Functional chromatin organisation in mammalian cells - lessons from 3D super-resolution imaging
Lothar Schermelleh, University of Oxford
Three-dimensional (3D) chromatin organisation plays a key role in regulating genome function in higher eukaryotes. Despite recognition that the genome partitions into ~1Mb-sized topological associated domains (TADs) based on ensemble Hi-C measurements, many features of the physical organisation at the single cell level remain underexplored. Using in vivo and in situ 3D super-resolution microscopy, supported by 3D scanning electron microscopy of cryo-preserved samples, we reveal a sequential curvilinear arrangement of irregular shaped ~200-300 nm diameter nucleosomal assemblies with viscoelastic properties (‘blobs’) juxtaposed to an RNA-populated chromatin-depleted interchromatin network. Quantitative mapping of genome function markers uncovers a zonal distribution, with strong confinement of structural proteins and transcriptionally active/permissive marks to a narrow region at blob surfaces, and enrichment of repressive marks towards the interior. This correlation between nanoscale topology and genome function is relaxed in postreplicative chromatin, and accentuated upon ATP depletion and hyperosmolarity induced chromatin condensation and, remarkably, after inactivation of cohesin. Our findings establish TAD-sized nanodomains (‘blobs’) as physical modules of mesoscale genome organization with functional chromatin states being defined by radial position and exposure to a phase-separated interchromatin space.
