ArticleGenome research2013
Quantitative proteomic analysis reveals concurrent RNA-protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
40 citing papers in PubMed, 59 citations in OpenAlex.
- Puf3 contributes to changes in mRNA solubility, translation elongation dynamics at rare arginine codons and loss of protein homeostasis in cells lacking Not4.RNA (New York, N.Y.) · 2026Article
- Genome-Wide Analysis ofInternational journal of molecular sciences · 2023Article
- RNA-dependent interactome allows network-based assignment of RNA-binding protein function.Nucleic acids research · 2023Article
- Stress granule-associated TaMBF1c confers thermotolerance through regulating specific mRNA translation in wheat (Triticum aestivum).The New phytologist · 2022Article
- Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast.RNA biology · 2021Article
- Discovering the RNA-Binding Proteome of Plant Leaves with an Improved RNA Interactome Capture Method.Biomolecules · 2020Article
- The plant MBF1 protein family: a bridge between stress and transcription.Journal of experimental botany · 2020Review
- Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation.Nature genetics · 2020Article
- Structure-function relationships in the Nab2 polyadenosine-RNA binding Zn finger protein family.Protein science : a publication of the Protein Society · 2019Review
- Multi-protein bridging factor 1(Mbf1), Rps3 and Asc1 prevent stalled ribosomes from frameshifting.eLife · 2018Article
- Long noncoding RNA licensing of obesity-linked hepatic lipogenesis and NAFLD pathogenesis.Nature communications · 2018Article
- The Lsm1-7/Pat1 complex binds to stress-activated mRNAs and modulates the response to hyperosmotic shock.PLoS genetics · 2018Article
- A brave new world of RNA-binding proteins.Nature reviews. Molecular cell biology · 2018Review
- Mbf1 ensures Polycomb silencing by protectingDevelopment (Cambridge, England) · 2018Article
- The lncRNA GATA6-AS epigenetically regulates endothelial gene expression via interaction with LOXL2.Nature communications · 2018Article
- Post-transcriptional gene silencing mediated by microRNAs is controlled by nucleoplasmic Sfpq.Nature communications · 2017Article
- RNA Binding by Histone Methyltransferases Set1 and Set2.Molecular and cellular biology · 2017Article
- Article
- Structural Characteristics of Simple RNA Repeats Associated with Disease and their Deleterious Protein Interactions.Frontiers in cellular neuroscience · 2017Review
- Identifying proteins that bind to specific RNAs - focus on simple repeat expansion diseases.Nucleic acids research · 2016Review
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
A growing body of evidence supports the existence of an extensive network of RNA-binding proteins (RBPs) whose combinatorial binding affects the post-transcriptional fate of every mRNA in the cell-yet we still do not have a complete understanding of which proteins bind to mRNA, which of these bind concurrently, and when and where in the cell they bind. We describe here a method to identify the proteins that bind to RNA concurrently with an RBP of interest, using quantitative mass spectrometry combined with RNase treatment of affinity-purified RNA-protein complexes. We applied this method to the known RBPs Pab1, Nab2, and Puf3. Our method significantly enriched for known RBPs and is a clear improvement upon previous approaches in yeast. Our data reveal that some reported protein-protein interactions may instead reflect simultaneous binding to shared RNA targets. We also discovered more than 100 candidate RBPs, and we independently confirmed that 77% (23/30) bind directly to RNA. The previously recognized functions of the confirmed novel RBPs were remarkably diverse, and we mapped the RNA-binding region of one of these proteins, the transcriptional coactivator Mbf1, to a region distinct from its DNA-binding domain. Our results also provided new insights into the roles of Nab2 and Puf3 in post-transcriptional regulation by identifying other RBPs that bind simultaneously to the same mRNAs. While existing methods can identify sets of RBPs that interact with common RNA targets, our approach can determine which of those interactions are concurrent-a crucial distinction for understanding post-transcriptional regulation.
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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.