ArticleNature biotechnology2021
Analysis of RNA-protein networks with RNP-MaP defines functional hubs on RNA.
Article in Nature biotechnology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
- Folding the message: mRNA structure as a regulatory layer of human mitochondrial gene expression.Biochimica et biophysica acta. Molecular cell research · 2026Review
- Characterizing RNA 3D structural features from DMS reactivity.Nucleic acids research · 2026Article
- Correlated protein-RNA associations and a requirement for HNRNPU in the long-range recruitment of Polycomb Repressive Complexes by the lncRNAs Airn and Kcnq1ot1.PLoS genetics · 2026Article
- Multi-site DMS probing reveals higher-order structure of RNA-protein complexes in living cells.Molecular cell · 2026Article
- Novel CuCLIP-seq for in situ covalently captured protein-binding RNAs.Nature communications · 2026Article
- Quantifying MgbioRxiv : the preprint server for biology · 2026Article
- Progress and challenges in profiling protein-RNA and protein-associated RNA-RNA interactions.RNA (New York, N.Y.) · 2026Review
- Decoding the lncRNA World: Comprehensive Approaches to lncRNA Structure and Interactome Studies.Cells · 2026Review
- BioLLMNet: enhancing RNA-interaction prediction with a specialized cross-LLM transformation network.Briefings in bioinformatics · 2025Article
- Mapping small molecule-RNA binding sites via Chem-CLIP synergized with capillary electrophoresis and nanopore sequencing.Nucleic acids research · 2025Article
- SARS-CoV-2 Is an Electricity-Driven Virus.Reviews of physiology, biochemistry and pharmacology · 2025Review
- Template switching enables chemical probing of native RNA structures.RNA (New York, N.Y.) · 2024Article
- Proximitomics by Reactive Species.ACS central science · 2024Review
- The role of Matrin-3 in physiology and its dysregulation in disease.Biochemical Society transactions · 2024Review
- ePRINT: exonuclease assisted mapping of protein-RNA interactions.Genome biology · 2024Article
- RNAvigate: efficient exploration of RNA chemical probing datasets.Nucleic acids research · 2024Article
- Specific protein-RNA interactions are mostly preserved in biomolecular condensates.Science advances · 2024Article
- Observation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing.Nature communications · 2023Article
- A task-specific encoding algorithm for RNAs and RNA-associated interactions based on convolutional autoencoder.Nucleic acids research · 2023Article
- Chemoproteomic capture of RNA binding activity in living cells.Nature communications · 2023Article
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5 authors.
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Abstract
RNA-protein interaction networks govern many biological processes but are difficult to examine comprehensively. We devised ribonucleoprotein networks analyzed by mutational profiling (RNP-MaP), a live-cell chemical probing strategy that maps cooperative interactions among multiple proteins bound to single RNA molecules at nucleotide resolution. RNP-MaP uses a hetero-bifunctional crosslinker to freeze interacting proteins in place on RNA and then maps multiple bound proteins on single RNA strands by read-through reverse transcription and DNA sequencing. RNP-MaP revealed that RNase P and RMRP, two sequence-divergent but structurally related non-coding RNAs, share RNP networks and that network hubs define functional sites in these RNAs. RNP-MaP also identified protein interaction networks conserved between mouse and human XIST long non-coding RNAs and defined protein communities whose binding sites colocalize and form networks in functional regions of XIST. RNP-MaP enables discovery and efficient validation of functional protein interaction networks on long RNAs in living cells.
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