ArticleNature biotechnology2021
RNA timestamps identify the age of single molecules in RNA sequencing.
Article in Nature biotechnology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed, 57 citations in OpenAlex.
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- Evolution of Engineered ADAR-Based RNA Editing Systems.International journal of molecular sciences · 2026Review
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- Post-transcriptional modular synthetic receptors.Nature chemical biology · 2025Article
- ADARs: pleiotropy in function, versatility in application.Nucleic acids research · 2025Review
- Emerging clinical applications of ADAR based RNA editing.Stem cells translational medicine · 2025Review
- Spatial Transcriptomics: Integrating Morphology and Molecular Mechanisms of Kidney Diseases.The American journal of pathology · 2025Review
- Post-Transcriptional Modular Synthetic Receptors.bioRxiv : the preprint server for biology · 2024Article
- Toward DNA-Based Recording of Biological Processes.International journal of molecular sciences · 2024Review
- Detection of transcriptome-wide microRNA-target interactions in single cells with agoTRIBE.Nature biotechnology · 2024Article
- The debranching enzyme Dbr1 regulates lariat turnover and intron splicing.Nature communications · 2024Article
- Spatiotemporal multi-omics: exploring molecular landscapes in aging and regenerative medicine.Military Medical Research · 2024Review
- A dynamical perspective: moving towards mechanism in single-cell transcriptomics.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Dissecting mammalian reproduction with spatial transcriptomics.Human reproduction update · 2023Review
- Profiling dynamic RNA-protein interactions using small-molecule-induced RNA editing.Nature chemical biology · 2023Article
- Spatial transcriptomics: recent developments and insights in respiratory research.Military Medical Research · 2023Review
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7 authors at 4 institutions in 1 country.
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Abstract
Current approaches to single-cell RNA sequencing (RNA-seq) provide only limited information about the dynamics of gene expression. Here we present RNA timestamps, a method for inferring the age of individual RNAs in RNA-seq data by exploiting RNA editing. To introduce timestamps, we tag RNA with a reporter motif consisting of multiple MS2 binding sites that recruit the adenosine deaminase ADAR2 fused to an MS2 capsid protein. ADAR2 binding to tagged RNA causes A-to-I edits to accumulate over time, allowing the age of the RNA to be inferred with hour-scale accuracy. By combining observations of multiple timestamped RNAs driven by the same promoter, we can determine when the promoter was active. We demonstrate that the system can infer the presence and timing of multiple past transcriptional events. Finally, we apply the method to cluster single cells according to the timing of past transcriptional activity. RNA timestamps will allow the incorporation of temporal information into RNA-seq workflows.
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