ArticleProceedings of the National Academy of Sciences of the United States of America2011
Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 195 papers, 1 of them a synthesis that pooled it.
What it found
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Who cites it
195 citing papers in PubMed, 1 synthesis or guideline pooled it, 315 citations in OpenAlex.
- Computational meta-analysis of ribosomal RNA fragments: potential targets and interaction mechanisms.Nucleic acids research · 2021Pooled it
- Elucidating structure-function relationships in the mammalian nucleolus.Nature reviews. Molecular cell biology · 2026Review
- Bacterial small regulatory RNAs.Nature reviews. Microbiology · 2026Review
- Small Regulatory RNAs in Prokaryotes: Key Features, Identification, Environmental Roles, and Applications.Microorganisms · 2026Review
- snoRNAs and their derived sdRNAs: Emerging regulators, biomarkers, and therapeutic targets in human cancers (Review).International journal of oncology · 2026Review
- High-Resolution Mapping of RNA-RNA Interactions Across the HIV-1 Genome With HicapR.Bio-protocol · 2026Article
- Progress and challenges in profiling protein-RNA and protein-associated RNA-RNA interactions.RNA (New York, N.Y.) · 2026Review
- RAPseq enables large-scale identification of RBP-RNA interactions and reveals essentials of post-transcriptional gene regulation.Nucleic acids research · 2026Article
- DRfold2 is a deep learning-based tool that enables efficient and accurate RNA structure prediction.PLoS biology · 2026Article
- Sni445 recruits box C/D snoRNPs snR4 and snR45 to guide ribosomal RNA acetylation by Kre33.Nucleic acids research · 2026Article
- NBSR: a Negative Binomial Softmax Regression model for microRNA-seq data analysis.Biostatistics (Oxford, England) · 2026Article
- From environmental signals to adaptive phenotypes: signal-responsive regulation and network logic of bacterial small RNAs.FEMS microbiology reviews · 2026Review
- Mapping of RBP-Mediated RNA-RNA Interactome with RIC-Seq.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Unveiling Functional Long-Range RNA Structures via RIC-seq Analysis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Systematic mapping of small nucleolar RNA interactions in human cells.RNA biology · 2025Article
- Direct circRNA-mRNA Binding Controls mRNA Fate: A New Mechanism for circRNAs.Non-coding RNA · 2025Review
- KSHV miRNAs target STING to evade innate immunity and facilitate KSHV lytic reactivation from latency.Cell reports · 2025Article
- Small regulatory RNAs as key modulators of antibiotic resistance in pathogenic bacteria.Journal of microbiology (Seoul, Korea) · 2025Review
- bpRNA-CosMoS: a robust and efficient RNA structural comparison method using k-mer based cosine similarity.Bioinformatics (Oxford, England) · 2025Article
- Mapping snoRNA-target RNA interactions in an RNA-binding protein-dependent manner with chimeric eCLIP.Genome biology · 2025Article
135 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Many protein-protein and protein-nucleic acid interactions have been experimentally characterized, whereas RNA-RNA interactions have generally only been predicted computationally. Here, we describe a high-throughput method to identify intramolecular and intermolecular RNA-RNA interactions experimentally by cross-linking, ligation, and sequencing of hybrids (CLASH). As validation, we identified 39 known target sites for box C/D modification-guide small nucleolar RNAs (snoRNAs) on the yeast pre-rRNA. Novel snoRNA-rRNA hybrids were recovered between snR4-5S and U14-25S. These are supported by native electrophoresis and consistent with previously unexplained data. The U3 snoRNA was found to be associated with sequences close to the 3' side of the central pseudoknot in 18S rRNA, supporting a role in formation of this structure. Applying CLASH to the yeast U2 spliceosomal snRNA led to a revised predicted secondary structure, featuring alternative folding of the 3' domain and long-range contacts between the 3' and 5' domains. CLASH should allow transcriptome-wide analyses of RNA-RNA interactions in many organisms.
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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.