ArticleNature methods2015
Protein-RNA networks revealed through covalent RNA marks.
Article in Nature methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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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
60 citing papers in PubMed, 97 citations in OpenAlex.
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- Synergistic Methods to Investigate Eukaryotic Translation and Its Quality Control.Journal of molecular biology · 2025Review
- Decoding RNA-Protein Interactions: Methodological Advances and Emerging Challenges.Advanced genetics (Hoboken, N.J.) · 2025Review
- Deaminase-based RNA recording enables high throughput mutational profiling of protein-RNA interactions.bioRxiv : the preprint server for biology · 2025Article
- Old players and new insights: unraveling the role of RNA-binding proteins in brain tumors.Theranostics · 2025Review
- CRISPR/Cas13 sgRNA-Mediated RNA-RNA Interaction Mapping in Live Cells with APOBEC RNA Editing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Beyond RNA-binding domains: determinants of protein-RNA binding.RNA (New York, N.Y.) · 2024Article
- Mapping subcellular RNA localization with proximity labeling.Acta biochimica et biophysica Sinica · 2024Review
- PUF partner interactions at a conserved interface shape the RNA-binding landscape and cell fate in Caenorhabditis elegans.Developmental cell · 2024Article
- A transient in planta editing assay identifies specific binding of the splicing regulator PTB as a prerequisite for cassette exon inclusion.Plant molecular biology · 2024Article
- Current progress in strategies to profile transcriptomic mFrontiers in cell and developmental biology · 2024Review
- RNA binding proteins in cardiovascular development and disease.Current topics in developmental biology · 2024Article
- Profiling dynamic RNA-protein interactions using small-molecule-induced RNA editing.Nature chemical biology · 2023Article
- Chemical Approaches To Investigate Post-transcriptional RNA Regulation.ACS chemical biology · 2023Review
- Identification of RNA-Binding Protein Targets with HyperTRIBE inInternational journal of molecular sciences · 2023Article
- Role of the RNA-binding protein family in gynecologic cancers.American journal of cancer research · 2023Review
- Analyzing RNA-Protein Interactions by Cross-Link Rates and CLIP-seq Libraries.Current protocols · 2023Article
- Single-molecule identification of the target RNAs of different RNA binding proteins simultaneously in cells.Genes & development · 2022Article
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4 authors at 1 institution in 1 country.
Funding
Abstract
Protein-RNA networks are ubiquitous and central in biological control. We present an approach termed RNA Tagging that enables the user to identify protein-RNA interactions in vivo by analyzing purified cellular RNA, without protein purification or cross-linking. An RNA-binding protein of interest is fused to an enzyme that adds uridines to the end of RNA. RNA targets bound by the chimeric protein in vivo are covalently marked with uridines and subsequently identified from extracted RNA via high-throughput sequencing. We used this approach to identify hundreds of RNAs bound by a Saccharomyces cerevisiae PUF protein, Puf3p. The results showed that although RNA-binding proteins productively bind specific RNAs to control their function, they also 'sample' RNAs without exerting a regulatory effect. We used the method to uncover hundreds of new and likely regulated targets for a protein without canonical RNA-binding domains, Bfr1p. RNA Tagging is well suited to detect and analyze protein-RNA networks in vivo.
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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.