Quantitative single-cell imaging suggests increased global chromatin accessibility in tumor versus non-tumor cell...

Cancer phenotypic plasticity is associated with poor prognosis. The mechanisms of phenotypic plasticity are not fully understood. Possibly, the degree of chromatin accessibility defines the easiness of cell transitions between phenotypes. To test this, a method to compare chromatin accessibility between cells is needed. We propose to measure the chromatin accessibility of a cell by total signal from nuclei stained with DNA-binding fluorescent molecules. This method is based on data that some small molecules bind nucleosome-free DNA better than nucleosomal DNA. Thus, fluorescence of these molecules is proportional to the amount of nucleosome-free DNA, serving as a measure of chromatin accessibility. We optimized the method using several DNA-binding molecules and known chromatin modulating agents. Using a set of tumor and non-tumor cells we observed the higher chromatin accessibility of tumor versus non-tumor cells. Chromatin accessibility was also increased upon oncogene-induced transformation of mouse and human cells.