Regulation of transcription and cell identity by FGF/ERK signaling dynamics in embryonic stem cells
Developmental Biology
Cell Biology
Final Report Abstract
Cells in a developing embryo must continuously make critical decisions: what type of cell to become, and when. This process - called cell differentiation - is largely guided by chemical signals from the cell's surroundings. These signals are transmitted from cell surface receptors via signal transduction systems to the cell nucleus, where they trigger changes in gene activity that define a cell’s identity and function. One of the most important signaling systems for cell differentiation in early embryos and embryonic stem cells is the Fibroblast Growth Factor (FGF) signaling pathway. While it is fairly well known how FGF signaling activates cytoplasmic signal transduction systems, is still not fully understood how these ultimately influence gene activity to drive cells toward different fates. It is also not known if and how different amounts of FGF lead to distinct gene expression responses. This research project set out to fill these gaps. Using both bulk and single-cell RNA sequencing, we first mapped out which genes respond to FGF signals in mouse embryonic stem cells. We found that FGF affects hundreds of genes, but not in neatly divided groups based on sensitivity. Instead, responses varied smoothly, challenging our initial idea that there are clearly separated “classes” of target genes. To better understand how FGF controls expression levels of its target genes, we next looked at their expression dynamics. Through a combination of RNA staining and single cell RNA sequencing, we found that the expression of FGF target genes is more bursty than that of control genes, i.e., periods with high gene expression are interspersed with longer periods of silence than seen for non-target genes. This led to more variation between individual cells. Such variability might be useful by allowing a population of cells to explore a range of possible future fates more effectively. Finally, to figure out how FGF signals control gene transcription molecularly, we performed a powerful CRISPR knock-out screen to find new genes involved in this process. One surprising discovery was the Med12 gene, part of a large protein complex that helps control gene activity. Our detailed studies revealed that Med12 not only relays FGF signals, but that it integrates multiple signals (like FGF, Wnt, and mTOR) that guide cell differentiation. While Med12 was not required for all types of cell fate decisions, its loss made stem cells slower to change into more specialized types, suggesting it fine-tunes how quickly cells move from one state to another. Taken together, our results provide new insight into how FGF signals are processed molecularly and dynamically, which could be relevant for a better understanding of FGF- dependent cell fate decisions beyond those in early development.
Publications
-
Tissue-intrinsic beta-catenin signals antagonize Nodal-driven anterior visceral endoderm differentiation. Nature Communications, 15(1).
Schumacher, Sina; Fernkorn, Max; Marten, Michelle; Chen, Rui; Kim, Yung Su; Bedzhov, Ivan & Schröter, Christian
-
Med12 cooperates with multiple differentiation signals to facilitate efficient lineage transitions in embryonic stem cells. Journal of Cell Science, 138(8).
Fernkorn, Max & Schröter, Christian
