Multiscale visualization of nucleolar chromatin in yeast Saccharomyces cerevisiae

Spatial organization of chromosomes is crucial for genome stability, transcription, and proper mitotic segregation. By employing a range of imaging technologies, including random illumination microscopy and single molecule localization microscopy (SMLM), we conducted an in-depth exploration of the chromatin organization in budding yeast, with optical resolutions ranging from 250 nm to 50 nm. In silico models based on passively moving polymer chains and local tethering to nuclear landmarks explained much of the experimental data in yeast chromatin. We compared these models with our new imaging data of the nucleoplasmic and nucleolar chromatin. Chromatin fibers observed in the nucleoplasm showed some similarity with model prediction with a resolution of 150 nm. However, we visualized local clustering of chromatin in both the nucleoplasm and nucleolus, rather than the tube-like appearance predicted by polymer chain models. In the nucleolus, local clustering of ribosomal DNA (rDNA) chromatin is consistently observed from 150 nm resolution down to 50 nm. We also observed that actively transcribed rDNA spatially segregates from bulk nucleolar chromatin. Using correlative light and electron microscopy (CLEM), we found that local rDNA clustering is forming a specific nucleolar subdomain visible in transmission electron microscopy, the yeast equivalent of metazoan fibrillar center. We conclude that nucleolar chromatin forms a distinct sub-nucleolar compartment in yeast, supporting the model of a tripartite structural organization of the yeast nucleolus.