ArticleNature communications2019
CAPRI enables comparison of evolutionarily conserved RNA interacting regions.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Bridging technical innovation and computational advances in studies of RNA-protein assemblies.Nature reviews. Genetics · 2026Review
- hnRNPUL1 has a dead polynucleotide kinase domain that regulates RNA and protein interactions.iScience · 2026Article
- PRRC2A, PRRC2B and PRRC2C are Stress Granule Proteins that Promote Translation Through Association with the eIF3 complex.bioRxiv : the preprint server for biology · 2026Article
- RBP2GO 2.0: Integrating disease associations and sequence features to explore RNA-binding protein functions.Nucleic acids research · 2026Article
- Diet-induced RKIP downregulation disrupts PC/PE-ER homeostasis to drive MASLD.Nature communications · 2025Article
- 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
- A highly sensitive protein-RNA cross-linking mass spectrometry workflow with enhanced structural modeling potential.Nucleic acids research · 2025Article
- Deep mutational scanning of the Trypanosoma brucei developmental regulator RBP6 reveals an essential disordered region influenced by positive residues.Nature communications · 2025Article
- Enzymatic synthesis of reactive RNA probes containing squaramate-linked cytidine or adenosine for bioconjugations and cross-linking with lysine-containing peptides and proteins.Communications chemistry · 2025Article
- Article
- Capture of RNA-binding proteins across mouse tissues using HARD-AP.Nature communications · 2024Article
- Refining the pool of RNA-binding domains advances the classification and prediction of RNA-binding proteins.Nucleic acids research · 2024Article
- Cytosolic RNA binding of the mitochondrial TCA cycle enzyme malate dehydrogenase.RNA (New York, N.Y.) · 2024Article
- RNA-binding proteins in cardiovascular biology and disease: the beat goes on.Nature reviews. Cardiology · 2024Review
- Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes.Nature communications · 2024Article
- RNA-binding protein Nocte regulates Drosophila development by promoting translation reinitiation on mRNAs with long upstream open reading frames.Nucleic acids research · 2024Article
- LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways.Nature communications · 2023Article
- Review
- Chloroacetamide-Modified Nucleotide and RNA for Bioconjugations and Cross-Linking with RNA-Binding Proteins.Angewandte Chemie (International ed. in English) · 2023Article
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7 authors.
Funding
Abstract
RNA-protein complexes play essential regulatory roles at nearly all levels of gene expression. Using in vivo crosslinking and RNA capture, we report a comprehensive RNA-protein interactome in a metazoan at four levels of resolution: single amino acids, domains, proteins and multisubunit complexes. We devise CAPRI, a method to map RNA-binding domains (RBDs) by simultaneous identification of RNA interacting crosslinked peptides and peptides adjacent to such crosslinked sites. CAPRI identifies more than 3000 RNA proximal peptides in Drosophila and human proteins with more than 45% of them forming new interaction interfaces. The comparison of orthologous proteins enables the identification of evolutionary conserved RBDs in globular domains and intrinsically disordered regions (IDRs). By comparing the sequences of IDRs through evolution, we classify them based on the type of motif, accumulation of tandem repeats, conservation of amino acid composition and high sequence divergence.
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