ArticleGenome research2020
Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms.
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 60 citations in OpenAlex.
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- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Transcript architecture predetermines m6A remodeling and sensory neuron vulnerability in chemotherapy-induced peripheral neuropathy.bioRxiv : the preprint server for biology · 2026Article
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods.Nature reviews. Molecular cell biology · 2026Review
- Advances and challenges in non-canonical nucleic acids data storage.Nature communications · 2026Review
- The new era of single-molecule RNA modification detection through nanopore base-calling models.Nature reviews. Molecular cell biology · 2026Review
- Integrated analysis of post-transcriptional regulations reveals insights into acute myeloid leukemia.Communications biology · 2025Article
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- The RMaP challenge of predicting RNA modifications by nanopore sequencing.Communications chemistry · 2025Article
- DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing.Genome biology · 2025Article
- Profiling the epigenome using long-read sequencing.Nature genetics · 2025Review
- Full-length direct RNA sequencing uncovers stress granule-dependent RNA decay upon cellular stress.eLife · 2024Article
- Nanodynamo quantifies subcellular RNA dynamics revealing extensive coupling between steps of the RNA life cycle.Nature communications · 2024Article
- Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics.NAR genomics and bioinformatics · 2024Article
- Full-length direct RNA sequencing uncovers stress-granule dependent RNA decay upon cellular stress.bioRxiv : the preprint server for biology · 2024Article
- Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation.Molecular systems biology · 2024Article
- Nanopore Direct RNA Sequencing for Modified Uridine Nucleotides Yields Signals Dependent on the Physical Properties of the Modified Base.Israel journal of chemistry · 2024Article
- Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Eukaryotic genes often generate a variety of RNA isoforms that can lead to functionally distinct protein variants. The synthesis and stability of RNA isoforms is poorly characterized because current methods to quantify RNA metabolism use short-read sequencing and cannot detect RNA isoforms. Here we present nanopore sequencing-based isoform dynamics (nano-ID), a method that detects newly synthesized RNA isoforms and monitors isoform metabolism. Nano-ID combines metabolic RNA labeling, long-read nanopore sequencing of native RNA molecules, and machine learning. Nano-ID derives RNA stability estimates and evaluates stability determining factors such as RNA sequence, poly(A)-tail length, secondary structure, translation efficiency, and RNA-binding proteins. Application of nano-ID to the heat shock response in human cells reveals that many RNA isoforms change their stability. Nano-ID also shows that the metabolism of individual RNA isoforms differs strongly from that estimated for the combined RNA signal at a specific gene locus. Nano-ID enables studies of RNA metabolism at the level of single RNA molecules and isoforms in different cell states and conditions.
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