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

Abstract

Metazoan genomes are spatially organized at multiple scales, from packaging of DNA around individual nucleosomes to segregation of whole chromosomes into distinct territories1–5. 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 mechanisms2–4,6–8, 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 expression9–11. 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. Remarkably, 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 chromatin shows the densest packing and most intriguing folding behaviour in which packing density increases with domain length. Distinct from the self-similar organization displayed by transcriptionally active and inactive chromatin, the Polycomb-repressed domains are characterized by a high degree of chromatin intermixing within the domain. Moreover, compared to inactive domains, Polycomb-repressed domains spatially exclude neighbouring active chromatin to a much stronger degree. Computational modelling and knockdown experiments suggest that reversible chromatin interactions mediated by Polycomb-group proteins plays an important role in these unique packaging properties of the repressed chromatin. Taken together, our super-resolution images reveal distinct chromatin packaging for different epigenetic states at the kilobase-to-megabase scale, a length scale that is directly relevant to genome regulation.

Transferable model for chromosome architecture

“…Interestingly, the A compartment tends to be less densely packed and to lie at the periphery of the chromosome territory. These observations are consistent with the findings of prior studies using both microscopy and Hi-C (9,29,30). Notably, a control model composed of a simple self-avoiding homopolymer chain failed to exhibit any of these results and, instead, recapitulated the expected properties for an equilibrium globule ( Fig.…”

Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast

“…4F), a power-law scaling behavior with a scaling exponent of 0.28 ± 0.03 can be clearly observed, which is consistent with the earlier proposed chromatin organization as a fractal globule with a fractal dimension of ∼3 (43,44). This result suggests, even at these deeply subdiffractional length scales (20-60 nm), the topology of nucleic acids within the nucleus follows the same power-law structure as that observed at higher length scales (100-250 nm) (44,45). At these length scales, one possible explanation is that individual genes selfassemble into discrete clusters that maximize their surface area while minimizing their volume occupancy.…”

Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells

“…residues. Polycomb-repressor complexes can induce chromatin folding independently of catalytic activity [30][31][32] . The co-associations of active genes or Polycomb-repressed genes have so far been studied separately, without assessing whether one type of association might have predominant contributions to chromatin folding at specific loci.…”