The Caenorhabditis elegans intestine - a clonally-derived, 20-cell organ - is a powerful model of organogenesis owing to its relative simplicity. We seek to map the gene regulatory networks that specify and differentiate the intestine. We want to understand how key transcription factors ELT-2 and ELT-7 work together to regulate intestine genes. ELT-2 is an intestine-specific GATA transcription factor necessary for larval viability and sufficient for C. elegans intestinal development. ELT-7 works redundantly with ELT-2, and deletion of both enhances intestine deformities observed in ELT-2 deletion alone. Despite extensive and fruitful study, it is still not well understood how ELT-2 engage different sets of target genes over time and how they compete with, cooperate with, or stimulate other transcription factors to execute stage-specific transcriptional outcomes within the intestine. One challenge in addressing these questions is that the field lacks a clear developmental time course of intestine-specific transcriptome profiles. To characterize the changing intestinal transcriptome, we have optimized FACS purification of intestine cells at embryo and L1 developmental stages and performed RNA-seq on populations of ~90% pure intestine cells. Comparative studies between our transcriptome profiles, published ELT-2 ChIP-seq data, and published sets of
elt-2 and/or
elt-7 dependent genes are leading us to insights into ELT-2 regulatory behavior. Though ELT-2 is generally associated with transcriptional activation, we have observed that ELT-2 directly binds and represses expression of intestine expressed transcription factors PQM-1 and ETS-4. This finding suggests that ELT-2 repression may tune or maintain proper gene expression levels for a subset of target genes. Additionally, we have observed a subset of ELT-2 repressed target genes that are intestine depleted and instead associated with neuronal or germline biology. This suggests that ELT-2 repression may play a role in protecting the intestine from inappropriate or competing cell fates. Finally, we identified over-expression of the
elt-2 promoter in the absence of ELT-2 protein, indicating that ELT-2 binding may down-regulates its own promoter through a negative feedback loop. We demonstrated that
elt-2 promoter over-expression is ELT-7 dependent. Together these data suggest that ELT-2 both represses and activates target intestine genes, with ELT-7 primarily serving as an activator.