ArticleRNA (New York, N.Y.)2016
Reproducible features of small RNAs in C. elegans reveal NU RNAs and provide insights into 22G RNAs and 26G RNAs.
Article in RNA (New York, N.Y.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Argonaute-siRNA loading via the RNA-binding protein RDE-4 in C. elegans.Current biology : CB · 2025Article
- WAGO-1 is a sexually dimorphic Argonaute protein required for proper germ granule structure and gametogenesis.bioRxiv : the preprint server for biology · 2025Article
- A guide to the biogenesis and functions of endogenous small non-coding RNAs in animals.Nature reviews. Molecular cell biology · 2025Review
- A low-abundance class of Dicer-dependent siRNAs produced from a variety of features inGenome research · 2024Article
- Article
- Target-specific requirements for RNA interference can arise through restricted RNA amplification despite the lack of specialized pathways.bioRxiv : the preprint server for biology · 2024Article
- piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode.Scientific reports · 2022Article
- Angiogenin promotes angiogenesis via the endonucleolytic decay of miR-141 in colorectal cancer.Molecular therapy. Nucleic acids · 2022Article
- stepRNA: Identification of Dicer cleavage signatures and passenger strand lengths in small RNA sequences.Frontiers in bioinformatics · 2022Article
- The RNA phosphatase PIR-1 regulates endogenous small RNA pathways in C. elegans.Molecular cell · 2021Article
- Review
- Article
- Gene silencing by double-stranded RNA from C. elegans neurons reveals functional mosaicism of RNA interference.Nucleic acids research · 2019Article
- Article
- Function and Evolution of Nematode RNAi Pathways.Non-coding RNA · 2019Review
- Article
- The double-stranded RNA binding protein RDE-4 can act cell autonomously during feeding RNAi in C. elegans.Nucleic acids research · 2017Article
- Removing bias against short sequences enables northern blotting to better complement RNA-seq for the study of small RNAs.Nucleic acids research · 2017Article
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Authors and funding
2 authors.
Funding
Abstract
Small RNAs regulate gene expression and most genes in the worm Caenorhabditis elegans are subject to their regulation. Here, we analyze small RNA data sets and use reproducible features of RNAs present in multiple data sets to discover a new class of small RNAs and to reveal insights into two known classes of small RNAs--22G RNAs and 26G RNAs. We found that reproducibly detected 22-nt RNAs, although are predominantly RNAs with a G at the 5' end, also include RNAs with A, C, or U at the 5' end. These RNAs are synthesized downstream from characteristic sequence motifs on mRNA and have U-tailed derivatives. Analysis of 26G RNAs revealed that they are processed from a blunt end of double-stranded RNAs and that production of one 26G RNA generates a hotspot immediately downstream for production of another. To our surprise, analysis of RNAs shorter than 18 nt revealed a new class of RNAs, which we call NU RNAs (pronounced "new RNAs") because they have a NU bias at the 5' end, where N is any nucleotide. NU RNAs are antisense to genes and originate downstream from U bases on mRNA. Although many genes have complementary NU RNAs, their genome-wide distribution is distinct from that of previously known classes of small RNAs. Our results suggest that current approaches underestimate reproducibly detected RNAs that are shorter than 18 nt, and theoretical considerations suggest that such shorter RNAs could be used for sequence-specific gene regulation in organisms like C. elegans that have small genomes.
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