ArticleRNA (New York, N.Y.)2015
Genome-wide profiling of the C. elegans dsRNAome.
Article in RNA (New York, N.Y.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
38 citing papers in PubMed.
- dsRNAscan maps human dsRNAome, revealing conservation, intermolecular dsRNA, and correlates of ADAR dependency.Molecular cell · 2026Article
- ADARs mediate distinct RNA editing activity and gene regulation in theRNA (New York, N.Y.) · 2026Article
- ADARs mediate distinct RNA editing activity and gene regulation in thebioRxiv : the preprint server for biology · 2025Article
- Article
- Comprehensive Mapping of Human dsRNAome Reveals Conservation, Neuronal Enrichment, and Intermolecular Interactions.bioRxiv : the preprint server for biology · 2025Article
- Full-length direct RNA sequencing reveals extensive remodeling of RNA expression, processing and modification in aging Caenorhabditis elegans.Nucleic acids research · 2024Article
- Article
- ADBP-1 regulates ADR-2 nuclear localization to control editing substrate selection.Nucleic acids research · 2024Article
- Full-length direct RNA sequencing reveals extensive remodeling of RNA expression, processing and modification in agingbioRxiv : the preprint server for biology · 2024Article
- Navigating the landscape of epitranscriptomics and host immunity.Genome research · 2024Review
- The competitive landscape of the dsRNA world.Molecular cell · 2024Review
- dsRID: in silico identification of dsRNA regions using long-read RNA-seq data.Bioinformatics (Oxford, England) · 2023Article
- dsRID: Editing-free in silico identification of dsRNA region using long-read RNA-seq data.bioRxiv : the preprint server for biology · 2023Article
- An essential role for the piRNA pathway in regulating the ribosomal RNA pool in C. elegans.Developmental cell · 2021Article
- Transient kinetic studies of the antiviraleLife · 2021Article
- Profiling neural editomes reveals a molecular mechanism to regulate RNA editing during development.Genome research · 2021Article
- Prevention of dsRNA-induced interferon signaling by AGO1x is linked to breast cancer cell proliferation.The EMBO journal · 2020Article
- mRNA Editing, Processing and Quality Control inGenetics · 2020Review
- The majority of A-to-I RNA editing is not required for mammalian homeostasis.Genome biology · 2019Article
- DUX4-induced bidirectional HSATII satellite repeat transcripts form intranuclear double-stranded RNA foci in human cell models of FSHD.Human molecular genetics · 2019Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Recent studies hint that endogenous dsRNA plays an unexpected role in cellular signaling. However, a complete understanding of endogenous dsRNA signaling is hindered by an incomplete annotation of dsRNA-producing genes. To identify dsRNAs expressed in Caenorhabditis elegans, we developed a bioinformatics pipeline that identifies dsRNA by detecting clustered RNA editing sites, which are strictly limited to long dsRNA substrates of Adenosine Deaminases that act on RNA (ADAR). We compared two alignment algorithms for mapping both unique and repetitive reads and detected as many as 664 editing-enriched regions (EERs) indicative of dsRNA loci. EERs are visually enriched on the distal arms of autosomes and are predicted to possess strong internal secondary structures as well as sequence complementarity with other EERs, indicative of both intramolecular and intermolecular duplexes. Most EERs were associated with protein-coding genes, with ∼1.7% of all C. elegans mRNAs containing an EER, located primarily in very long introns and in annotated, as well as unannotated, 3' UTRs. In addition to numerous EERs associated with coding genes, we identified a population of prospective noncoding EERs that were distant from protein-coding genes and that had little or no coding potential. Finally, subsets of EERs are differentially expressed during development as well as during starvation and infection with bacterial or fungal pathogens. By combining RNA-seq with freely available bioinformatics tools, our workflow provides an easily accessible approach for the identification of dsRNAs, and more importantly, a catalog of the C. elegans dsRNAome.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.