ArticlePLoS genetics2019
Quantitative mapping of DNA phosphorothioatome reveals phosphorothioate heterogeneity of low modification frequency.
Article in PLoS genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 20 citations in OpenAlex.
- Optimized Multi-Phosphorothioate Linkers Enable Efficient Iodine-Induced Cleavage of Surface-Immobilized DNA for Genomic Applications.ACS omega · 2026Article
- A Convenient Fluorogenic Detection Strategy for Phosphorothioate Modification of DNA Through Photocatalytic Oligonucleotide-Templated Reaction.Biomolecules · 2025Article
- KinMethyl: robust methylation detection in prokaryotic SMRT sequencing via kinetic signal modeling and deep feature integration.Bioinformatics advances · 2025Article
- PT-seq: A method for metagenomic analysis of phosphorothioate epigenetics in complex microbial communities.bioRxiv : the preprint server for biology · 2024Article
- High-throughput sequencing of EcoWI restriction fragments maps the genome-wide landscape of phosphorothioate modification at base resolution.PLoS genetics · 2022Article
- Origin of iodine preferential attack at sulfur in phosphorothioate and subsequent P-O or P-S bond dissociation.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Quantification and mapping of DNA modifications.RSC chemical biology · 2021Review
- Development of Methods Derived from Iodine-Induced Specific Cleavage for Identification and Quantitation of DNA Phosphorothioate Modifications.Biomolecules · 2020Article
- DNA Phosphorothioate Modifications Are Widely Distributed in the Human Microbiome.Biomolecules · 2020Article
- Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Bacterial genetics and molecular pathogenesis in the age of high throughput DNA sequencing.Current opinion in microbiology · 2020Review
- Protein Domain Guided Screen for Sequence Specific and Phosphorothioate-Dependent Restriction Endonucleases.Frontiers in microbiology · 2020Article
Corrections and comments
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phosphorothioate (PT) modifications of the DNA backbone, widespread in prokaryotes, are first identified in bacterial enteropathogens Escherichia coli B7A more than a decade ago. However, methods for high resolution mapping of PT modification level are still lacking. Here, we developed the PT-IC-seq technique, based on iodine-induced selective cleavage at PT sites and high-throughput next generation sequencing, as a mean to quantitatively characterizing the genomic landscape of PT modifications. Using PT-IC-seq we foud that most PT sites are partially modified at a lower PT frequency (< 5%) in E. coli B7A and Salmonella enterica serovar Cerro 87, and both show a heterogeneity pattern of PT modification similar to those of the typical methylation modification. Combining the iodine-induced cleavage and absolute quantification by droplet digital PCR, we developed the PT-IC-ddPCR technique to further measure the PT modification level. Consistent with the PT-IC-seq measurements, PT-IC-ddPCR analysis confirmed the lower PT frequency in E. coli B7A. Our study has demonstrated the heterogeneity of PT modification in the bacterial population and we also established general tools for rigorous mapping and characterization of PT modification events at whole genome level. We describe to our knowledge the first genome-wide quantitative characterization of PT landscape and provides appropriate strategies for further functional studies of PT modification.
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