Live monitoring uncovers divergent epigenetic remodeling during osteogenic and adipogenic differentiation of mesenchymal stem cells.

Abstract

Histone post-translational modifications represent a central mechanism of epigenetic regulation, upholding chromatin architecture and genomic function. Elucidating the dynamic relationship between epigenetic modifications and chromatin remodeling requires sensitive tools for live-cell analysis. To address this, we developed K9-MILo (K9-Methylated Inhibitory Locus), a genetically encoded fluorescent sensor for visualizing the heterochromatin mark H3K9me3 in living cells. K9-MILo incorporates the MPP8 chromodomain, the mTurquoise2 fluorescent protein, and a nuclear localization signal. Expression of K9-MILo in immortalized mesenchymal stem cells and its translocation in the nucleus did not compromise their ability to differentiate into adipogenic and osteogenic lineages. Using K9-MILo in conjunction with automatically mapped long-term live-cell imaging and machine learning-based analysis, we tracked heterochromatin dynamics during adipogenic and osteogenic differentiation. Comparative analysis revealed that the different dynamics of heterochromatin patterns in adipogenic and osteogenic differentiation are entirely distinct between lineages. Furthermore, we showed that the trajectory of epigenetic remodeling is unaltered by the PPARγ activator indomethacin. Despite enhancing lipid droplet formation, the PPARγ activator indomethacin did not alter the overall trajectory of heterochromatin remodeling during adipogenic differentiation. Our findings establish K9-MILo as a sensitive probe for epigenetic dynamics and demonstrate that the integration of reader domain-based sensors with quantitative image analysis provides a powerful platform for investigating chromatin function and screening for epigenetically active compounds.