Reconstructing a metazoan genetic pathway with transcriptome-wide epistasis measurements

RNA-seq is commonly used to identify genetic modules that respond to perturbations. In single cells, transcriptomes have been used as phenotypes, but this concept has not been applied to whole-organism RNA-seq. Linear models can quantify expression effects of individual mutants and identify epistatic effects in double mutants. To make interpretation of these high-dimensional measurements intuitive, we developed a single coefficient to quantify transcriptome-wide epistasis that accurately reflects the underlying interactions. To demonstrate our approach, we sequenced four single and two double mutants of Caenorhabditis elegans . From these mutants, we reconstructed the known hypoxia pathway. In addition, we uncovered a class of 56 genes that have opposing changes in expression in egl-9(lf) compared to vhl-1(lf) but the egl-9(lf); vhl-1(lf) mutant has the same phenotype as egl-9(lf) . This class violates the classical model of HIF-1 regulation, but can be explained by postulating a role of hydroxylated HIF-1 in transcriptional control.