mRNA-seq of worms and the mitochondrial unfolded protein response (UPRmt)

To cope with a challenging and unpredictable environment, living systems have evolved several organelle-specific stress responses, e.g. the cytosolic heat shock response (HSR), the endoplasmic reticulum unfolded protein response (UPRER) and the mitochondrial unfolded protein response (UPRmt). UPRmt monitors mitochondrial function and homeostasis in general. However, the mechanism of UPRmt remains largely unexplored. Here we identified that histone deacetylase HDA-1 is associated with homeobox domain-containing protein DVE-1 in UPRmt activation in Caenorhabditis elegans. Knocking down ATP synthase subunit atp-2 generates mitochondrial stress and induces UPRmt. After analyzing the mRNA profiles of worms on L4440 RNAi, hda-1 RNAi or dve-1 RNAi and untreated or treated with atp-2 RNAi, we found that 283 hda-1_dependent genes and 218 dve-1_dependent genes were upregulated in response to atp-2 RNAi. Overall design: mRNA profiles of worms were generated by deep sequencing, in duplicate, using Illumina HiSeq2500. Worms on L4440 RNAi, hda-1 RNAi or dve-1 RNAi were untreated or treated with atp-2 RNAi