Super-Resolution Imaging Of Chromatin Organization in Individual Chromosomes

The spatial organization of chromatin plays an important role in many essential genome functions from gene regulation to genome replication. However, many gaps remain in our understanding of the three-dimensional (3D) organization of chromatin and chromosomes, partly because of the lack of proper imaging tools. Recently, we developed a super-resolution chromatin-imaging approach and applied this method to study chromatins in different epigenetic states that are essential for regulating gene expression. We studied three major epigenetic states: transcriptionally active, inactive, and Polycomb-repressed states. Our results revealed distinct chromatin structures for these different states, molecular mechanisms underlying these structural differences, and implications of these structural differences in gene regulation. Moreover, we developed a multiplexed FISH method that enables the imaging and localization of numerous genomic loci for tracing the 3D conformation of chromatin in individual chromosomes. We applied this method to study the spatial organizations of topologically-associating domains (TADs) and chromatin compartments. Our results revealed novel organizations of TADs and compartments in individual chromosomes and suggest that the organization of chromatin domains and compartments can change in response to regulation.