ArticleNature communications2024
Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 21 citations in OpenAlex.
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- Single-cell profiling reveals pervasive heterogeneity in subcellular RNA localization.bioRxiv : the preprint server for biology · 2026Article
- Systematic characterization of the composition and dynamics of processing body-associated mRNAs.Nature communications · 2025Article
- Noncanonical target-strand cytosine base editing via engineered Un1Cas12f1 platform.Nature communications · 2025Article
- Decoding the interactions and functions of non-coding RNA with artificial intelligence.Nature reviews. Molecular cell biology · 2025Review
- Decoding Cardiac Maturation Program: Insights from RNA Splicing Regulation.Current cardiology reports · 2025Review
- RNA-binding proteins orchestrating immunity in plants.The Plant journal : for cell and molecular biology · 2025Review
- APOBEC1-Dependent RNA Eiting of TNF Signaling Orchestrates Ileal Villus Morphogenesis in Pigs: Integrative Transcriptomic and Editomic Insights.Animals : an open access journal from MDPI · 2025Article
- Deaminase-based RNA recording enables high throughput mutational profiling of protein-RNA interactions.bioRxiv : the preprint server for biology · 2025Article
- Identification of RBP binding sites using RNA deaminases.Methods in enzymology · 2025Article
- Decoding protein-RNA interactions using CLIP-based methodologies.Nature reviews. Genetics · 2024Review
- Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution.Genome research · 2024Article
- LoDEI: a robust and sensitive tool to detect transcriptome-wide differential A-to-I editing in RNA-seq data.Nature communications · 2024Article
- High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues.Nature communications · 2024Article
- Revealing the hidden RBP-RNA interactions with RNA modification enzyme-based strategies.Wiley interdisciplinary reviews. RNAReview
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Authors and funding
15 authors at 2 institutions in 1 country.
Funding
Abstract
RNA binding proteins (RBPs) are key regulators of RNA processing and cellular function. Technologies to discover RNA targets of RBPs such as TRIBE (targets of RNA binding proteins identified by editing) and STAMP (surveying targets by APOBEC1 mediated profiling) utilize fusions of RNA base-editors (rBEs) to RBPs to circumvent the limitations of immunoprecipitation (CLIP)-based methods that require enzymatic digestion and large amounts of input material. To broaden the repertoire of rBEs suitable for editing-based RBP-RNA interaction studies, we have devised experimental and computational assays in a framework called PRINTER (protein-RNA interaction-based triaging of enzymes that edit RNA) to assess over thirty A-to-I and C-to-U rBEs, allowing us to identify rBEs that expand the characterization of binding patterns for both sequence-specific and broad-binding RBPs. We also propose specific rBEs suitable for dual-RBP applications. We show that the choice between single or multiple rBEs to fuse with a given RBP or pair of RBPs hinges on the editing biases of the rBEs and the binding preferences of the RBPs themselves. We believe our study streamlines and enhances the selection of rBEs for the next generation of RBP-RNA target discovery.
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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.