Common modes of ERK induction resolve into context specific signalling via a combination of signal duration and cell type specific transcriptional repression [RSC_RNA]
Fibroblast Growth Factor (FGF) signalling via ERK exerts diverse roles in development and disease. In mammalian preimplantation embryos and naïve pluripotent stem cells ERK promotes differentiation, whereas in primed pluripotent states closer to somatic differentiation ERK sustains self-renewal. How can the same pathway produce different outcomes in two related cell types? To explore context-dependent ERK signalling in embryonic development and differentiation we generated cell and mouse lines that allow for tissue- and time-specific cell intrinsic ERK activation. Using these tools, we find variations in response to ERK are mostly mediated by repression of transcriptional targets that occur in tandem with reductions in chromatin accessibility at regulatory regions. Furthermore, immediate early ERK responses are largely shared by different cell types but become refined producing cell-specific programs as increasing durations of signalling interface with cell specific gene regulatory networks. Induction in naïve pluripotency is accompanied by chromatin changes, whereas in later stages it is not, suggesting that chromatin context doesn't shape signalling response. Altogether, our data suggest that cell-type specific responses to ERK signalling exploit the same immediate early response, but then sculpt it to specific lineages via repression of distinct cellular programs and downstream indirect stimulation of available enhancer networks. Overall design: To map the transcriptional response to ERK in pluripotent cell types, we targeted mESCs with a version of the cRAF inducible model in Hamilton et al., 2019. The construct allows for rapid and homogeneous ERK induction upon tamoxifen supplementation. We differentiated targeted ESC towards RSC and collected samples for RNA-seq before induction (0h), after 2h and 4h of ERK induction, and then treated for an additional 2h with MEK inhibitor (rev), to explore reversion of ERK targets. For each condition, 2 replicates were collected from 2 biological clones (clone 4 and 8), as a total of 4 replicates per condition.