Tracking induced pluripotent stem cells differentiation with a fluorescent genetically encoded epigenetic probe

Abstract

Abstract Epigenetic modifications (methylation, acetylation, etc.) of core histones play a key role in regulation of gene expression. Thus, the epigenome changes strongly during various biological processes such as cell differentiation and dedifferentiation. Classical methods of analysis of epigenetic modifications such as mass-spectrometry and chromatin immuno-precipitation, work with fixed cells only. Here we present a genetically encoded fluorescent probe, MPP8-Green, for detecting H3K9me3, a histone modification associated with gene repression. This probe, based on the chromodomain of MPP8, allows for visualization of H3K9me3 epigenetic landscapes in single live cells. We used this probe to track changes in H3K9me3 landscapes during the differentiation of induced pluripotent stem cells (iPSCs) into induced neurons. Our findings revealed two major waves of global H3K9me3 reorganization during this process. The first wave occurred 16-24 hours after the induction, followed by a minor change on the second day. Then, on the third day, cells underwent another significant epigenetic change. By combining live visualization of epigenetic landscapes via genetically encoded probes and machine learning approaches, we can identify and characterize multiparametric epigenetic signatures of single cells during stem cell differentiation. This approach provides valuable insights into the dynamics of epigenetic changes during cellular differentiation processes.