ArticleNucleic acids research2017
Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed, 117 citations in OpenAlex.
- Massively Parallel In Vitro Functional Analysis of Evolution-Derived Transcriptional Riboswitch Sequences.Bio-protocol · 2026Article
- High-throughput functional profiling and evolutionary covariation analysis of entire riboswitch sequences.Nucleic acids research · 2026Article
- Recent Advances in Chemical Probing Strategies for RNA Structure Determination In Vivo.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- DMS-informed secondary structure modeling of Epstein-Barr Virus LMP-1 pre-mRNA defines novel elements spanning introns.PloS one · 2026Article
- High-throughput functional profiling and evolutionary covariation analysis of entire riboswitch sequences.bioRxiv : the preprint server for biology · 2025Article
- Cryo-EM study and in vivo chemical mapping of the Methanosarcina acetivorans ribosome and its dimerization via a repurposed enzyme and translation factor.The Journal of biological chemistry · 2025Article
- Ribosome-induced mRNA pseudoknot interactions visualized by DMS MaP-Seq.bioRxiv : the preprint server for biology · 2025Article
- Identification of a conserved RNA structure in thebioRxiv : the preprint server for biology · 2025Article
- Rapid discovery of functional RNA domains.Nucleic acids research · 2025Article
- bpRNA-CosMoS: a robust and efficient RNA structural comparison method using k-mer based cosine similarity.Bioinformatics (Oxford, England) · 2025Article
- Consistent features observed in structural probing data of eukaryotic RNAs.NAR genomics and bioinformatics · 2025Article
- RNA Structure: Past, Future, and Gene Therapy Applications.International journal of molecular sciences · 2024Review
- RNA structure: implications in viral infections and neurodegenerative diseases.Advanced biotechnology · 2024Review
- Observation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing.Nature communications · 2023Article
- In vivo-like nearest neighbor parameters improve prediction of fractional RNA base-pairing in cells.Nucleic acids research · 2023Article
- A transient intermediate RNA structure underlies the regulatory function of theRNA (New York, N.Y.) · 2023Article
- In vivo structure probing of RNA inRNA (New York, N.Y.) · 2023Article
- RNA folding studies inside peptide-rich droplets reveal roles of modified nucleosides at the origin of life.Science advances · 2023Article
- Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS.Nucleic acids research · 2023Article
- Transcriptome-wide probing reveals RNA thermometers that regulate translation of glycerol permease genes inRNA (New York, N.Y.) · 2023Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA serves many functions in biology such as splicing, temperature sensing, and innate immunity. These functions are often determined by the structure of RNA. There is thus a pressing need to understand RNA structure and how it changes during diverse biological processes both in vivo and genome-wide. Here, we present Structure-seq2, which provides nucleotide-resolution RNA structural information in vivo and genome-wide. This optimized version of our original Structure-seq method increases sensitivity by at least 4-fold and improves data quality by minimizing formation of a deleterious by-product, reducing ligation bias, and improving read coverage. We also present a variation of Structure-seq2 in which a biotinylated nucleotide is incorporated during reverse transcription, which greatly facilitates the protocol by eliminating two PAGE purification steps. We benchmark Structure-seq2 on both mRNA and rRNA structure in rice (Oryza sativa). We demonstrate that Structure-seq2 can lead to new biological insights. Our Structure-seq2 datasets uncover hidden breaks in chloroplast rRNA and identify a previously unreported N1-methyladenosine (m1A) in a nuclear-encoded Oryza sativa rRNA. Overall, Structure-seq2 is a rapid, sensitive, and unbiased method to probe RNA in vivo and genome-wide that facilitates new insights into RNA biology.
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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.