Tracking induced pluripotent stem cell differentiation with a fluorescent genetically encoded epigenetic probe
Afanasii I Stepanov1,2, Alexandra A Shuvaeva1,2,3, Lidia V Putlyaeva1,2
1Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia.
Cellular and Molecular Life Sciences : CMLS
|September 2, 2024
Summary
Researchers developed a fluorescent probe to visualize epigenetic landscapes in living cells. This probe tracked changes in histone modification (H3K9me3) during stem cell differentiation, revealing key reorganization events.
Area of Science:
- Molecular Biology
- Epigenetics
- Cell Biology
Background:
- Epigenetic modifications, such as histone methylation and acetylation, are crucial for gene expression regulation.
- Epigenomic changes are dynamic during biological processes like cell differentiation.
- Existing methods for analyzing epigenetic modifications typically require fixed cells, limiting real-time observation.
Purpose of the Study:
- To develop a genetically encoded fluorescent probe for visualizing H3K9me3, a marker of inactive chromatin, in living cells.
- To track dynamic changes in H3K9me3 epigenetic landscapes during induced pluripotent stem cell (iPSC) differentiation into induced neurons.
- To establish a novel method (LiveMIEL) combining epigenetic probes and machine learning for analyzing single-cell epigenetic signatures.
Main Methods:
- Development of MPP8-Green, a genetically encoded fluorescent probe based on the MPP8 chromodomain, for detecting H3K9me3.
- Live-cell imaging of H3K9me3 epigenetic landscapes in differentiating iPSCs.
- Application of machine learning approaches within the LiveMIEL framework for multiparametric epigenetic signature classification.
Main Results:
- MPP8-Green successfully visualized H3K9me3 dynamics in single living cells.
- Two significant waves of global H3K9me3 reorganization were observed during a 4-day iPSC to induced neuron differentiation process, occurring on days 1 and 3.
- Minimal changes in H3K9me3 landscapes were detected on days 2 and 4 of differentiation.
Conclusions:
- The MPP8-Green probe enables real-time monitoring of H3K9me3 dynamics in living cells.
- The LiveMIEL method offers a powerful approach for classifying single-cell epigenetic states during differentiation.
- This technology has broad potential for studying epigenomic regulation in various biological models and disease states.
