Genome function in the nucleus is organised through membrane-less compartments enriched with specific proteins and nucleic acids. Promyelocytic leukemia (PML) bodies regulate telomere maintenance and DNA damage responses, but their internal molecular organisation remains poorly understood. We visualised the molecular composition of PML bodies directly within the nucleus using an advanced cryogenic-correlative light and electron microscopy (cryo-CLEM) pipeline. Cryo-electron tomography revealed eYFP-PML-I bodies as compartments with a molecular makeup distinct from the surrounding nucleoplasm. Cryogenic super-resolution correlative light and electron microscopy showed these comprise a diffuse PML-protein shell enclosing an inner core. A visual proteomics comparison of the core and surrounding regions through template matching and sub-tomogram averaging mapped nucleosomes, TRiC chaperonin complexes in both closed and open conformations, and single-capped PA28 proteasomes. Membrane structures of unknown function were additionally detected within some eYFP-PML-I bodies. Remarkably, the nucleosomes included density consistent with columnar trinucleosome assemblies (1), revealing that PML body interiors harbour discrete chromatin domains. Moreover, vault complexes were detected in poised positions in the proximal nucleoplasm. Together, these first in situ higher-resolution structural insights of PML bodies identify their critical functional components and an interior porous architecture that suggests a mechanism for content selection based on physical partitioning akin to size-exclusion chromatography.
Prazak, V., Harley, I., Falckenhayn, J., Boutell, C., Thomason, P. A., Davis, B. G., Kaufmann, R., Carter, S. D.
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