Research Programme Image Figure 1. Long-range interactions (arrowed) detected between genomic regions being repressed by the polycomb epigenetic machinery. Adapted from Boyle et al., Genes Dev., 2020, 34:931. Summary We aim to understand the mechanisms that drive the spatial organisation of the mammalian genome, and how 3D organisation contributes to the repression and activation of gene expression and to enhancer function. We have developed computational tools to investigate chromosome conformation and experimental methods to assay enhancer function and the dysfunction caused by mutations in enhancers. 3D Genome Organisation and Heterochromatin 3D Genome Organisation and Enhancer Function 3D Genome Organisation and Heterochromatin We have used microscopy and chromosome capture assays to show that an important epigenetic machine - polycomb - mediates very long-range interactions between polycomb target genomic loci at larger length scales (over many megabases) than other levels of 3D genome organisation such as topologically associating domains (TADs) (Fig. 1). Polycomb creates facultative heterochromatin. We are also investigating how constitutive heterochromatin is organised and re-organised in the cell nucleus.Figure 2. Model of chromatin folding that may underlie enhancer-promoter communication. Image Figure 2. Microscopy reveals a loss of spatial proximity between a gene and its enhancer upon gene activation. Adapted from Benabdallah et al., Mol. Cell, 2019, 76:473. 3D Genome Organisation and Enhancer Function The complexity of human development, health and disease is dependent on the precise and responsive control of gene expression driven by regulatory elements – termed enhancers - embedded in the vast swathes of the non-coding human genome. We do not understand how enhancers work at locations in the genome distant from the genes they regulate, but the three-dimensional (3D) folding of the genome is thought to be important. Nor do we understand how to interpret most DNA sequence changes in enhancers found in patients and populations. Addressing this knowledge gap, we have identified unexpected changes in the 3D relationship of genes and their enhancers that have stimulated new thinking about mechanisms of long-range enhancer function. We also developed a new assay, using the zebrafish, that can detect human disease-causing mutations in enhancers. We have also developed a searchable Nuclear protein database that contains information on protein structure, function and sub-cellular localisation for >2500 mammalian proteins. Nuclear protein database Purpose Our work is aimed at understanding the genome at a level beyond that of the DNA sequence alone. We are investigating how the genome is organised within the nuclear space, both within normal, and diseased, cells and also how this organisation changes during development. Approach, Progress and Future Work We take a multidisciplinary approach, using cytological, genetic, biochemical and synthetic biology methods to understand genome spatial organisation. However, a prominent feature of our work is the use of visual assays to investigate how the genome is folded up. To do this we combine fluorescence in situ hybridisation (FISH) and digital microscopy with the use of automated image analysis software. This article was published on 2024-09-23
