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RNA–protein interaction detection in living cells

https://doi.org/10.1038/nmeth.4601
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Designed Arginine-Rich RNA-Binding Peptides with Picomolar Affinity
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The Xist lncRNA interacts with SHARP to silence transcription through HDAC3
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Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes
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Roquin recognizes a non-canonical hexaloop structure in the 3′-UTR of Ox40
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Invasive three-dimensional organotypic neoplasia from multiple normal human epithelia
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The CRAPome: a contaminant repository for affinity purification–mass spectrometry data
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Directed evolution of APEX2 for electron microscopy and proximity labeling
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irCLIP platform for efficient characterization of protein–RNA interactions
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Human cerebral cortex development from pluripotent stem cells to functional excitatory synapses
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Aptamers as therapeutics
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RNA regulons: coordination of post-transcriptional events
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Structural basis for RNA recognition in roquin-mediated post-transcriptional gene regulation
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RNA-Protein Interaction Detection (RaPID)
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Zika Virus Associated with Microcephaly
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Unbiased RNA–protein interaction screen by quantitative proteomics
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Probing nuclear pore complex architecture with proximity-dependent biotinylation
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Clinical Severity and Thermodynamic Effects of Iron-responsive Element Mutations in Hereditary Hyperferritinemia-Cataract Syndrome
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A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells
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An improved smaller biotin ligase for BioID proximity labeling
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Structural insights into the targeting of mRNA GU-rich elements by the three RRMs of CELF1
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New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes
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From Birth to Death: The Complex Lives of Eukaryotic mRNAs
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Epigenetic Regulation by Long Noncoding RNAs
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Dynamically Reshaping Signaling Networks to Program Cell Fate via Genetic Controllers
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The STAT3-Binding Long Noncoding RNA lnc-DC Controls Human Dendritic Cell Differentiation
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Tissue-based map of the human proteome
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Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal
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Iron-Dependent Degradation of Apo-IRP1 by the Ubiquitin-Proteasome Pathway
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The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data
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Human Induced Pluripotent Stem Cell–Derived Cardiomyocytes as an In Vitro Model for Coxsackievirus B3–Induced Myocarditis and Antiviral Drug Screening Platform
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Efficient precise knockin with a double cut HDR donor after CRISPR/Cas9-mediated double-stranded DNA cleavage
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Specific RNP capture with antisense LNA/DNA mixmers
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Evidence for reassociation of RNA-binding proteins after cell lysis: Implications for the interpretation of immunoprecipitation analyses
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Successful Conversion of the Bacillus subtilis BirA Group II Biotin Protein Ligase into a Group I Ligase
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Linking white and grey matter in schizophrenia: Oligodendrocyte and neuron pathology in the prefrontal cortex
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Diverse roles of host RNA binding proteins in RNA virus replication

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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RNA –Protein Interactomics
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Photocatalytic Chemical Crosslinking for Profiling RNA–Protein Interactions in Living Cells
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Two‐Level Spatially Localized Proximity Labeling for Cross‐Biological‐Hierarchy Measurement and Manipulation
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Photocatalytic Chemical Crosslinking for Profiling RNA–Protein Interactions in Living Cells
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SLC38A2 Overexpression Induces a Cancer‐like Metabolic Profile and Cooperates with SLC1A5 in Pan‐cancer Prognosis
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On-Demand Proximity Labeling Using Light-Activated BioID
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Spatiotemporally Resolved Profiling of Protein Movement by TransitID
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LAP2 Proteins Chaperone GLI1 Movement between the Lamina and Chromatin to Regulate Transcription
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Functional viromic screens uncover regulatory RNA elements
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Recent Advances in Proximity Labeling-Based Subcellular Proteomic Mapping
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SAFB2 Enables the Processing of Suboptimal Stem-Loop Structures in Clustered Primary miRNA Transcripts
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Hybridization-proximity labeling reveals spatially ordered interactions of nuclear RNA compartments
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Spatial omics advances for in situ RNA biology
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Exploring the expanding universe of host-virus interactions mediated by viral RNA
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TurboCas: A method for locus-specific labeling of genomic regions and isolating their associated protein interactome
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QKI deficiency in macrophages protects mice against JEV infection by regulating cell migration and antiviral response
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Unveiling the role of PUS7-mediated pseudouridylation in host protein interactions specific for the SARS-CoV-2 RNA genome
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Direct and noninvasive fluorescence analysis of an RNA-protein interaction based on a CRISPR/Cas12a-powered assay
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Computational approaches to macromolecular interactions in the cell
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Addressing the challenge of in situ structural studies of RNP granules in light of emerging opportunities
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Challenges in structural modeling of RNA-protein interactions
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Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell
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Studying the ubiquitin code through biotin-based labelling methods
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Exploring protein-protein interactions at the proteome level
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Cross-linking and mass spectrometry as a tool for studying the structural biology of ribonucleoproteins
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Revealing lncRNA Structures and Interactions by Sequencing-Based Approaches
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In-Cell Discovery of RNA–Protein Interactions
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RNA-Centric Methods: Toward the Interactome of Specific RNA Transcripts
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Bacterial enzymes: powerful tools for protein labeling, cell signaling, and therapeutic discovery
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Landscape of Noncoding RNA in Prostate Cancer
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Revolutionary applications of proximity labeling for cell analysis and functional regulation from multi-dimensional perspectives
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Liquid–liquid phase separation at the frontline of plant–pathogen battles
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eCRUIS captures RNA-protein interaction in vitro and in vivo
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Study on the interaction protein of transcription factor Smad3 based on TurboID proximity labeling technology
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Mass Spectrometry for Assessing Protein–Nucleic Acid Interactions
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Proximity-Based Phospho-Interactome (Prob-PhI) Characterization Reveals Distinct Signaling Activities of MEK1 and MEK2
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Characterizations of G-Quadruplex RNA-Protein Interactions in Living Cells
inferred← citeshttps://doi.org/10.1021/acs.biochem.5c00660openalex-snapshot
Mapping RNA-Binding Proteins on the Ribosome by Tethered Micrococcal Nuclease
inferred← citeshttps://doi.org/10.1021/acs.chemrev.1c00223openalex-snapshot
In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology
inferred← citeshttps://doi.org/10.1021/acs.jproteome.0c00068openalex-snapshot
The Development of RNA-KISS, a Mammalian Three-Hybrid Method to Detect RNA–Protein Interactions in Living Mammalian Cells
inferred← citeshttps://doi.org/10.1021/acs.jproteome.6c00523openalex-snapshot
Proximity Labeling: An Empowering Tool for Deciphering Molecular Mechanisms
inferred← citeshttps://doi.org/10.1021/acs.jproteome.9b00609openalex-snapshot
Combining Proximity Labeling and Cross-Linking Mass Spectrometry for Proteomic Dissection of Nuclear Envelope Interactome
inferred← citeshttps://doi.org/10.1021/acscentsci.4c00373openalex-snapshot
Proximitomics by Reactive Species
inferred← citeshttps://doi.org/10.1021/acschembio.5c00471openalex-snapshot
CRISPR RiPCA for Investigating eIF4E-m7GpppX Capped mRNA Interactions
inferred← citeshttps://doi.org/10.1021/acschembio.8b00919openalex-snapshot
Directed Evolution of Split APEX2 Peroxidase
inferred← citeshttps://doi.org/10.1021/acsinfocus.7e5010openalex-snapshot
Functional Proteomics
inferred← citeshttps://doi.org/10.1021/jacs.2c01384openalex-snapshot
μMap-Red: Proximity Labeling by Red Light Photocatalysis
inferred← citeshttps://doi.org/10.1021/jasms.9b00024openalex-snapshot
Signature Fragment Ions of Biotinylated Peptides
inferred← citeshttps://doi.org/10.1038/nbt.4201openalex-snapshot
Efficient proximity labeling in living cells and organisms with TurboID
inferred← citeshttps://doi.org/10.1038/nmeth0518-394bopenalex-snapshot
Erratum: Corrigendum: RNA–protein interaction detection in living cells
inferred← citeshttps://doi.org/10.1038/s41377-023-01335-8openalex-snapshot
Submonolayer biolasers for ultrasensitive biomarker detection
inferred← citeshttps://doi.org/10.1038/s41422-021-00581-yopenalex-snapshot
Comparison of viral RNA–host protein interactomes across pathogenic RNA viruses informs rapid antiviral drug discovery for SARS-CoV-2
inferred← citeshttps://doi.org/10.1038/s41422-024-00938-zopenalex-snapshot
The rapid proximity labeling system PhastID identifies ATP6AP1 as an unconventional GEF for Rheb
inferred← citeshttps://doi.org/10.1038/s41467-025-58979-wopenalex-snapshot
TblncRNA-23, a long non-coding RNA transcribed by RNA polymerase I, regulates developmental changes in Trypanosoma brucei
inferred← citeshttps://doi.org/10.1038/s41477-023-01371-7openalex-snapshot
TurboID-based proteomic profiling of meiotic chromosome axes in Arabidopsis thaliana
inferred← citeshttps://doi.org/10.1038/s41556-021-00835-2openalex-snapshot
METTL16 exerts an m6A-independent function to facilitate translation and tumorigenesis
inferred← citeshttps://doi.org/10.1038/s41573-022-00505-4openalex-snapshot
Modulating biomolecular condensates: a novel approach to drug discovery
inferred← citeshttps://doi.org/10.1038/s41576-024-00749-3openalex-snapshot
Decoding protein–RNA interactions using CLIP-based methodologies
inferred← citeshttps://doi.org/10.1038/s41576-026-00931-9openalex-snapshot
Bridging technical innovation and computational advances in studies of RNA–protein assemblies
inferred← citeshttps://doi.org/10.1038/s41580-025-00914-4openalex-snapshot
Regulation of RNA-binding proteins by small biomolecules
inferred← citeshttps://doi.org/10.1038/s41586-022-04727-9openalex-snapshot
Gibbin mesodermal regulation patterns epithelial development
inferred← citeshttps://doi.org/10.1038/s41587-019-0341-6openalex-snapshot
Probing and engineering liquid-phase organelles
inferred← citeshttps://doi.org/10.1038/s41587-020-0434-2openalex-snapshot
ChromID identifies the protein interactome at chromatin marks
inferred← citeshttps://doi.org/10.1038/s41587-025-02780-zopenalex-snapshot
Genome-wide mapping of RNA-protein associations through sequencing
inferred← citeshttps://doi.org/10.1038/s41587-025-02891-7openalex-snapshot
RNA stability enhancers for durable base-modified mRNA therapeutics
inferred← citeshttps://doi.org/10.1038/s41589-023-01530-zopenalex-snapshot
Profiling the interactome of oligonucleotide drugs by proximity biotinylation
inferred← citeshttps://doi.org/10.1038/s41589-025-01993-2openalex-snapshot
In situ proximity labeling of proteins associated with circRNA and RNA G-quadruplexes
inferred← citeshttps://doi.org/10.1038/s41592-019-0330-1openalex-snapshot
Methods to study RNA–protein interactions
inferred← citeshttps://doi.org/10.1038/s41592-020-01010-5openalex-snapshot
Deciphering molecular interactions by proximity labeling
inferred← citeshttps://doi.org/10.1038/s41592-020-0866-0openalex-snapshot
CRISPR-assisted detection of RNA–protein interactions in living cells
inferred← citeshttps://doi.org/10.1038/s41592-022-01552-wopenalex-snapshot
PROBER identifies proteins associated with programmable sequence-specific DNA in living cells
inferred← citeshttps://doi.org/10.1038/s41592-022-01553-9openalex-snapshot
PROBER: overcoming the high noise of DNA–protein interactions studies
inferred← citeshttps://doi.org/10.1038/s41592-024-02181-1openalex-snapshot
TREX reveals proteins that bind to specific RNA regions in living cells
inferred← citeshttps://doi.org/10.1038/s41592-024-02457-6openalex-snapshot
Multiomic characterization of RNA microenvironments by oligonucleotide-mediated proximity-interactome mapping
inferred← citeshttps://doi.org/10.1038/s41596-020-0399-0openalex-snapshot
Proximity labeling in mammalian cells with TurboID and split-TurboID
inferred← citeshttps://doi.org/10.1038/s41596-021-00609-yopenalex-snapshot
Capture of the newly transcribed RNA interactome using click chemistry
inferred← citeshttps://doi.org/10.1038/s41598-021-84612-zopenalex-snapshot
Validation of a multicellular tumor microenvironment system for modeling patient tumor biology and drug response
inferred← citeshttps://doi.org/10.1038/s41598-022-05405-6openalex-snapshot
Orthogonal proteomics methods to unravel the HOTAIR interactome
inferred← citeshttps://doi.org/10.1038/s41598-022-15438-6openalex-snapshot
In-resin CLEM of Epon-embedded cells using proximity labeling
inferred← citeshttps://doi.org/10.1038/s42003-020-0758-yopenalex-snapshot
Biotin proximity tagging favours unfolded proteins and enables the study of intrinsically disordered regions
inferred← citeshttps://doi.org/10.1038/s42003-022-03604-5openalex-snapshot
Engineering of ultraID, a compact and hyperactive enzyme for proximity-dependent biotinylation in living cells
inferred← citeshttps://doi.org/10.1038/s43586-021-00023-4openalex-snapshot
CLIP and complementary methods
inferred← citeshttps://doi.org/10.1038/s43586-021-00029-yopenalex-snapshot
Subcellular proteomics
inferred← citeshttps://doi.org/10.1038/s44320-024-00049-2openalex-snapshot
A proximity proteomics pipeline with improved reproducibility and throughput
inferred← citeshttps://doi.org/10.1039/d0cs01366hopenalex-snapshot
Reactive intermediates for interactome mapping
inferred← citeshttps://doi.org/10.1042/bcj20180440openalex-snapshot
lncRedibly versatile: biochemical and biological functions of long noncoding RNAs
inferred← citeshttps://doi.org/10.1042/bcj20220382openalex-snapshot
Proteomic mapping and optogenetic manipulation of membrane contact sites
inferred← citeshttps://doi.org/10.1042/bsr20250116openalex-snapshot
Proteomic investigation of signaling dynamics: from static maps to network rewiring
inferred← citeshttps://doi.org/10.1042/bst20191059openalex-snapshot
Zooming in on protein–RNA interactions: a multi-level workflow to identify interaction partners
inferred← citeshttps://doi.org/10.1051/medsci/2025094openalex-snapshot
Les protéines cellulaires de liaison à l’ARN et leur interaction avec les ARN viraux
inferred← citeshttps://doi.org/10.1063/5.0083875openalex-snapshot
Biotin-painted proteins have thermodynamic stability switched by kinetic folding routes
inferred← citeshttps://doi.org/10.1073/pnas.1820737116openalex-snapshot
β-Actin mRNA interactome mapping by proximity biotinylation
inferred← citeshttps://doi.org/10.1073/pnas.2006617117openalex-snapshot
RNA–protein interaction mapping via MS2- or Cas13-based APEX targeting
inferred← citeshttps://doi.org/10.1073/pnas.2305211120openalex-snapshot
LOV thy neighbor: Mapping protein interactomes by genetically encodable photoproximity labeling
inferred← citeshttps://doi.org/10.1074/jbc.ra118.004928openalex-snapshot
The 40S ribosomal protein uS5 (RPS2) assembles into an extraribosomal complex with human ZNF277 that competes with the PRMT3–uS5 interaction
inferred← citeshttps://doi.org/10.1074/jbc.ra118.006004openalex-snapshot
Profiling of rotavirus 3′UTR-binding proteins reveals the ATP synthase subunit ATP5B as a host factor that supports late-stage virus replication
inferred← citeshttps://doi.org/10.1074/mcp.r120.001941openalex-snapshot
Proximity Dependent Biotinylation: Key Enzymes and Adaptation to Proteomics Approaches
inferred← citeshttps://doi.org/10.1080/07388551.2019.1709798openalex-snapshot
Advanced strategy for metabolite exploration in filamentous fungi
inferred← citeshttps://doi.org/10.1080/14737159.2023.2187289openalex-snapshot
Molecular predictors of metastasis in patients with prostate cancer
inferred← citeshttps://doi.org/10.1080/14789450.2019.1638769openalex-snapshot
Protein interactions study through proximity-labeling
inferred← citeshttps://doi.org/10.1080/15476286.2019.1703069openalex-snapshot
The RNA binding protein Quaking represses host interferon response by downregulating MAVS
inferred← citeshttps://doi.org/10.1080/15476286.2020.1868754openalex-snapshot
Identification of host factors binding to dengue and Zika virus subgenomic RNA by efficient yeast three-hybrid screens of the human ORFeome
inferred← citeshttps://doi.org/10.1080/15476286.2021.1873620openalex-snapshot
CBRPP: a new RNA-centric method to study RNA–protein interactions
inferred← citeshttps://doi.org/10.1080/15476286.2023.2287302openalex-snapshot
Multiple Oligo assisted RNA Pulldown via Hybridization followed by Mass Spectrometry (MORPH-MS) for exploring the RNA-Protein interactions
inferred← citeshttps://doi.org/10.1080/15548627.2020.1847461openalex-snapshot
Protein complexes and neighborhoods driving autophagy
inferred← citeshttps://doi.org/10.1091/mbc.e19-10-0568openalex-snapshot
Spatial proximity of proteins surrounding zyxin under force-bearing conditions
inferred← citeshttps://doi.org/10.1093/bib/bbaf292openalex-snapshot
Graph-RPI: predicting RNA–protein interactions via graph autoencoder and self-supervised learning strategies
inferred← citeshttps://doi.org/10.1093/bioinformatics/btz478openalex-snapshot
P3DOCK: a protein–RNA docking webserver based on template-based and template-free docking
inferred← citeshttps://doi.org/10.1093/g3journal/jkab077openalex-snapshot
Highly effective proximate labeling in Drosophila
inferred← citeshttps://doi.org/10.1093/g3journal/jkae221openalex-snapshot
Characterization of BioID tagging systems in budding yeast and exploring the interactome of the Ccr4-Not complex
inferred← citeshttps://doi.org/10.1093/jb/mvab123openalex-snapshot
Biotinylation-based proximity labelling proteomics: basics, applications and technical considerations
inferred← citeshttps://doi.org/10.1093/jb/mvaf042openalex-snapshot
Comprehensive identification of proteins interacting with long non-coding RNA TUG1 in R-loop regulation
inferred← citeshttps://doi.org/10.1093/nar/gkaa1108openalex-snapshot
PDCD2 functions as an evolutionarily conserved chaperone dedicated for the 40S ribosomal protein uS5 (RPS2)
inferred← citeshttps://doi.org/10.1093/nar/gkab614openalex-snapshot
Visualization and characterization of RNA–protein interactions in living cells
inferred← citeshttps://doi.org/10.1093/nar/gkab732openalex-snapshot
The RNA binding protein Quaking represses splicing of the Fibronectin EDA exon and downregulates the interferon response
inferred← citeshttps://doi.org/10.1093/nar/gkae038openalex-snapshot
SHIFTR enables the unbiased identification of proteins bound to specific RNA regions in live cells
inferred← citeshttps://doi.org/10.1093/nar/gkae1097openalex-snapshot
Glucose binds and activates NSUN2 to promote translation and epidermal differentiation
inferred← citeshttps://doi.org/10.1093/nar/gkae1165openalex-snapshot
RNA binding by Periphilin plays an essential role in initiating silencing by the HUSH complex
inferred← citeshttps://doi.org/10.1093/nar/gkag086openalex-snapshot
HCR-Proxy resolves site-specific proximal RNA microenvironments at subcompartmental resolution
inferred← citeshttps://doi.org/10.1093/nar/gkag601openalex-snapshot
Dual function of ERH in primary miRNA biogenesis
inferred← citeshttps://doi.org/10.1093/nar/gkz295openalex-snapshot
Beyond CLIP: advances and opportunities to measure RBP–RNA and RNA–RNA interactions
inferred← citeshttps://doi.org/10.1093/plphys/kiab479openalex-snapshot
Advances in enzyme-mediated proximity labeling and its potential for plant research
inferred← citeshttps://doi.org/10.1098/rspb.2020.1397openalex-snapshot
The increasing diversity and complexity of the RNA-binding protein repertoire in plants
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