Mutation and RNAi-based muscle enrichment impact gene expression levels. (A) Muscle troponin T tnt-3 exemplifies genes enriched in muscle-enhanced embryos (red). Muscle-normal expression (black) is nonzero since these animals retain significant muscle. (B) Non-BWM troponin C tnc-2 exemplifies genes depleted in muscle-enriched embryos. BWM-enriched animals (red) have reduced non-BWM tissue, so little expression is seen. (C) Troponin pat-10, which is expressed in both BWM and non-BWM, exhibits a negligible net change. (D) dhp-2 (dihydropyrimidinase) and (E) lbp-3 (lipid-binding) are both muscle-enriched. dhp-2 is affected by hlh-1 loss of function, and lbp-3 is affected by unc-120 loss-of-function, suggesting positive regulation by the BWM transcription factors. (F) Group averages of the ratiometric change for the muscle-enriched genes (those significantly up-regulated in muscle-enriched animals), nonmuscle-enriched (those significantly down-regulated in muscle-enriched animals) genes, and annotated BWM genes (which significantly overlap with NSM and PhM genes and are, therefore, more broadly expressed) are plotted against the RNAi feeding conditions. (G) Overlap of hlh-1 and unc-120 regulated genes, both positively and negatively regulated, including the 441 genes positively regulated by both unc-120 and hlh-1. The number of genes in the other intersects are listed. (H) BWM transcription factors regulate more broadly expressed RNAs than BWM-specific ones. A total of 1139 genes whose RNA levels are significantly regulated by hlh-1 and/or unc-120 are expressed exclusively in BWM; hlh-1 and unc-120 significantly regulated 1068 and 2694 broadly expressed genes. (RPKM) Reads per kilobase of gene structure model per million reads.
