. Zudem zeigte sich die Bildung von Clustern zwischen mehreren, weit auseinander liegenden, regulatorischen Elementen. Dies lässt unter Umständen auf das Entstehen von regulatorischen Zentren zwischen diesen Enhancer-reichen Regionen schließen. Weitere Untersuchungen zeigten Veränderung der sogenannten Super-Enhancer Cluster in unterschiedlichen Zelltypen. Des Weiteren sind Super-Enhancer TADs sehr dekondensiert und wurden häufig an Splicing-Speckle Regionen vorgefunden. / Chromatin needs to organize gene regulation whilst fitting into the confined space of the nucleus. Chromatin organization is therefore intertwined with gene activation and silencing. In recent years many advances in the field of chromatin architecture have been made showing that chromatin is organized hierarchically. Folding occurs in subsequent units, where each level of organization contributes to the spatial compaction of DNA and gene regulation. In this dissertation different levels of 3D chromatin organization were analysed using single-cell, high-resolution imaging. On the smallest scale, the 3D organization of two neighbouring Topologically Associating Domains (TADs) at the Sox9 locus was investigated. Performing Fluorescence in situ Hybridization (FISH) in 3D and cryosectioned mouse embryonic stem cells, extensive contacts between the two neighbouring TADs across the TAD boundary were detected. Applying FISH in a cell line bearing a genomic duplication within the Sox9 locus, the occurrence of two different conformations that result from the duplication was shown. Recent evidence from GAM showed the formation of long-range, multimer contacts between distal regulatory elements. Investigating the occurrence of long-range contacts between super-enhancer TADs in single cells by FISH, showed that they establish frequent interactions at close spatial distances. Furthermore the formation of clusters containing distal super-enhancer TADs could be demonstrated, indicating the possibility of higher-order regulatory hubs between these enhancer-rich regions. Further investigation showed that super-enhancer regions form different clusters in different cell types. Finally, it was shown that super-enhancers are highly decondensed and preferentially located at splicing speckles.