Perturbations that compromise specification generally result in developmental arrest, making it difficult to address questions of whether or not differentiation gene networks can correct for these in later development. We are using "hypomorphic gut specification" (HGS) strains in which activation of the gut specification factors
end-1 and/or
end-3 in the E (gut) lineage has been compromised. In HGS strains, development of gut becomes stochastic, manifested as a delay in activation of
elt-2, a gene whose product maintains the intestinal fate, and changes in the E lineage. Surviving HGS adults have normal levels of ELT-2, but they variably have excess numbers of gut cells (hyperplasia) and store excess fat, as detected by the presence of abnormally large lipid storage granules revealed by Oil Red O staining and localization of ATGL-1::GFP. Other pleiotropic effects, including a shorter life span, variable sterility and morphological changes, suggest that animals are undernourished. We do not find hyperlipidemia in
cdc-25.1(
rr31) adults, which contain an even greater number of gut cells than HGS animals, suggesting that hyperplasia is not the cause of hyperlipidemia. We observe an increase in expression and nuclear localization of DAF-16, a primary regulator of lipid storage. However, a
daf-16 null mutant background only partially reduces lipid accumulation in HGS animals, suggesting that other genes are the primary cause of the hyperlipidemia. To identify such genes, we performed tissue-specific RNA-Seq on isolated intestines from control and HGS adults. Only a small set of intestinal genes appears to be differentially expressed. One of these, a previously uncharacterized nuclear hormone receptor (NHR) gene, is strongly activated in the anterior gut in controls but downregulated in HGS animals. A null mutant in the gene induced by CRISPR/Cas9 results in adults that retain abnormally high amounts of lipids, suggesting that a major component of the fat accumulation in HGS strains is lack of expression of this NHR. Our results suggest two models by which HGS leads to hyperlipidemia and changed metabolism. First, compromised activation of specification through END-1,3 may prevent robust establishment of normal metabolism due to a failure to activate some early factors other than
elt-2. In a second model, the anterior cells of the gut may undergo a transformation in fate to a more posterior type of gut cell, resulting in a failure to adequately digest bacteria arriving from the pharynx. This might cause a decrease in digestive capacity of the gut, resulting in starvation-like defects. Together, our results connect progenitor specification with function of the differentiated organ, showing that a failure of robust early gene expression can result in abnormalities that are not corrected by activation of a terminal organ identity gene.