A Streamlined Protocol for Single-Molecule Localization Microscopy in Arabidopsis Nuclei

While confocal fluorescence microscopy has provided valuable insights into chromatin organization in plant nuclei, its diffraction-limited resolution constrains the investigation of chromatin architecture, motivating the use of super-resolution techniques such as Single-Molecule Localization Microscopy (SMLM). Among these approaches, direct stochastic optical reconstruction microscopy (dSTORM) provides nanoscale resolution in individual cells, enabling precise visualization of chromatin domains, histone modifications, and nuclear organization. While such methods are increasingly applied in mammalian systems, their use in plant biology remains limited, largely due to technical challenges in sample preparation. Here, we present a streamlined and reproducible workflow for SMLM imaging of nuclei isolated from Arabidopsis thaliana. This protocol starts with seedling fixation to preserve nuclear morphology, followed by gentle tissue chopping and centrifugation to enrich intact nuclei. Isolated nuclei are then fluorophore-labeled in liquid medium and immobilized on low-melting agarose pads, a strategy that enhances stability during prolonged single-molecule imaging sessions. These steps collectively minimize background fluorescence, improve labeling consistency, and increase reproducibility across biological replicates. The resulting preparations provide enhanced clarity for visualizing chromatin modifications and nuclear architecture in plants. By lowering the technical barriers to implement SMLM imaging in Arabidopsis, this protocol provides a versatile means to investigate epigenetic regulation, chromatin organization, and nuclear topological variations at the nanoscale. This work establishes a methodological foundation for applying SMLM to plants, bridging the gap with mammalian cell biology and opening new opportunities to study how nuclear architecture contributes to genome regulation in response to developmental and environmental cues in plant systems.