ArticleNucleic acids research2019
Assaying RNA structure with LASER-Seq.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Multi-site DMS probing reveals higher-order structure of RNA-protein complexes in living cells.Molecular cell · 2026Article
- Recent Advances in Chemical Probing Strategies for RNA Structure Determination In Vivo.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- Single-cell transcriptome analysis reveals regulatory programs of prognosis-associated RNA binding proteins during LIHC development.Cancer cell international · 2025Article
- Review
- Sequential structure probing of cotranscriptional RNA folding intermediates.Nature communications · 2025Article
- bpRNA-CosMoS: a robust and efficient RNA structural comparison method using k-mer based cosine similarity.Bioinformatics (Oxford, England) · 2025Article
- RNA infrastructure profiling illuminates transcriptome structure in crowded spaces.Cell chemical biology · 2024Article
- Recent advances in and applications of ex vivo drug sensitivity analysis for blood cancers.Blood research · 2024Review
- txtools: an R package facilitating analysis of RNA modifications, structures, and interactions.Nucleic acids research · 2024Article
- RNA structure: implications in viral infections and neurodegenerative diseases.Advanced biotechnology · 2024Review
- Systematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq.Nature communications · 2023Article
- Cycloaddition enabled mutational profiling of 5-vinyluridine in RNA.Chemical communications (Cambridge, England) · 2023Article
- Probing the dynamic RNA structurome and its functions.Nature reviews. Genetics · 2023Review
- Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives.Briefings in bioinformatics · 2022Review
- Ataluren binds to multiple protein synthesis apparatus sites and competitively inhibits release factor-dependent termination.Nature communications · 2022Article
- Article
- Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing.Nucleic acids research · 2021Article
- Review
- Rapid structure-function insights via hairpin-centric analysis of big RNA structure probing datasets.NAR genomics and bioinformatics · 2021Article
- RNA structure probing uncovers RNA structure-dependent biological functions.Nature chemical biology · 2021Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Chemical probing methods are crucial to our understanding of the structure and function of RNA molecules. The majority of chemical methods used to probe RNA structure report on Watson-Crick pairing, but tertiary structure parameters such as solvent accessibility can provide an additional layer of structural information, particularly in RNA-protein complexes. Herein we report the development of Light Activated Structural Examination of RNA by high-throughput sequencing, or LASER-Seq, for measuring RNA structure in cells with deep sequencing. LASER relies on a light-generated nicotinoyl nitrenium ion to form covalent adducts with the C8 position of adenosine and guanosine. Reactivity is governed by the accessibility of C8 to the light-generated probe. We compare structure probing by RT-stop and mutational profiling (MaP), demonstrating that LASER can be integrated with both platforms for RNA structure analyses. We find that LASER reactivity correlates with solvent accessibility across the entire ribosome, and that LASER can be used to rapidly survey for ligand binding sites in an unbiased fashion. LASER has a particular advantage in this last application, as it readily modifies paired nucleotides, enabling the identification of binding sites and conformational changes in highly structured RNA.
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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.