MINFLUX dissects nucleosome and compacting chromatin structures in living cells

The chromatin structure is fundamental for genome compaction and gene transcriptional regulation in the nucleus. Although in vitro studies suggest a classical model that 11-nm nucleosome polymers fold into 30 nm fibers, such structures have not been observed in situ. In contrast, disordered chains or condensed liquid-like chromatin domains are reported in cells by EM studies and by super-resolution fluorescence microscopy. Do condensed chromatin fibers indeed exist in the cell? We identified a fluorescent dye that preferentially binds to AT-rich regions of DNA and blinks spontaneously to allow single probe visualization. Using three-dimensional (3D) MINFLUX localization, which is extremely low in phototoxicity and high-speed, we observed that a subset of DNA molecules assembles into fiber-like structures co-localized with histones. Native chromatin fibers in living cells are detected in the middle of the nucleus with segments that are variable in width. Most of the chromatin fibers are dismissed after Trichostatin A (TSA) treatment. In some cases, DNA localization even reveals the 3D ultrastructure of individual nucleosomes as 5-10 probes wrapping around an 11-nm cylinder in living cells. Therefore, chromatin fibers (∼30 nm) do exist in living cells, at least in AT-rich regions of the genome. The MINFLUX nanoscopy reveals the native chromatin ultrastructure and its folding to achieve structural compaction in the nucleus.