ArticleGenome biology2023
Intronic small nucleolar RNAs regulate host gene splicing through base pairing with their adjacent intronic sequences.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 36 citations in OpenAlex.
- InteRRact: a web server for the interactive exploration and comparison of transcriptome-wide RNA-RNA interactions.NAR genomics and bioinformatics · 2026Article
- Integrative multi-omics analyses reveal nuclear noncoding RNA-mediated regulatory landscape in Alzheimer's disease.Archives of pharmacal research · 2026Article
- Transcriptional readthrough precedes alternative splicing programs triggered in CML cells by imatinib.Science advances · 2026Article
- Nonsense-mediated decay controls a negative feedback loop in innate immune sensing.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- snoCLASH Reveals Extensive snoRNA-mRNA Interaction Networks.bioRxiv : the preprint server for biology · 2025Article
- Coupling mechanisms coordinating mRNA translation with stages of the mRNA lifecycle.RNA biology · 2025Review
- Systematic mapping of small nucleolar RNA interactions in human cells.RNA biology · 2025Article
- Transcriptional readthrough precedes alternative splicing programs triggered in CML cells by imatinib.bioRxiv : the preprint server for biology · 2025Article
- Snord15b Maintains Stemness of Intestinal Stem Cells via Enhancement of Alternative Splicing of Btrc Short Isoform for Suppression of β-Catenin Ubiquitination.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- The role of cGAS-STING signaling pathway in ferroptosis.Journal of advanced research · 2025Review
- A U3 snoRNA is required for the regulation of chromatin dynamics and antiviral response in Drosophila melanogaster.Nucleic acids research · 2025Article
- SnoBIRD: a tool to identify C/D box snoRNAs and refine their annotation across all eukaryotes.Nucleic acids research · 2025Article
- Small Nucleolar RNAs: Biological Functions and Diseases.MedComm · 2025Review
- Small nucleolar RNAs: the hidden precursors of cancer ribosomes.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- The zebrafish (NAR genomics and bioinformatics · 2025Article
- Small Nucleolar RNAs and the Brain: Growing Evidence Supporting Their Role in Psychiatric Disorders.Biological psychiatry global open science · 2025Review
- SNORA37/CMTR1/ELAVL1 feedback loop drives gastric cancer progression via facilitating CD44 alternative splicing.Journal of experimental & clinical cancer research : CR · 2025Article
- SnoRNAs: The promising targets for anti-tumor therapy.Journal of pharmaceutical analysis · 2024Review
- SNORD3A Regulates STING Transcription to Promote Ferroptosis in Acute Kidney Injury.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- RNA structure in alternative splicing regulation: from mechanism to therapy.Acta biochimica et biophysica Sinica · 2024Review
Corrections and comments
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Authors and funding
13 authors at 3 institutions in 3 countries.
Funding
Abstract
backgroundSmall nucleolar RNAs (snoRNAs) are abundant noncoding RNAs best known for their involvement in ribosomal RNA maturation. In mammals, most expressed snoRNAs are embedded in introns of longer genes and produced through transcription and splicing of their host. Intronic snoRNAs were long viewed as inert passengers with little effect on host expression. However, a recent study reported a snoRNA influencing the splicing and ultimate output of its host gene. Overall, the general contribution of intronic snoRNAs to host expression remains unclear.
resultsComputational analysis of large-scale human RNA-RNA interaction datasets indicates that 30% of detected snoRNAs interact with their host transcripts. Many snoRNA-host duplexes are located near alternatively spliced exons and display high sequence conservation suggesting a possible role in splicing regulation. The study of the model SNORD2-EIF4A2 duplex indicates that the snoRNA interaction with the host intronic sequence conceals the branch point leading to decreased inclusion of the adjacent alternative exon. Extended SNORD2 sequence containing the interacting intronic region accumulates in sequencing datasets in a cell-type-specific manner. Antisense oligonucleotides and mutations that disrupt the formation of the snoRNA-intron structure promote the splicing of the alternative exon, shifting the EIF4A2 transcript ratio away from nonsense-mediated decay.
conclusionsMany snoRNAs form RNA duplexes near alternative exons of their host transcripts, placing them in optimal positions to control host output as shown for the SNORD2-EIF4A2 model system. Overall, our study supports a more widespread role for intronic snoRNAs in the regulation of their host transcript maturation.
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