Heat shock in C. elegans induces downstream of gene transcription and accumulation of double-stranded RNA

• DOI: 10.1371/journal.pone.0206715
• Publication Date: 2019-04-08T17:25:21Z
• Authors: Marko Melnick; Patrick Gonzales; Joseph Cabral; Mary A. Allen; Robin D. Dowell; Christopher D. Link
• Keywords: Cell Nucleus; 0301 basic medicine; 0303 health sciences; Transcription, Genetic; Science; Q; R; RNA-Binding Proteins; 03 medical and health sciences; Medicine; Animals; RNA, Helminth; Caenorhabditis elegans; Caenorhabditis elegans Proteins; Heat-Shock Response; Research Article; RNA, Double-Stranded

AbstractWe observed that heat shock of Caenorhabditis elegans leads to the formation of nuclear double-stranded RNA (dsRNA) foci, detectable with a dsRNA-specific monoclonal antibody. These foci significantly overlap with nuclear HSF-1 granules. To investigate the molecular mechanism(s) underlying dsRNA foci formation, we used RNA-seq to globally characterize total RNA and immunoprecipitated dsRNA from control and heat shocked worms. We find antisense transcripts are generally increased after heat shock, and a subset of both sense and antisense transcripts enriched in the dsRNA pool by heat shock overlap with dsRNA transcripts enriched by deletion of tdp-1, which encodes the C. elegans ortholog of TDP-43. Interestingly, transcripts involved in translation are over-represented in the dsRNAs induced by either heat shock or deletion of tdp-1. Also enriched in the dsRNA transcripts are sequences downstream of annotated genes (DoGs), which we globally quantified with a new algorithm. To validate these observations, we used fluorescence in situ hybridization (FISH) to confirm both antisense and downstream of gene transcription for eif-3.B, one of the affected loci we identified.