DVE-1_ChIP-seq and HDA-1_ChIP-seq of worms

Mitochondria are important organelles, but their function is often challenged by toxic products of metabolism as well as by pathogen attack. The mitochondrial unfolded protein response (UPRmt) monitors mitochondrial function in general: it is responsible for buffering the mitochondrial protein folding environment, and controlling mitochondria-nuclear balance of the electron transport chain (ETC) components. Besides, UPRmt plays essential roles in aging and lifespan. Here we found that knocking down histone deacetylase hda-1 robustly attenuated UPRmt and lifespan extension. We identified HDA-1 as a required factor for UPRmt activation and HDA-1 is associated with the homeobox domain-containing protein DVE-1.So, we performed ChIP-seq of worms to find DNA regions on which HDA-1 and DVE-1 bound, and if their binding depend on each other. Overall design: hda-1p::hda-1::gfp worms and dve-1p::dve-1::gfp worms were used for HDA-1-ChIP and DVE-1-ChIP. Worms on L4440 RNAi, hda-1 RNAi or dve-1 RNAi were untreated or treated with atp-2 RNAi. ChIP-seq data were generated by deep sequencing, using Illumina HiSeqXten. HDA-1_input/ChIP (dve-1); HG-D.repOverlap.finalPeak.bed3 HDA-1_input/ChIP (dve-1+atp-2); HG-DA.repOverlap.finalPeak.bed3 DVE-1_input/ChIP (hda-1); DG-H.repOverlap.finalPeak.bed3 DVE-1_input/ChIP (hda-1+atp-2); DG-HA.repOverlap.finalPeak.bed3