ArticleNature protocols2014
Transcriptome-wide target profiling of RNA cytosine methyltransferases using the mechanism-based enrichment procedure Aza-IP.
Article in Nature protocols, 2014. 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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Who cites it
37 citing papers in PubMed, 61 citations in OpenAlex.
- Article
- Role of RNA 5‑methylcytosine modification in cancer: Insights from coding and non‑coding RNAs (Review).Molecular medicine reports · 2026Review
- 5-Azacytidine incorporation into mRNAs disrupts translation and induces ribosome collisions.bioRxiv : the preprint server for biology · 2026Article
- m5C RNA methylation is dysregulated by oncogenic herpesviruses via c-Myc signaling to counteract host antiviral factors.Nucleic acids research · 2026Article
- TCN-5mC: a predictor of 5-methylcytosine sites based on multi-feature fusion and TCN-inspired block networks.Frontiers in genetics · 2026Article
- m5C RNA modification in colorectal cancer: mechanisms and therapeutic targets.Journal of translational medicine · 2025Review
- Detection, molecular function and mechanisms of m5C in cancer.Clinical and translational medicine · 2025Review
- Transcriptomic era of cancers in females: new epigenetic perspectives and therapeutic prospects.Frontiers in oncology · 2024Review
- The Quiet Giant: Identification, Effectors, Molecular Mechanism, Physiological and Pathological Function in mRNA 5-methylcytosine Modification.International journal of biological sciences · 2024Review
- Chemical Proteomic Discovery of Isotype-Selective Covalent Inhibitors of the RNA Methyltransferase NSUN2.Angewandte Chemie (International ed. in English) · 2023Article
- Current technical advancements in plant epitranscriptomic studies.The plant genome · 2023Review
- RNA modifications in hematological malignancies.International journal of hematology · 2023Review
- The Transition from Cancer "omics" to "epi-omics" through Next- and Third-Generation Sequencing.Life (Basel, Switzerland) · 2022Review
- Harnessing Nature's Molecular Recognition Capabilities to Map and Study RNA Modifications.Accounts of chemical research · 2022Article
- Chemical biology and medicinal chemistry of RNA methyltransferases.Nucleic acids research · 2022Article
- Differential viral RNA methylation contributes to pathogen blocking in Wolbachia-colonized arthropods.PLoS pathogens · 2022Article
- The role of RNA modification in hepatocellular carcinoma.Frontiers in pharmacology · 2022Review
- The role of RNA modification in the generation of acquired drug resistance in glioma.Frontiers in genetics · 2022Review
- BiLSTM-5mC: A Bidirectional Long Short-Term Memory-Based Approach for Predicting 5-Methylcytosine Sites in Genome-Wide DNA Promoters.Molecules (Basel, Switzerland) · 2021Article
- Advances in mRNA 5-methylcytosine modifications: Detection, effectors, biological functions, and clinical relevance.Molecular therapy. Nucleic acids · 2021Review
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Cytosine methylation within RNA is common, but its full scope and functions are poorly understood, as the RNA targets of most mammalian cytosine RNA methyltransferases (m(5)C-RMTs) remain uncharacterized. To enable their characterization, we developed a mechanism-based method for transcriptome-wide m(5)C-RMT target profiling. All characterized mammalian m(5)C-RMTs form a reversible covalent intermediate with their cytosine substrate-a covalent linkage that is trapped when conducted on the cytosine analog 5-azacytidine (5-aza-C). We used this property to develop Aza-immunoprecipitation (Aza-IP), a methodology to form stable m(5)C-RMT-RNA linkages in cell culture, followed by IP and high-throughput sequencing, to identify direct RNA substrates of m(5)C-RMTs. Remarkably, a cytosine-to-guanine (C→G) transversion occurs specifically at target cytosines, allowing the simultaneous identification of the precise target cytosine within each RNA. Thus, Aza-IP reports only direct RNA substrates and the C→G transversion provides an important criterion for target cytosine identification, which is not available in alternative approaches. Here we present a step-by-step protocol for Aza-IP and downstream analysis, designed to reveal identification of substrate RNAs and precise cytosine targets of m(5)C-RMTs. The entire protocol takes 40-50 d to complete.
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