Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells

Summary

Cell populations can be strikingly heterogeneous, composed of multiple cellular states, each exhibiting stochastic noise in its gene expression. A major challenge is to disentangle these two types of variability and to understand the dynamic processes and mechanisms that control them. Embryonic stem cells (ESCs) provide an ideal model system to address this issue because they exhibit heterogeneous and dynamic expression of functionally important regulatory factors. We analyzed gene expression in individual ESCs using single-molecule RNA-FISH and quantitative time-lapse movies. These data discriminated stochastic switching between two coherent (correlated) gene expression states and burst-like transcriptional noise. We further showed that the “2i” signaling pathway inhibitors modulate both types of variation. Finally, we found that DNA methylation plays a key role in maintaining these metastable states. Together, these results show how ESC gene expression states and dynamics arise from a combination of intrinsic noise, coherent cellular states, and epigenetic regulation.

Graphical Abstract

Highlights

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  smFISH in ESCs reveals two transcriptional states and highly stochastic expression

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  Live-cell expression dynamics reveal the in situ transition rates between states

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  DNA methylation regulates state-switching dynamics

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  “2i” signaling inhibitors impact both gene expression noise and state transitions

Abstract

Using single-molecule RNA-FISH and quantitative time-lapse movies, Singer et al. discriminate two primary sources of gene expression heterogeneity in embryonic stem cells: random switching between correlated gene expression states and burst-like transcriptional noise. Perturbing specific signaling pathways modulates both processes, and DNA methylation is key to maintaining these states.