GSE134164
The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [RNA-seq2]
Post-transcriptional mechanisms have the potential to influence complex changes in gene expression, yet their role in cell fate transitions remain largely unexplored. Here, we show that the RNA helicase DDX6 is crucial for the dissolution of the pluripotency-specific transcriptional network in mouse and human embryonic stem cells (ESCs). We further demonstrate that epigenetic silencing of DDX6 endows primed ESCs with a differentiation-resistant, “hyper-pluripotent” state, which readily reprograms to a naïve state resembling the preimplantation embryo. In addition to directing cell fate in ESCs, we find that DDX6 plays a key role in adult progenitors where it controls the balance between self-renewal and differentiation in a context-dependent manner. Specifically, DDX6 loss blocks the differentiation of mouse intestinal stem cells and human neural stem cells, while it favors exit from the progenitor state in human muscle and mesenchymal progenitors. Mechanistically, we show that DDX6 coordinates the storage and translational suppression of target mRNAs in P-bodies. Upon loss of DDX6 or mutation of its helicase domain, P-bodies dissolve and release mRNAs encoding fate-instructive transcription and chromatin factors that subsequently re-enter the ribosome pool. Increased translation of these targets impacts cell fate by rewiring the enhancer, heterochromatin and DNA methylation landscapes of human undifferentiated cell types. Collectively, our data establish a novel link between P-body homeostasis, chromatin organization and cellular potency across diverse stem and progenitor cell populations. Overall design: DDX6 overexpression in the GEN1C hiPSCs cells (GEN1C DDX6 OE) was achieved by infection with a lentiviral vector expressing the wt DDX6 cDNA (Vector Builder). For the TGFßi assay, cells were incubated in differentiation media for 48 hours for the TGFßi condition.