ArticleNature methods2023
RNA molecular recording with an engineered RNA deaminase.
Article in Nature methods, 2023. 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.
- Post-transcriptional regulatory networks: The dynamic interplay of RNA-binding proteins.The FEBS journal · 2026Review
- Probing RNA-protein interactions in the early mouse embryo.bioRxiv : the preprint server for biology · 2026Article
- Physiologic variation in sperm miRNAs tune embryonic gene regulatory programs and developmental outcomes.bioRxiv : the preprint server for biology · 2026Article
- RNA editing: an emerging frontier in cancer therapy - explorations, opportunities, and challenges.International journal of surgery (London, England) · 2026Article
- Co-profiling of in situ RNA-protein interactions and transcriptome in single cells and tissues.Nature methods · 2025Article
- Deaminase-based RNA recording enables high throughput mutational profiling of protein-RNA interactions.bioRxiv : the preprint server for biology · 2025Article
- SENP1 inhibits aerobic glycolysis in AβCell biology and toxicology · 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
- Mapping the future of oxidative RNA damage in neurodegeneration: Rethinking the status quo with new tools.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Programmed RNA editing with an evolved bacterial adenosine deaminase.Nature chemical biology · 2024Article
- Toward DNA-Based Recording of Biological Processes.International journal of molecular sciences · 2024Review
- R2Dtool: integration and visualization of isoform-resolved RNA features.Bioinformatics (Oxford, England) · 2024Article
- Challenges to mapping and defining mRNA (New York, N.Y.) · 2024Article
- Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies.Nature communications · 2024Article
- Characterization of Pumilio gene expression during early neural crest development.Differentiation; research in biological diversityArticle
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
RNA deaminases are powerful tools for base editing and RNA molecular recording. However, the enzymes used in currently available RNA molecular recorders such as TRIBE, DART or STAMP have limitations due to RNA structure and sequence dependence. We designed a platform for directed evolution of RNA molecular recorders. We engineered an RNA A-to-I deaminase (an RNA adenosine base editor, rABE) that has high activity, low bias and low background. Using rABE, we present REMORA (RNA-encoded molecular recording in adenosines), wherein deamination by rABE writes a molecular record of RNA-protein interactions. By combining rABE with the C-to-U deaminase APOBEC1 and long-read RNA sequencing, we measured binding by two RNA-binding proteins on single messenger RNAs. Orthogonal RNA molecular recording of mammalian Pumilio proteins PUM1 and PUM2 shows that PUM1 competes with PUM2 for a subset of sites in cells. Furthermore, we identify transcript isoform-specific RNA-protein interactions driven by isoform changes distal to the binding site. The genetically encodable RNA deaminase rABE enables single-molecule identification of RNA-protein interactions with cell type specificity.
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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.