How the epigenetic landscape is connected to the multiscalearchitecture of the genome and how this regulates the functioning ofthe nuclear machinery (e.g. replication and transcription)remains a crucial question in chromatin biology.Here, we employed 3D multicolor super-resolutionmicroscopy technologies to study the nanoscale organization ofepigenetic marks in single cells and during embryogenesis inDrosophila melanogaster. We found that active (H3K4me3) andinactive (H3K27me3) chromatin marks segregate at the nanoscale,forming discrete compartments of distinctive sizes. The 1D epigeneticlandscape correlates well with the multiscale physical sizes ofactive compartments. In contrast, inactive marks assemble intoclusters larger than those predicted from epigenetic domains,suggesting that long-range contacts between inactive domains mayact as an structural regulatory mechanism during development.Simultaneous imaging of 69 topologically associating domain (TAD)boundaries shows that TADs regroup as a function of embryonicdevelopment. Pairwise imaging of TAD boundaries revealed that thesedifferent architectural rearrangements during development do notderive from specific contacts (or loops) between TAD borders.Interestingly pairwise distance measurements of sequential andnon-sequential boundaries were highly correlated with epigenetictypes of the encompassing TADs. The power-law dependence of physicalversus genomic distance was unaltered in different cell types, butnon-specific long-range contact frequencies depended strongly on celltype and had a large effect in chromosome folding at the single-celllevel. Our findings reveal that the epigenetic landscape shapes thechromatin fiber at the nanoscale and suggest that the dynamic andstochastic rearrangement of chromosome architectures may play a rolein transcriptional regulation during development.
