ArticleNature methods2010
FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing.
Article in Nature methods, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 192 papers.
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Who cites it
192 citing papers in PubMed.
- Transcriptomic characterization of Coccidioides morphological states using RiboMarker-enhanced RNA sequencing.G3 (Bethesda, Md.) · 2026Article
- Direct circRNA-mRNA Binding Controls mRNA Fate: A New Mechanism for circRNAs.Non-coding RNA · 2025Review
- Enhanced RNA secondary structure prediction through integrative deep learning and structural context analysis.Nucleic acids research · 2025Article
- Biomolecules Interacting with Long Noncoding RNAs.Biology · 2025Review
- Non-transgenic RNAi strategies for sustainable plant viral disease control: a review.Molecular biology reports · 2025Review
- Identification of RNA structures and their roles in RNA functions.Nature reviews. Molecular cell biology · 2024Review
- Exploring the challenges of RNAi-based strategies for crop protection.Advanced biotechnology · 2024Review
- Isoform-specific RNA structure determination using Nano-DMS-MaP.Nature protocols · 2024Review
- Navigating the landscape of epitranscriptomics and host immunity.Genome research · 2024Review
- Global identification of mRNA-interacting circular RNAs by CLiPPR-Seq.Nucleic acids research · 2024Article
- RNA structure profiling at single-cell resolution reveals new determinants of cell identity.Nature methods · 2024Article
- Probing RNA structural landscapes acrossFrontiers in microbiology · 2024Article
- Long noncoding RNA study: Genome-wide approaches.Genes & diseases · 2023Review
- The plant noncoding transcriptome: a versatile environmental sensor.The EMBO journal · 2023Review
- Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA.Nucleic acids research · 2023Article
- Systematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq.Nature communications · 2023Article
- Article
- Recent advances in RNA structurome.Science China. Life sciences · 2022Review
- UFold: fast and accurate RNA secondary structure prediction with deep learning.Nucleic acids research · 2022Article
- Oxidative RNA Damage in the Pathogenesis and Treatment of Type 2 Diabetes.Frontiers in physiology · 2022Review
132 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Classical approaches to determine structures of noncoding RNA (ncRNA) probed only one RNA at a time with enzymes and chemicals, using gel electrophoresis to identify reactive positions. To accelerate RNA structure inference, we developed fragmentation sequencing (FragSeq), a high-throughput RNA structure probing method that uses high-throughput RNA sequencing of fragments generated by digestion with nuclease P1, which specifically cleaves single-stranded nucleic acids. In experiments probing the entire mouse nuclear transcriptome, we accurately and simultaneously mapped single-stranded RNA regions in multiple ncRNAs with known structure. We probed in two cell types to verify reproducibility. We also identified and experimentally validated structured regions in ncRNAs with, to our knowledge, no previously reported probing data.
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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.