ArticleNature methods2014
Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins.
Article in Nature methods, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 150 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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Who cites it
150 citing papers in PubMed, 270 citations in OpenAlex.
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- Signal or noise? RNA-binding proteins and the challenges of binding site assignments.Nucleic acids research · 2026Review
- 2'-O-methylation-dependent installation of NNature communications · 2026Article
- Novel CuCLIP-seq for in situ covalently captured protein-binding RNAs.Nature communications · 2026Article
- RNA-induced PRC2 inhibition depends on the sequence of bound RNA.Nature communications · 2026Article
- Rapid photo-crosslinking in living cells reveals protein-nucleic acid dynamics on a timescale of minutes.Nucleic acids research · 2026Article
- Phosphoproteomic Landscape of HDLBP: Insights into Function and Disease Associations.International journal of molecular sciences · 2026Article
- Distinct steps of nuclear maturation of human pre-60S complexes require the activity of GTPases including GNL3L.Nucleic acids research · 2026Article
- GlycoRNA research: from unknown unknowns to known unknowns.Protein & cell · 2026Review
- Nucleolar MED19 regulates 2'-O-methylation of rRNA in supporting cancer cell growth.Nucleic acids research · 2025Article
- Visualizing liquid-liquid phase separation and protein aggregates.Communications chemistry · 2025Review
- RNA-induced PRC2 inhibition depends on the sequence of bound RNA.Research square · 2025Article
- Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid-protein interaction sites by mass spectrometry.Nucleic acids research · 2025Article
- A highly sensitive protein-RNA cross-linking mass spectrometry workflow with enhanced structural modeling potential.Nucleic acids research · 2025Article
- Malonate promotes CD8Cellular & molecular immunology · 2025Article
- c-di-GMP inhibits rRNA methylation and impairs ribosome assembly in the presence of kanamycin.EMBO reports · 2025Article
- Direct observation of ultrafast symmetry reduction during internal conversion of 2-thiouracil using Coulomb explosion imaging.Nature communications · 2025Article
- Identification and characterization of a human MORC2 DNA binding region that is required for gene silencing.Nucleic acids research · 2025Article
90 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
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA-protein complexes play pivotal roles in many central biological processes. Although methods based on high-throughput sequencing have advanced our ability to identify the specific RNAs bound by a particular protein, there is a need for precise and systematic ways to identify RNA interaction sites on proteins. We have developed an experimental and computational workflow combining photo-induced cross-linking, high-resolution mass spectrometry and automated analysis of the resulting mass spectra for the identification of cross-linked peptides, cross-linking sites and the cross-linked RNA oligonucleotide moieties of such RNA-binding proteins. The workflow can be applied to any RNA-protein complex of interest or to whole proteomes. We applied the approach to human and yeast mRNA-protein complexes in vitro and in vivo, demonstrating its powerful utility by identifying 257 cross-linking sites on 124 distinct RNA-binding proteins. The open-source software pipeline developed for this purpose, RNP(xl), is available as part of the OpenMS project.
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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.