Now You See Me: Visualizing nuclear complexity by selective staining

Transmission electron microscopy (TEM) enables nanoscale resolution of cellular structures, yet its biological interpretability in cell biology critically depends on the staining protocols. Here, we present an integrated TEM workflow applied to mammalian erythropoiesis, an established model for the study of nuclear remodeling, to dissect chromatin condensation and large-scale nuclear reorganization. We systematically compare multiple staining strategies, including uranyl acetate and lead citrate for general morphology, EDTA regressive for ribonucleoproteins, osmium ammine for DNA, terbium citrate vapors for RNA, and immunogold labeling for the heterochromatin marker H3K9me3. Each method reveals distinct structural features and, when combined with segmentation tools, enables their high-resolution mapping. We demonstrate that the choice of protocol markedly influences image interpretation and semi-quantitative image analysis. To our knowledge, this is the first systematic study to integrate these cytochemical protocols into a standardized imaging pipeline with potential applicability across biological systems. Our findings establish a methodological reference for nanoscale nuclear imaging and offer insights into the spatial organization of chromatin at the ultrastructural level.