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A Protein-Protein Interaction Underlies the Molecular Basis for Substrate Recognition by an Adenosine to Inosine RNA Editing Enzyme

ABSTRACT: We report an unbiased analysis of ADR-2 binding across the C. elegans transcriptome, which indicates that ADR-1 is required for ADR-2 to stably bind a majority of target mRNAs in vivo. By obtaining 30-50 million reads from immunoprecipitated RNA and input samples from wild type and adr-2(-) strains, we identified 1235 ADR-2 bound targets in wild-type worms. Comparing these ADR-2 bound targets with a list of all known edited targets in C. elegans, we determined ~65% of them are edited. Additionally sequencing reads from an ADR-2 RIP assay performed in the adr-1(-) strain were used to determine that the majority of ADR-2 targets (80%) have significantly reduced binding by ADR-2 in the absence of adr-1.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE112367 | GEO | 2018/08/23

REPOSITORIES: GEO

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Project description:A-to-I RNA editing is widespread in eukaryotic transcriptomes and plays an essential role in the creation of proteomic and phenotypic diversity. Loss of ADARs, the proteins responsible for A-to-I editing, results in lethality in mammals. In C. elegans, knocking out both ADARs, ADR-1 and ADR-2, results in aberrant behavior and abnormal development. Studies have shown that ADR-2 can actively deaminate dsRNA while ADR-1 cannot. However, as most studies of C. elegans ADARs were performed on worms mutated in both ADAR genes, the effects observed cannot be attributed to a single ADAR or to the interactions between ADAR genes. Therefore, we set to study the effects of each C. elegans ADAR on RNA editing, gene expression, protein levels and the contribution of each of ADAR to the phenotypes observed in worms mutated in both genes, in order to elucidate their distinct functions. We found significant differences in the phenotypes observed in worms mutated in a single ADAR gene. Worms harboring adr-1 mutations have a significant reduction in their lifespan, while worms harboring adr-2 mutations have extended lifespan. We also observed severe abnormalities in vulva formation mainly in adr-1 mutants, and we suggest that these phenotypes are a result of an RNA editing independent function of ADR-1. Mutations in each ADAR resulted in expressional changes in hundreds of genes, and a significant downregulation of edited genes. However, very few changes in the protein levels were observed. In addition, we found that ADR-1 binds many edited genes. Our results suggest that ADR-1 has a significant function in the RNA editing process and by altering editing levels it causes the severe phenotypes that we observed. In contrast, a complete lack of RNA editing is less harmful to the worms. Furthermore, our results indicate that the effect of RNA editing on the protein content in the cell is minor and probably the main purpose of these modifications is to antagonize or enhance other gene regulatory mechanisms that act on RNA.

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A Protein-Protein Interaction Underlies the Molecular Basis for Substrate Recognition by an Adenosine to Inosine RNA Editing Enzyme

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