ArticleJournal of nanobiotechnology2013
Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription.
Article in Journal of nanobiotechnology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers.
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Who cites it
89 citing papers in PubMed, 160 citations in OpenAlex.
- Multi-omics-driven precision medicine.iMeta · 2026Review
- Epitranscriptomic Analysis of A-to-I RNA Editing and mInternational journal of molecular sciences · 2026Review
- SM-NucSeq, Genetic and Epigenetic Sequencing of Nucleosomes with Single-Molecule Real-Time Sequencing.Nano letters · 2026Article
- Veterinary Herpesviruses: Experimental Tools for Transcriptomics and Neuroscience.Veterinary sciences · 2026Review
- Tissue-specific biosynthesis and spatial distribution of xanthones in Garcinia oblongifolia revealed by integrated metabolomic and full-length transcriptomic analyses.BMC genomics · 2025Article
- Nanopore direct RNA sequencing reveals METTL2A-mediated mGenome research · 2025Article
- Investigating RNA dynamics from single molecule transcriptomes.Trends in genetics : TIG · 2025Review
- The Mysterious World of Non-Canonical Caps - What We Know and Why We Need New Sequencing Techniques.Chembiochem : a European journal of chemical biology · 2025Review
- Next-Generation Sequencing Methods to Determine the Accuracy of Retroviral Reverse Transcriptases: Advantages and Limitations.Viruses · 2025Review
- Review
- Detecting a wide range of epitranscriptomic modifications using a nanopore-sequencing-based computational approach with 1D score-clustering.Nucleic acids research · 2025Article
- Mapping epigenetic modifications by sequencing technologies.Cell death and differentiation · 2025Review
- Epigenetics and plant hormone dynamics: a functional and methodological perspective.Journal of experimental botany · 2024Review
- Advances in single-cell long-read sequencing technologies.NAR genomics and bioinformatics · 2024Article
- Epitranscriptome insights into Riccia fluitans L. (Marchantiophyta) aquatic transition using nanopore direct RNA sequencing.BMC plant biology · 2024Article
- Decoding epitranscriptomic regulation of viral infection: mapping of RNA NCellular & molecular biology letters · 2024Review
- General Principles and Limitations for Detection of RNA Modifications by Sequencing.Accounts of chemical research · 2024Article
- Current progress in strategies to profile transcriptomic mFrontiers in cell and developmental biology · 2024Review
- Current technical advancements in plant epitranscriptomic studies.The plant genome · 2023Review
- Analysis approaches for the identification and prediction ofEpigenetics · 2023Review
29 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundZero-mode waveguides (ZMWs) are photonic nanostructures that create highly confined optical observation volumes, thereby allowing single-molecule-resolved biophysical studies at relatively high concentrations of fluorescent molecules. This principle has been successfully applied in single-molecule, real-time (SMRT®) DNA sequencing for the detection of DNA sequences and DNA base modifications. In contrast, RNA sequencing methods cannot provide sequence and RNA base modifications concurrently as they rely on complementary DNA (cDNA) synthesis by reverse transcription followed by sequencing of cDNA. Thus, information on RNA modifications is lost during the process of cDNA synthesis.
resultsHere we describe an application of SMRT technology to follow the activity of reverse transcriptase enzymes synthesizing cDNA on thousands of single RNA templates simultaneously in real time with single nucleotide turnover resolution using arrays of ZMWs. This method thereby obtains information from the RNA template directly. The analysis of the kinetics of the reverse transcriptase can be used to identify RNA base modifications, shown by example for N6-methyladenine (m6A) in oligonucleotides and in a specific mRNA extracted from total cellular mRNA. Furthermore, the real-time reverse transcriptase dynamics informs about RNA secondary structure and its rearrangements, as demonstrated on a ribosomal RNA and an mRNA template.
conclusionsOur results highlight the feasibility of studying RNA modifications and RNA structural rearrangements in ZMWs in real time. In addition, they suggest that technology can be developed for direct RNA sequencing provided that the reverse transcriptase is optimized to resolve homonucleotide stretches in RNA.
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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.