Deconstructing transcriptional heterogeneity in pluripotent stem cells

Abstract

Pluripotent stem cells (PSCs) are capable of dynamic interconversion between distinct substates; however, the regulatory circuits specifying these states and enabling transitions between them are not well understood. Here we set out to characterize transcriptional heterogeneity in mouse PSCs by single-cell expression profiling under different chemical and genetic perturbations. Signalling factors and developmental regulators show highly variable expression, with expression states for some variable genes heritable through multiple cell divisions. Expression variability and population heterogeneity can be influenced by perturbation of signalling pathways and chromatin regulators. Notably, either removal of mature microRNAs or pharmacological blockage of signalling pathways drives PSCs into a low-noise ground state characterized by a reconfigured pluripotency network, enhanced self-renewal and a distinct chromatin state, an effect mediated by opposing microRNA families acting on the Myc/Lin28/let-7 axis. These data provide insight into the nature of transcriptional heterogeneity in PSCs. This study uses single-cell expression profiling of pluripotent stem cells after various perturbations, and uncovers a high degree of variability that can be inherited through cell divisions—modulating microRNA or external signalling pathways induces a ground state with reduced gene expression heterogeneity and a distinct chromatin profile. Although it is recognized that pluripotent stem cells switch dynamically between distinct substates, the gene regulatory networks specifying the states and governing transitions between them are not well defined. Using single-cell expression profiling of mouse pluripotent stem cells subjected to chemical and genetic perturbations, George Daley and colleagues establish how transcriptional networks are dynamically reconfigured to drive distinct states of pluripotency. They observe a high degree of variability that can be inherited through cell divisions and find that modulating microRNA or external signalling pathways lowers the heterogeneity in gene expression and induces a distinct epigenetic state.