Quantifying the spatial distribution of post-translational histone modifications using 3D spectroscopic single-molecule localization microscopy

Super-resolution microscopy has enabled studies that probe protein spatial distribution at the nanoscale. This, in turn, has made it possible to study the distribution of post-translational modifications in the nucleus. Cancer is associated with widespread alterations in gene expression. It is of interest to classify the resulting change in the spatial distribution of post-translational modifications. However, there is a lack of studies that examine the interactions of multiple histone modifications in a single nucleus. We quantified the individual distribution and clustering behaviors of H3K27me3 and H3K27ac and classified the level of contact between these histone modifications using spectroscopic single-molecule localization microscopy (sSMLM). We also associated the detected changes in these parameters with degrees of cancer malignancy and with drug-induced perturbations in methylation machinery.