ArticleRNA (New York, N.Y.)2014
Mod-seq: high-throughput sequencing for chemical probing of RNA structure.
Article in RNA (New York, N.Y.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 110 papers.
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Who cites it
110 citing papers in PubMed.
- Recent Advances in Chemical Probing Strategies for RNA Structure Determination In Vivo.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- In vivo structure profiling reveals human cytosolic and mitochondrial tRNA structurome and interactome in response to stress.Nature communications · 2025Article
- bpRNA-CosMoS: a robust and efficient RNA structural comparison method using k-mer based cosine similarity.Bioinformatics (Oxford, England) · 2025Article
- Isoform-specific RNA structure determination using Nano-DMS-MaP.Nature protocols · 2024Review
- RNA structure: implications in viral infections and neurodegenerative diseases.Advanced biotechnology · 2024Review
- Late consolidation of rRNA structure during co-transcriptional assembly inbioRxiv : the preprint server for biology · 2024Article
- Molecular pathways and therapeutic strategies in dermatofibrosarcoma protuberans (DFSP): unravelling the tumor's genetic landscape.EXCLI journal · 2024Review
- RNA molecular recording with an engineered RNA deaminase.Nature methods · 2023Article
- Review
- Navigating the pitfalls of mapping DNA and RNA modifications.Nature reviews. Genetics · 2023Review
- The Evaluation of SHAPE-MaP RNA Structure Probing Protocols Reveals a Novel Role of MnInternational journal of molecular sciences · 2023Article
- RNA Structure Determination by High-Throughput Structural Analysis.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives.Briefings in bioinformatics · 2022Review
- 3D Modeling of Non-coding RNA Interactions.Advances in experimental medicine and biology · 2022Article
- An ultra low-input method for global RNA structure probing uncovers Regnase-1-mediated regulation in macrophages.Fundamental research · 2022Article
- In vivo architecture of the telomerase RNA catalytic core in Trypanosoma brucei.Nucleic acids research · 2021Article
- Review
- RNA structure probing uncovers RNA structure-dependent biological functions.Nature chemical biology · 2021Review
- Global in situ profiling of RNA-RNA spatial interactions with RIC-seq.Nature protocols · 2021Article
- diffBUM-HMM: a robust statistical modeling approach for detecting RNA flexibility changes in high-throughput structure probing data.Genome biology · 2021Article
50 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
The functions of RNA molecules are intimately linked to their ability to fold into complex secondary and tertiary structures. Thus, understanding how these molecules fold is essential to determining how they function. Current methods for investigating RNA structure often use small molecules, enzymes, or ions that cleave or modify the RNA in a solvent-accessible manner. While these methods have been invaluable to understanding RNA structure, they can be fairly labor intensive and often focus on short regions of single RNAs. Here we present a new method (Mod-seq) and data analysis pipeline (Mod-seeker) for assaying the structure of RNAs by high-throughput sequencing. This technique can be utilized both in vivo and in vitro, with any small molecule that modifies RNA and consequently impedes reverse transcriptase. As proof-of-principle, we used dimethyl sulfate (DMS) to probe the in vivo structure of total cellular RNAs in Saccharomyces cerevisiae. Mod-seq analysis simultaneously revealed secondary structural information for all four ribosomal RNAs and 32 additional noncoding RNAs. We further show that Mod-seq can be used to detect structural changes in 5.8S and 25S rRNAs in the absence of ribosomal protein L26, correctly identifying its binding site on the ribosome. While this method is applicable to RNAs of any length, its high-throughput nature makes Mod-seq ideal for studying long RNAs and complex RNA mixtures.
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