Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

Using super-resolution imaging to directly observe the three-dimensional organization of Drosophila chromatin at a scale spanning sizes from individual genes to entire gene regulatory domains, the authors find that transcriptionally active, inactive and Polycomb-repressed chromatin states each have a distinct spatial organisation. Direct imaging of chromatin organization How chromatin is folded in the nucleus has important implications for many biological processes, from the regulation of gene expression to DNA replication. Here Xiaowei Zhuang and colleagues use super-resolution imaging to directly observe the organization of Drosophila chromatin at a scale spanning the sizes of individual genes and gene regulatory domains. They find that transcriptionally active, inactive, and Polycomb-repressed chromatin states each have a distinct spatial organization. Transcriptionally inactive chromatin resembles the fractal globule state of a polymer, whereas Polycomb domains have a unique compact organization and spatial isolation from other domains, explaining why gene expression is so strongly repressed in this state. Metazoan genomes are spatially organized at multiple scales, from packaging of DNA around individual nucleosomes to segregation of whole chromosomes into distinct territories 1 , 2 , 3 , 4 , 5 . At the intermediate scale of kilobases to megabases, which encompasses the sizes of genes, gene clusters and regulatory domains, the three-dimensional (3D) organization of DNA is implicated in multiple gene regulatory mechanisms 2 , 3 , 4 , 6 , 7 , 8 , but understanding this organization remains a challenge. At this scale, the genome is partitioned into domains of different epigenetic states that are essential for regulating gene expression 9 , 10 , 11 . Here we investigate the 3D organization of chromatin in different epigenetic states using super-resolution imaging. We classified genomic domains in Drosophila cells into transcriptionally active, inactive or Polycomb-repressed states, and observed distinct chromatin organizations for each state. All three types of chromatin domains exhibit power-law scaling between their physical sizes in 3D and their domain lengths, but each type has a distinct scaling exponent. Polycomb-repressed domains show the densest packing and most intriguing chromatin folding behaviour, in which chromatin packing density increases with domain length. Distinct from the self-similar organization displayed by transcriptionally active a