ArticleNature biotechnology2021
Determination of isoform-specific RNA structure with nanopore long reads.
Article in Nature biotechnology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 63 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
63 citing papers in PubMed, 117 citations in OpenAlex.
- Advanced deep learning strategies in nanopore RNA sequencing.RNA biology · 2026Review
- Review
- DeCoRE: A computational method to resolve RNA structural heterogeneity from RNA structure probing data by direct RNA sequencing.Science advances · 2026Article
- DMS-MaPseq and DREEM Analyses Implicate the Critical Role of RNA Structural Dynamics in Turnip Yellow Mosaic Virus Pathogenicity.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- FIRST-seq: a nanopore-based cDNA sequencing platform for RNA modification and structure profiling.Genome biology · 2026Article
- Direct RNA sequencing and signal alignment reveal RNA structure ensembles in a eukaryotic cell.Nature methods · 2026Article
- Recent Advances in Chemical Probing Strategies for RNA Structure Determination In Vivo.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- Investigating RNA dynamics from single molecule transcriptomes.Trends in genetics : TIG · 2025Review
- Knowing when to fold 'em.Nature methods · 2025Article
- DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing.Genome biology · 2025Article
- Long-read RNA sequencing: A transformative technology for exploring transcriptome complexity in human diseases.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- De novo basecalling of RNA modifications at single molecule and nucleotide resolution.Genome biology · 2025Article
- Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing.GigaScience · 2025Article
- The role of structure in regulatory RNA elements.Bioscience reports · 2024Review
- Identification of RNA structures and their roles in RNA functions.Nature reviews. Molecular cell biology · 2024Review
- m6ATM: a deep learning framework for demystifying the m6A epitranscriptome with Nanopore long-read RNA-seq data.Briefings in bioinformatics · 2024Article
- R2Dtool: integration and visualization of isoform-resolved RNA features.Bioinformatics (Oxford, England) · 2024Article
- Advances in environmental DNA monitoring: standardization, automation, and emerging technologies in aquatic ecosystems.Science China. Life sciences · 2024Review
- Isoform-specific RNA structure determination using Nano-DMS-MaP.Nature protocols · 2024Review
3 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
- Erratum issued
Authors and funding
14 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Current methods for determining RNA structure with short-read sequencing cannot capture most differences between distinct transcript isoforms. Here we present RNA structure analysis using nanopore sequencing (PORE-cupine), which combines structure probing using chemical modifications with direct long-read RNA sequencing and machine learning to detect secondary structures in cellular RNAs. PORE-cupine also captures global structural features, such as RNA-binding-protein binding sites and reactivity differences at single-nucleotide variants. We show that shared sequences in different transcript isoforms of the same gene can fold into different structures, highlighting the importance of long-read sequencing for obtaining phase information. We also demonstrate that structural differences between transcript isoforms of the same gene lead to differences in translation efficiency. By revealing isoform-specific RNA structure, PORE-cupine will deepen understanding of the role of structures in controlling gene regulation.
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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.