ArticleNature protocols2020
Identification, quantification and bioinformatic analysis of RNA-dependent proteins by RNase treatment and density gradient ultracentrifugation using R-DeeP.
Article in Nature protocols, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 31 citations in OpenAlex.
- Cross-species R-DeeP profiling reveals a conserved core of RNA-dependent proteins in yeast.Nucleic acids research · 2026Article
- AURORA A interacts with DICER and SETD2 to promote S-phase progression.EMBO reports · 2026Article
- Strategies for constructing context-specific protein-protein interaction networks.Briefings in bioinformatics · 2026Review
- RBP2GO 2.0: Integrating disease associations and sequence features to explore RNA-binding protein functions.Nucleic acids research · 2026Article
- Uncomplexed-TSC1 deploys novel mTORC1-independent pathway to exacerbate the liver glycogen storage in TSC.Cell death & disease · 2025Article
- Translational repression by 4E-T is crucial to maintain the prophase-I arrest in vertebrate oocytes.Nature communications · 2025Article
- An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions.Nature communications · 2025Article
- Nucleotide-induced hyper-oligomerization inactivates transcription termination factor ρ.Nature communications · 2025Article
- R-DeeP/TripepSVM identifies the RNA-binding OB-fold-like protein PatR as regulator of heterocyst patterning.Nucleic acids research · 2025Article
- An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions.bioRxiv : the preprint server for biology · 2024Article
- Refining the pool of RNA-binding domains advances the classification and prediction of RNA-binding proteins.Nucleic acids research · 2024Article
- Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes.Nature communications · 2024Article
- Exploring new roles for RNA-binding proteins in epigenetic and gene regulation.Current opinion in genetics & development · 2024Review
- Identification of G-quadruplex structures in MALAT1 lncRNA that interact with nucleolin and nucleophosmin.Nucleic acids research · 2023Article
- The impact of RNA binding proteins and the associated long non-coding RNAs in the TCA cycle on cancer pathogenesis.RNA biology · 2023Review
- Article
- Protein Interactome Profiling of Stable Molecular Complexes in Biomaterial Lysate.International journal of molecular sciences · 2022Review
- Alternative splicing modulation mediated by G-quadruplex structures in MALAT1 lncRNA.Nucleic acids research · 2022Article
- RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions.Nucleic acids research · 2021Article
- Emerging Roles of Long Noncoding RNAs in the Cytoplasmic Milieu.Non-coding RNA · 2020Review
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
Analysis of RNA-protein complexes is central to understanding the molecular circuitry governing cellular processes. In recent years, several proteome-wide studies have been dedicated to the identification of RNA-binding proteins. Here, we describe in detail R-DeeP, an approach built on RNA dependence, defined as the ability of a protein to engage in protein complexes only in the presence of RNA, involving direct or indirect interaction with RNA. This approach provides-for the first time, to our knowledge-quantitative information on the fraction of a protein associated with RNA-protein complexes. R-DeeP is independent of any potentially biased purification procedures. It is based on cellular lysate fractionation by density gradient ultracentrifugation and subsequent analysis by proteome-wide mass spectrometry (MS) or individual western blotting. The comparison of lysates with and without previous RNase treatment enables the identification of differences in the apparent molecular weight and, hence, the size of the complexes. In combination with information from databases of protein-protein complexes, R-DeeP facilitates the computational reconstruction of protein complexes from proteins migrating in the same fraction. In addition, we developed a pipeline for the statistical analysis of the MS dataset to automatically identify RNA-dependent proteins (proteins whose interactome depends on RNA). With this protocol, the individual analysis of proteins of interest by western blotting can be completed within 1-2 weeks. For proteome-wide studies, additional time is needed for the integration of the proteomic and statistical analyses. In the future, R-DeeP can be extended to other fractionation techniques, such as chromatography.
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