Abstract
Three-dimensional (3D) chromatin organization plays a key role in regulating mammalian genome function; however, many of its physical features at the single-cell level remain underexplored. Here, we use live- and fixed-cell 3D super-resolution and scanning electron microscopy to analyze structural and functional nuclear organization in somatic cells. We identify chains of interlinked ~200- to 300-nm-wide chromatin domains (CDs) composed of aggregated nucleosomes that can overlap with individual topologically associating domains and are distinct from a surrounding RNA-populated interchromatin compartment. High-content mapping uncovers confinement of cohesin and active histone modifications to surfaces and enrichment of repressive modifications toward the core of CDs in both hetero- and euchromatic regions. This nanoscale functional topography is temporarily relaxed in postreplicative chromatin but remarkably persists after ablation of cohesin. Our findings establish CDs as physical and functional modules of mesoscale genome organization.
Highlights
The genome in mammalian cell nuclei is hierarchically organized at various scales correlating with diverse genomic functions [1, 2]
Advances in super-resolution microscopy put these structures within visual reach [17, 24]. 3D-structured illumination microscopy (SIM) enables fast multicolor 3D acquisition of whole cells with eightfold higher volumetric resolution and strongly enhanced contrast compared to conventional fluorescence microscopy [25]
We suggest that the packing of nucleosomes into mesoscale chromatin domains (CDs) may lead to the physical exclusion of chromatin-associated complexes according to their size, providing a possible explanation for the ordered functional zonation as a consequence of physical accessibility [23]
Summary
The genome in mammalian cell nuclei is hierarchically organized at various scales correlating with diverse genomic functions [1, 2]. At the 100-Mb scale, entire chromosomes harbor distinct territories within the nucleus with transcriptionally active euchromatic and inactive heterochromatic segments tending to segregate into specific nuclear subregions [4]. Advances in next-generation sequencing–based chromosome conformation capturing methods (3C/Hi-C) have revealed partitioning into several hundred kilobases to a few megabase-sized topologically associating domains (TADs) [6, 7]. At higher levels of organization, TADs group into ~10- to 20-Mb genomic A and B compartments. Compartments are generally correlated with euchromatin or heterochromatin, and nuclear interior or lamina/ nucleolar contacts for A and B compartments, respectively [9]
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