Multiplexed single molecule localization microscopy platform for gene specific iNVestigation of chromatin organization

Super-resolution microscopy has revolutionized our ability to visualize structures below the diffraction limit, crucial for studying complex targets like chromatin. Chromatin's hierarchical organization, ranging from nanometers to micrometers, is effectively examined using SMLM methods such as STORM. Our sequential immunolabeling protocol enables reliable multi-label investigations in the dense nuclear environment, combining multiplexed localization datasets with robust spatial analysis and joint density analysis algorithms. By coupling this multi-label SMLM with gene-specific labeling using RASER-FISH, we can analyze transcriptional activity and chromatin reorganization at sub 200-nm length scales and understand the role of transcription in chromatin organization.