ArticleNature communications2021
Photoactivatable ribonucleosides mark base-specific RNA-binding sites.
Article in Nature communications, 2021. 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.
- Bridging technical innovation and computational advances in studies of RNA-protein assemblies.Nature reviews. Genetics · 2026Review
- Rapid photo-crosslinking in living cells reveals protein-nucleic acid dynamics on a timescale of minutes.Nucleic acids research · 2026Article
- RBP2GO 2.0: Integrating disease associations and sequence features to explore RNA-binding protein functions.Nucleic acids research · 2026Article
- Article
- Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid-protein interaction sites by mass spectrometry.Nucleic acids research · 2025Article
- Imaging and Tracking RNA in Live Mammalian Cells via Fluorogenic Photoaffinity Labeling.ACS chemical biology · 2025Article
- Intrastrand Photo-Crosslinking of 5-Fluoro-2'-O-methyl-4-thiouridine-Modified Oligonucleotides and Its Implication for Fluorescence-Based Detection of DNA Sequences.The Journal of organic chemistry · 2024Article
- Article
- pyRBDome: a comprehensive computational platform for enhancing RNA-binding proteome data.Life science alliance · 2024Article
- RNA-binding proteins in cardiovascular biology and disease: the beat goes on.Nature reviews. Cardiology · 2024Review
- DNA-Histone Cross-Link Formation via Hole Trapping in Nucleosome Core Particles.Journal of the American Chemical Society · 2023Article
- Detecting diagnostic features in MS/MS spectra of post-translationally modified peptides.Nature communications · 2023Article
- MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics.Molecular & cellular proteomics : MCP · 2023Article
- Review
- Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA.Nucleic acids research · 2023Article
- Characterizing crosstalk in epigenetic signaling to understand disease physiology.The Biochemical journal · 2023Article
- SP3-Enabled Rapid and High Coverage Chemoproteomic Identification of Cell-State-Dependent Redox-Sensitive Cysteines.Molecular & cellular proteomics : MCP · 2022Article
- Photoactivatable ribonucleosides mark base-specific RNA-binding sites.Nature communications · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA-protein interaction can be captured by crosslinking and enrichment followed by tandem mass spectrometry, but it remains challenging to pinpoint RNA-binding sites (RBSs) or provide direct evidence for RNA-binding. To overcome these limitations, we here developed pRBS-ID, by incorporating the benefits of UVA-based photoactivatable ribonucleoside (PAR; 4-thiouridine and 6-thioguanosine) crosslinking and chemical RNA cleavage. pRBS-ID robustly detects peptides crosslinked to PAR adducts, offering direct RNA-binding evidence and identifying RBSs at single amino acid-resolution with base-specificity (U or G). Using pRBS-ID, we could profile uridine-contacting RBSs globally and discover guanosine-contacting RBSs, which allowed us to characterize the base-specific interactions. We also applied the search pipeline to analyze the datasets from UVC-based RBS-ID experiments, altogether offering a comprehensive list of human RBSs with high coverage (3,077 RBSs in 532 proteins in total). pRBS-ID is a widely applicable platform to investigate the molecular basis of posttranscriptional regulation.
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Registered trials
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