ArticleNucleic acids research2020
Lead-seq: transcriptome-wide structure probing in vivo using lead(II) ions.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 34 citations in OpenAlex.
- Long Noncoding RNA Isoform Specificity and Chemical Modification on tRNA-Derived Fragments Leading to Divergent Functions.The American journal of pathology · 2026Review
- Recent Advances in Chemical Probing Strategies for RNA Structure Determination In Vivo.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- bpRNA-CosMoS: a robust and efficient RNA structural comparison method using k-mer based cosine similarity.Bioinformatics (Oxford, England) · 2025Article
- Two temperature-responsive RNAs act in concert: the small RNA CyaR and the mRNA ompX.Nucleic acids research · 2025Article
- RNA structure: implications in viral infections and neurodegenerative diseases.Advanced biotechnology · 2024Review
- Transcriptome-wide probing reveals RNA thermometers that regulate translation of glycerol permease genes inRNA (New York, N.Y.) · 2023Article
- The oxidative stress response, in particular the katY gene, is temperature-regulated in Yersinia pseudotuberculosis.PLoS genetics · 2023Article
- Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA.Nucleic acids research · 2023Article
- Genome-wide analysis of theProceedings of the National Academy of Sciences of the United States of America · 2022Article
- The life and death of RNA across temperatures.Computational and structural biotechnology journal · 2022Review
- The in vivo RNA structurome of the malaria parasite Plasmodium falciparum, a protozoan with an A/U-rich transcriptome.PloS one · 2022Article
- cyPhyRNA-seq: a genome-scale RNA-seq method to detect active self-cleaving ribozymes by capturing RNAs with 2',3'RNA biology · 2021Article
- The gatekeeper of Yersinia type III secretion is under RNA thermometer control.PLoS pathogens · 2021Article
- Accurate detection of RNA stem-loops in structurome data reveals widespread association with protein binding sites.RNA biology · 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
- OmpA, a Common Virulence Factor, Is Under RNA Thermometer Control inFrontiers in microbiology · 2021Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The dynamic conformation of RNA molecules within living cells is key to their function. Recent advances in probing the RNA structurome in vivo, including the use of SHAPE (Selective 2'-Hydroxyl Acylation analyzed by Primer Extension) or kethoxal reagents or DMS (dimethyl sulfate), provided unprecedented insights into the architecture of RNA molecules in the living cell. Here, we report the establishment of lead probing in a global RNA structuromics approach. In order to elucidate the transcriptome-wide RNA landscape in the enteric pathogen Yersinia pseudotuberculosis, we combined lead(II) acetate-mediated cleavage of single-stranded RNA regions with high-throughput sequencing. This new approach, termed 'Lead-seq', provides structural information independent of base identity. We show that the method recapitulates secondary structures of tRNAs, RNase P RNA, tmRNA, 16S rRNA and the rpsT 5'-untranslated region, and that it reveals global structural features of mRNAs. The application of Lead-seq to Y. pseudotuberculosis cells grown at two different temperatures unveiled the first temperature-responsive in vivo RNA structurome of a bacterial pathogen. The translation of candidate genes derived from this approach was confirmed to be temperature regulated. Overall, this study establishes Lead-seq as complementary approach to interrogate intracellular RNA structures on a global scale.
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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.