Dynamic lineage priming is driven via direct enhancer regulation by ERK

• Published in: Nature (London) 2019-11, Vol.575 (7782), p.355-360
• Main Authors: Hamilton, William B., Mosesson, Yaron, Monteiro, Rita S., Emdal, Kristina B., Knudsen, Teresa E., Francavilla, Chiara, Barkai, Naama, Olsen, Jesper V., Brickman, Joshua M.
• Format: Article
• Language: English
• Subjects: 38/39; 38/61; 38/71; 38/91; 631/136/142; 631/136/2444; 631/337/458/1733; 631/337/572/2102; 631/532/2117; 82; 82/1; 82/58; 96; 96/100; 96/106; Analysis; Animals; Binding; Bioinformatics; Cell differentiation; Cell Lineage; Cell self-renewal; Control; Distribution; DNA-directed RNA polymerase; Embryo cells; Embryonic stem cells; Embryos; Endoderm; Enhancers; Experiments; Extracellular signal-regulated kinase; Extracellular signal-regulated kinases; Extracellular Signal-Regulated MAP Kinases - genetics; Extracellular Signal-Regulated MAP Kinases - metabolism; Fibroblast growth factors; Gene expression; Gene regulation; Gene silencing; Genes; Genetic aspects; Genetic transcription; Growth factors; Heterogeneity; Humanities and Social Sciences; Implantation; Kinases; Mediator Complex - deficiency; Mediator Complex - metabolism; Mice; Mouse Embryonic Stem Cells - cytology; Mouse Embryonic Stem Cells - metabolism; multidisciplinary; Occupancy; Paracrine signalling; Pluripotency; Priming; Protein Binding; Protein turnover; Proteins; Proteomics; RNA polymerase; RNA polymerases; Science; Science (multidisciplinary); Signaling; Stem cell transplantation; Stem cells; Transcription activation; Transcription factors; Transcription, Genetic
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/s41586-019-1732-z

Central to understanding cellular behaviour in multi-cellular organisms is the question of how a cell exits one transcriptional state to adopt and eventually become committed to another. Fibroblast growth factor-extracellular signal-regulated kinase (FGF -ERK) signalling drives differentiation of mouse embryonic stem cells (ES cells) and pre-implantation embryos towards primitive endoderm, and inhibiting ERK supports ES cell self-renewal 1 . Paracrine FGF–ERK signalling induces heterogeneity, whereby cells reversibly progress from pluripotency towards primitive endoderm while retaining their capacity to re-enter self-renewal 2 . Here we find that ERK reversibly regulates transcription in ES cells by directly affecting enhancer activity without requiring a change in transcription factor binding. ERK triggers the reversible association and disassociation of RNA polymerase II and associated co-factors from genes and enhancers with the mediator component MED24 having an essential role in ERK-dependent transcriptional regulation. Though the binding of mediator components responds directly to signalling, the persistent binding of pluripotency factors to both induced and repressed genes marks them for activation and/or reactivation in response to fluctuations in ERK activity. Among the repressed genes are several core components of the pluripotency network that act to drive their own expression and maintain the ES cell state; if their binding is lost, the ability to reactivate transcription is compromised. Thus, as long as transcription factor occupancy is maintained, so is plasticity, enabling cells to distinguish between transient and sustained signals. If ERK signalling persists, pluripotency transcription factor levels are reduced by protein turnover and irreversible gene silencing and commitment can occur. ERK reversibly regulates embryonic stem cell transcription via selective redistribution of co-factors and RNA polymerase from pluripotency to early differentiation enhancers, while leaving transcription factors bound to their enhancers, thus preserving plasticity.