ArticleNature biotechnology2019
Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS).
Article in Nature biotechnology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 217 papers.
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Who cites it
217 citing papers in PubMed, 394 citations in OpenAlex.
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- High-throughput identification of endogenous biomolecular condensates and phase-separating proteins.Nature protocols · 2026Review
- The isolated HEPN domain of SACSIN exhibits RNA-binding activity.Cellular and molecular life sciences : CMLS · 2026Article
- SERIPH: a two-step extraction protocol for selective enrichment of semi-extractable RNAs.RNA (New York, N.Y.) · 2026Article
- Cross-species R-DeeP profiling reveals a conserved core of RNA-dependent proteins in yeast.Nucleic acids research · 2026Article
- The HIV-1 restriction factor RPRD2 does not inhibit transcription of HIV-1 or endogenous retroelements.bioRxiv : the preprint server for biology · 2026Article
- Dissecting autonomous enzymatic variability in single cells.Nature communications · 2026Article
- RNA-binding protein transcripts reflect composition of target mRNAs.Nucleic acids research · 2026Article
- Bridging technical innovation and computational advances in studies of RNA-protein assemblies.Nature reviews. Genetics · 2026Review
- Post-transcriptional regulatory networks: The dynamic interplay of RNA-binding proteins.The FEBS journal · 2026Review
- An approach for the systematic profiling of drug-induced remodeling of RNA-RBP (RNA-binding protein) interactions.RSC advances · 2026Article
- RNA-binding proteins and ribonucleoproteins as determinants of immunity.Nature reviews. Immunology · 2026Review
- A framework for the exploration of subcellular compartmentalization of RNA-binding proteins.Nature communications · 2026Article
- Rapid photo-crosslinking in living cells reveals protein-nucleic acid dynamics on a timescale of minutes.Nucleic acids research · 2026Article
- Dynamic Mapping of RNA-Binding Proteins DuringBio-protocol · 2026Article
- Recent Advances in Proximity Labeling-Based Subcellular Proteomic Mapping.Molecular & cellular proteomics : MCP · 2026Review
- RAPseq enables large-scale identification of RBP-RNA interactions and reveals essentials of post-transcriptional gene regulation.Nucleic acids research · 2026Article
- An intrinsically disordered region mediates RNA-binding selectivity and cellular activities of LARP6.Nature communications · 2026Article
- Integrative profiling of condensation-prone RNAs during early development.Cell genomics · 2026Article
157 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
13 authors at 3 institutions in 1 country.
Funding
Abstract
Existing high-throughput methods to identify RNA-binding proteins (RBPs) are based on capture of polyadenylated RNAs and cannot recover proteins that interact with nonadenylated RNAs, including long noncoding RNA, pre-mRNAs and bacterial RNAs. We present orthogonal organic phase separation (OOPS), which does not require molecular tagging or capture of polyadenylated RNA, and apply it to recover cross-linked protein-RNA and free protein, or protein-bound RNA and free RNA, in an unbiased way. We validated OOPS in HEK293, U2OS and MCF10A human cell lines, and show that 96% of proteins recovered were bound to RNA. We show that all long RNAs can be cross-linked to proteins, and recovered 1,838 RBPs, including 926 putative novel RBPs. OOPS is approximately 100-fold more efficient than existing methods and can enable analyses of dynamic RNA-protein interactions. We also characterize dynamic changes in RNA-protein interactions in mammalian cells following nocodazole arrest, and present a bacterial RNA-interactome for Escherichia coli. OOPS is compatible with downstream proteomics and RNA sequencing, and can be applied in any organism.
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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.