Tracking Epigenetic Changes in Single Cells

Histone modification is an important epigenetic feature that can regulate gene activity and ultimately determine cell fate. Tracking epigenetic changes in single cells can reveal dynamic changes in histone modifications responding to various external stimuli. The existing tools, however, are limited to fixed cell applications, exhibit no or limited spatial resolution, and/or requires extensive preparations. To address these limitations, we engineered a new set of probes based on epigenetic “reader” domains for H3K9me3 and H3K27ac. The probes capture epigenetic features with similar resolutions to commercial antibodies but are live-cell compatible. Cell images were collected to generate features i.e., texture, size, intensity of the illuminated nuclei and foci within the nuclear area. Clustering-based analysis were applied to identify key features induced by various epigenetic drug treatments. Our clustering approach identified key features that differentiate among cells treated with various known epigenetic enzyme inhibitors, e.g., BIX 01294. The selected image features can be used to quantify changes in histone modifications and exhibited agreement with immuno-stained cells. The engineered probes were used to track epigenetic changes in single cells.