Epigenetic optical sensing of 5-hydroxymethylcytosine at the single-molecule level

While single-molecule imaging is a powerful tool to detect and study epigenetic modifications, currently imaging methods are unable to detect the genomic locations of epigenetic modifications. Here we develop a selective chemical labeling-based single-molecule imaging method, single-molecule epigenetic localization (SMEL), which is capable of detecting loci-specific and strand-specific detection of 5-hydroxymethylcytosine, a major mammalian DNA epigenetic modification and biomarker involved in biological processes ranging from embryogenesis to tumorigenesis. We then apply SMEL to mouse embryonic stem cell genomic DNA to demonstrate the ultra-sensitivity and potential clinical application of this method.