Effects of HOE-1 (RNase Z/ELAC2) nuclear hyperactivation on gene expression in Caenorhabditis elegans.

We previously reported that the RNA endonculease HOE-1 (RNaseZ/ELAC2) is necessary and sufficient for activation of the mitochondrial unfolded protein response (UPRmt) in C. elegans (PMID: 35451962). To comprehensively assess the broader cellular consequences of increased nuclear activity of HOE-1, we conducted RNA sequencing on day 2 adult wildtype animals vs animals in which endogenous HOE-1 is elevated in the nucleus via perturbation of its nuclear export signal (hoe-1(?NES)). Additionally, wildtype and hoe-1(?NES) animals were grown on both control and atfs-1 RNAi (ATFS-1 is the central transcription factor for UPRmt) to determine gene expression that is atfs-1 dependent. This analysis revealed that differential gene expression in hoe-1(?NES) animals exhibits a strong mitochondrial signature. Notably, gene ontology (GO) analysis of significantly upregulated genes showed a significant overrepresentation of mitochondrial associated genes. Moreover, knockdown of atfs-1 strongly compromised the differentially expressed gene profile. Together these data suggest that increased nuclear activity of HOE-1 preferential impacts expression of mitochondrial genes. Overall design: hoe-1(?NES) animals were generated via CRISPR/Cas9 (validation and characterization can be found in PMID: 35451962). hoe-1(?NES) animals were then crossed to a conditional sterility mutant (glp-1(e2144). The wildtype condition submitted for RNAseq were glp-1(e2144) animals with wildtype hoe-1. Animals were grown for 72 hours at a non-permissive temperature (25°C) to confer sterility. This allowed for synchronization of adult populations and assessment of only somatic differential gene expression. Both wildtype and hoe-1(?NES) animals were grown on control and atfs-1 RNAi (HT115 bacterial background). Three biological replicates of 800 animals each were collected for each condition: wildtype on control RNAi, wildtype on atfs-1 RNAi, hoe-1(?NES) on control RNAi, and hoe-1(?NES) on atfs-1 RNAi.