ArticleNucleic acids research2022
Long-read single-molecule RNA structure sequencing using nanopore.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 36 citations in OpenAlex.
- Direct detection of alternative DNA conformations with long-read sequencing and machine learning approaches.bioRxiv : the preprint server for biology · 2026Article
- A whole-genome sequencing dataset of nanopore raw signals for bacterial genotyping and methylation analysis.Scientific data · 2025Article
- Past, present, and future of genomic technologies in cerebellar ataxias.Journal of neurology · 2025Review
- Investigating RNA dynamics from single molecule transcriptomes.Trends in genetics : TIG · 2025Review
- Bringing Attomolar Detection to the Point-of-Care with Nanopatterned DNA Origami Nanoantennas.Advanced materials (Deerfield Beach, Fla.) · 2025Article
- Translational Regulation of Plant Stress Responses: Mechanisms, Pathways, and Applications in Bioengineering.Annual review of phytopathology · 2025Review
- A new compression strategy to reduce the size of nanopore sequencing data.Genome research · 2025Article
- Biomolecular condensates control and are defined by RNA-RNA interactions that arise in viral replication.Research square · 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
- The enduring advantages of the SLOW5 file format for raw nanopore sequencing data.GigaScience · 2025Article
- The conformational space of RNase P RNA in solution.Nature · 2025Article
- RNA encodes physical information.bioRxiv : the preprint server for biology · 2024Article
- Direct RNA sequencing in plants: Practical applications and future perspectives.Plant communications · 2024Review
- Triplex H-DNA structure: the long and winding road from the discovery to its role in human disease.NAR molecular medicine · 2024Article
- Reduction of Ribosomal Expansion Segments in Yeast Species of the Magnusiomyces/Saprochaete Clade.Genome biology and evolution · 2024Article
- Interactive visualization of nanopore sequencing signal data with Squigualiser.Bioinformatics (Oxford, England) · 2024Article
- Isoform-specific RNA structure determination using Nano-DMS-MaP.Nature protocols · 2024Review
- Molecular insights into regulatory RNAs in the cellular machinery.Experimental & molecular medicine · 2024Review
- Detection of alternative DNA structures and its implications for human disease.Molecular cell · 2023Review
- Nano-DMS-MaP allows isoform-specific RNA structure determination.Nature methods · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA molecules can form secondary and tertiary structures that can regulate their localization and function. Using enzymatic or chemical probing together with high-throughput sequencing, secondary structure can be mapped across the entire transcriptome. However, a limiting factor is that only population averages can be obtained since each read is an independent measurement. Although long-read sequencing has recently been used to determine RNA structure, these methods still used aggregate signals across the strands to detect structure. Averaging across the population also means that only limited information about structural heterogeneity across molecules or dependencies within each molecule can be obtained. Here, we present Single-Molecule Structure sequencing (SMS-seq) that combines structural probing with native RNA sequencing to provide non-amplified, structural profiles of individual molecules with novel analysis methods. Our new approach using mutual information enabled single molecule structural interrogation. Each RNA is probed at numerous bases enabling the discovery of dependencies and heterogeneity of structural features. We also show that SMS-seq can capture tertiary interactions, dynamics of riboswitch ligand binding, and mRNA structural features.
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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.