Highlights d Real-time single-molecule detection in high-background, crowded cellular locales d Imaging and tracking Pol II at single genes during the transcription cycle d Organization, dynamics, and interdependencies of enhancer-bound regulatory factors d Dissection of enhancer mechanisms at the endogenous

We demonstrate a cryogenic super-resolution correlative light and electron microscopy of vitrified specimens which were prepared by high pressure freezing and cryo-sectioning to maintain a close-to-native state with better fluorescence preservation. Several fluorescent proteins were found photoswitchable and emitted much more photons under cryo-condition, hence resulting in higher localization precision. We observed nice correlation of a mitochondria protein with mitochondria outer membrane at nanometer resolution in three dimensional.