Erk signaling dynamics and their role in germ layer patterning

Abstract

While living creatures possess many different cell types, only a handful of core signaling pathways are required for developmental patterning, meaning that the effectors of these pathways are interpreted differently in different contexts. One way such differential interpretation can be achieved is through enhancer-level interpretation of signaling dynamics. In this work, we investigate the mechanisms used to generate and interpret phosphorylated Erk, a time-varying developmental signal, in the context of germ layer patterning, one of the first cell specification events to occur in development. First, we examine how mutations alter Erk signaling dynamics in vitro and find that mutations to Erk’s activator, MEK, can overactivate the pathway through multiple means: by altering the way MEK interacts with Erk, and by altering the way MEK interacts with its own activator, Raf (Chapter 2). We then address the question of how Erk signaling dynamics are interpreted during germ layer specification—the choice to become either endoderm, mesoderm, or ectoderm (Chapter 3, Chapter 4). In Chapter 3, we optogenetically alter the duration of Erk signaling in Drosophila embryos and identify a critical time window during which cells decide whether to become endoderm or mesoderm. In Chapter 4, we examine how differences in enhancer sensitivity among genes are used to interpret Erk signaling level in the endoderm vs. ectoderm decision. Finally, in Chapter 5, we compare and contrast Erk signal interpretation in Drosophila and vertebrate mesodermal specification. We believe that this work, which pairs signal perturbation with transcriptional quantification, characterization of cellular behavior, and mechanistic modeling, brings us one step closer to a mechanistic understanding of how cells interpret time-varying signals in developmental contexts.