ArticleMolecular cell2019
R-DeeP: Proteome-wide and Quantitative Identification of RNA-Dependent Proteins by Density Gradient Ultracentrifugation.
Article in Molecular cell, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
What it found
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Who cites it
74 citing papers in PubMed, 117 citations in OpenAlex.
- SAF-A/HNRNPU regulates euchromatin dynamics and is required for nuclear envelope integrity.bioRxiv : the preprint server for biology · 2026Article
- High-throughput identification of endogenous biomolecular condensates and phase-separating proteins.Nature protocols · 2026Review
- 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
- Bridging technical innovation and computational advances in studies of RNA-protein assemblies.Nature reviews. Genetics · 2026Review
- MeCP2 NID interaction with RNA: implications for Rett syndrome-relevant protein regulation.Human molecular genetics · 2026Article
- RBP2GO 2.0: Integrating disease associations and sequence features to explore RNA-binding protein functions.Nucleic acids research · 2026Article
- PROCA11 early activation fuels prostate cancer neuroendocrine traits by regulating cell survival and migration.iScience · 2025Article
- The Incoming Influenza Genome Assembles a Host RBP Network that Orchestrates Viral RNA Synthesis.bioRxiv : the preprint server for biology · 2025Article
- The RNA-binding protein PRRC2B preserves 5' TOP mRNA during starvation to maintain ribosome biogenesis during nutrient recovery.Nucleic acids research · 2025Article
- Pseudouridine selects RNAs for extracellular transport.bioRxiv : the preprint server for biology · 2025Article
- RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets.Nature communications · 2025Article
- Global profiling of protein complex dynamics with an experimental library of protein interaction markers.Nature biotechnology · 2025Article
- Hexokinase 2 is an RNA-binding protein that regulates mRNA translation independently of glycolysis and induces melanoma cell proliferation.PLoS biology · 2025Article
- An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions.Nature communications · 2025Article
- R-DeeP/TripepSVM identifies the RNA-binding OB-fold-like protein PatR as regulator of heterocyst patterning.Nucleic acids research · 2025Article
- Cellular RNA interacts with MAVS to promote antiviral signaling.Science (New York, N.Y.) · 2024Article
- RNA fine-tunes estrogen receptor-alpha binding on low-affinity DNA motifs for transcriptional regulation.The EMBO journal · 2024Article
- NEAT1 promotes genome stability via mGenes & development · 2024Article
- Large-scale map of RNA-binding protein interactomes across the mRNA life cycle.Molecular cell · 2024Article
14 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
The comprehensive but specific identification of RNA-binding proteins as well as the discovery of RNA-associated protein functions remain major challenges in RNA biology. Here we adapt the concept of RNA dependence, defining a protein as RNA dependent when its interactome depends on RNA. We converted this concept into a proteome-wide, unbiased, and enrichment-free screen called R-DeeP (RNA-dependent proteins), based on density gradient ultracentrifugation. Quantitative mass spectrometry identified 1,784 RNA-dependent proteins, including 537 lacking known links to RNA. Exploiting the quantitative nature of R-DeeP, proteins were classified as not, partially, or completely RNA dependent. R-DeeP identified the transcription factor CTCF as completely RNA dependent, and we uncovered that RNA is required for the CTCF-chromatin association. Additionally, R-DeeP allows reconstruction of protein complexes based on co-segregation. The whole dataset is available at http://R-DeeP.dkfz.de, providing proteome-wide, specific, and quantitative identification of proteins with RNA-dependent interactions and aiming at future functional discovery of RNA-protein complexes.
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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.