Mapping Absolute DNA Density in Cell Nuclei using Single-molecule Localization Microscopy

Within the cell nucleus, silent genes are generally located in chromatin areas of high density called heterochromatin, whereas active genes can be mostly found at the interface between chromatin and the interchromatin space called euchromatin. At present, the characterization of eu- and heterochromatin is mostly based on epigenetic modifications of histone proteins along the DNA sequence, while little is known about absolute DNA densities across the cell nucleus and their functional implications. Models of the nucleus solely based on biochemical data and assumptions about the nature of chromatin as a polymer still differ fundamentally from imaging data generated by high-resolution microscopy. This indicates that there is still important structurally relevant information missing. We believe that spatial constraints might be involved in gene regulation and have therefore developed a method that allows the measurement of absolute DNA densities in mammalian cell nuclei by transforming super-resolution localization data into true-to-scale density maps by Voronoi tessellation.