C. elegans ADARs antagonize silencing of cellular dsRNAs by the antiviral RNAi pathway

Genes Dev. 2018 Feb 1;32(3-4):271-282. doi: 10.1101/gad.310672.117. Epub 2018 Feb 26.

Abstract

Cellular dsRNAs are edited by adenosine deaminases that act on RNA (ADARs). While editing can alter mRNA-coding potential, most editing occurs in noncoding sequences, the function of which is poorly understood. Using dsRNA immunoprecipitation (dsRIP) and RNA sequencing (RNA-seq), we identified 1523 regions of clustered A-to-I editing, termed editing-enriched regions (EERs), in four stages of Caenorhabditis elegans development, often with highest expression in embryos. Analyses of small RNA-seq data revealed 22- to 23-nucleotide (nt) siRNAs, reminiscent of viral siRNAs, that mapped to EERs and were abundant in adr-1;adr-2 mutant animals. Consistent with roles for these siRNAs in silencing, EER-associated genes (EAGs) were down-regulated in adr-1;adr-2 embryos, and this was dependent on associated EERs and the RNAi factor RDE-4. We observed that ADARs genetically interact with the 26G endogenous siRNA (endo-siRNA) pathway, which likely competes for RNAi components; deletion of factors required for this pathway (rrf-3 or ergo-1) in adr-1;adr-2 mutant strains caused a synthetic phenotype that was rescued by deleting antiviral RNAi factors. Poly(A)+ RNA-seq revealed EAG down-regulation and antiviral gene induction in adr-1;adr-2;rrf-3 embryos, and these expression changes were dependent on rde-1 and rde-4 Our data suggest that ADARs restrict antiviral silencing of cellular dsRNAs.

Keywords: Dicer; RNA editing; deaminase; self–nonself; siRNA.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adenosine / metabolism
  • Adenosine Deaminase / genetics*
  • Animals
  • Caenorhabditis elegans / embryology
  • Caenorhabditis elegans / genetics
  • Caenorhabditis elegans / growth & development
  • Caenorhabditis elegans / metabolism
  • Caenorhabditis elegans Proteins / genetics*
  • Caenorhabditis elegans Proteins / metabolism
  • Inosine / metabolism
  • Mutation
  • RNA Editing*
  • RNA Interference*
  • RNA, Double-Stranded / metabolism*
  • RNA, Small Interfering / metabolism
  • RNA-Dependent RNA Polymerase / genetics
  • Ribonuclease III / metabolism

Substances

  • Caenorhabditis elegans Proteins
  • RNA, Double-Stranded
  • RNA, Small Interfering
  • Inosine
  • RNA-Dependent RNA Polymerase
  • RNA-directed RNA polymerase RRF-3, C elegans
  • dcr-1 protein, C elegans
  • Ribonuclease III
  • Adenosine Deaminase
  • Adr-1 protein, C elegans
  • Adr-2 protein, C elegans
  • Adenosine