Signaling pathways achieve specificity in target gene activation through the dependence on additional inputs, commonly referred to as “context”, such cell-specific transcription factors and appropriate chromatin states. To evaluate whether quantitative differences in activity of the Wnt pathway could also contribute to context-specific regulation, we measured the nuclear localization of the Wnt signaling pathway effectors, TCF and β-catenin, in all cells throughout development in C. elegans embryos. We found that the effect of Wnt compounds over successive exposures: we observed significantly increased nuclear localization of TCF and β-catenin in Wnt-signaled cells whose parents had also received a Wnt signal. This trans-generational “memory” of Wnt signaling influences target gene regulation suggesting that the level of signaling pathway activity can act an additional form of context.
To better understand how context information is encoded in Wnt target enhancers, we are investigating the dependence of enhancer activity on the organization and affinity of binding sites for TCF and other co-regulatory, cell-specific transcription factors. We identified 20 novel targets of the Wnt signaling pathway in C. elegans embryonic development, each expressed in a different subset of Wnt-signaled cells. We used modENCODE data and sequence conservation to identify 88 putative Wnt target enhancers and created a pipeline to test their activity in embryos. We image transgenic worms carrying fluorescent enhancer reporter constructs and a ubiquitously expressed GFP-histone at ~1 minute temporal resolution. Image analysis software identifies the nuclei and measures the reporter intensity, generating quantitative expression data for each individual cell at each timepoint from a single-celled zygote to a 600-cell elongating embryo, which we then compare with the expression of reporters driven by the full locus. Combining motif analysis of these enhancers with expression of candidate regulators from the EPIC database predicts specific regulators of each context-dependent enhancer, which we are currently testing experimentally.