Open AccessHeat shock in C. elegans induces downstream of gene transcription and accumulation of double-stranded RNA
Author(s) -
Marko Melnick,
Patrick Gonzales,
Joseph Cabral,
Mary A. Allen,
Robin D. Dowell,
Christopher D. Link
Publication year - 2019
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0206715
Subject(s) - rna silencing , biology , rna , microbiology and biotechnology , caenorhabditis elegans , transcription (linguistics) , gene , messenger rna , gene expression , heat shock , heat shock protein , genetics , rna interference , linguistics , philosophy
We 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 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.