ArticleNature communications2014
Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences.
Article in Nature communications, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
66 citing papers in PubMed, 109 citations in OpenAlex.
- Phage hijacks host phosphorothioate DNA modification machinery to circumvent bacterial Ssp defences.Nature microbiology · 2026Article
- Article
- Phosphorothioate DNA modification by BREX type 4 systems in the human gut microbiome.Nature communications · 2026Article
- Biology of host-dependent restriction-modification in prokaryotes.EcoSal Plus · 2025Review
- Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome.Microbiome · 2025Article
- Understanding prokaryotic adaptation through advanced DNA methylation detection techniques.The ISME journal · 2025Review
- KinMethyl: robust methylation detection in prokaryotic SMRT sequencing via kinetic signal modeling and deep feature integration.Bioinformatics advances · 2025Article
- Molecular basis of the phosphorothioation-sensing antiphage defense system IscS-DndBCDE-DndI.Nucleic acids research · 2024Article
- A widespread phage-encoded kinase enables evasion of multiple host antiphage defence systems.Nature microbiology · 2024Article
- PT-seq: A method for metagenomic analysis of phosphorothioate epigenetics in complex microbial communities.bioRxiv : the preprint server for biology · 2024Article
- Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome.bioRxiv : the preprint server for biology · 2024Article
- Reappraisal of the DNA phosphorothioate modification machinery: uncovering neglected functional modalities and identification of new counter-invader defense systems.Nucleic acids research · 2024Article
- Article
- Recurring and emerging themes in prokaryotic innate immunity.Current opinion in microbiology · 2023Review
- The DNA Phosphorothioation Restriction-Modification System Influences the Antimicrobial Resistance of Pathogenic Bacteria.Microbiology spectrum · 2023Article
- Nicking mechanism underlying the DNA phosphorothioate-sensing antiphage defense by SspE.Nature communications · 2022Article
- High-throughput sequencing of EcoWI restriction fragments maps the genome-wide landscape of phosphorothioate modification at base resolution.PLoS genetics · 2022Article
- Full-length transcriptome-referenced analysis reveals crucial roles of hormone and wounding during induction of aerial bulbils in lily.BMC plant biology · 2022Article
- Article
- Article
6 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
21 authors at 5 institutions in 2 countries.
Funding
Abstract
Bacterial phosphorothioate (PT) DNA modifications are incorporated by Dnd proteins A-E and often function with DndF-H as a restriction-modification (R-M) system, as in Escherichia coli B7A. However, bacteria such as Vibrio cyclitrophicus FF75 lack dndF-H, which points to other PT functions. Here we report two novel, orthogonal technologies to map PTs across the genomes of B7A and FF75 with >90% agreement: single molecule, real-time sequencing and deep sequencing of iodine-induced cleavage at PT (ICDS). In B7A, we detect PT on both strands of GpsAAC/GpsTTC motifs, but with only 12% of 40,701 possible sites modified. In contrast, PT in FF75 occurs as a single-strand modification at CpsCA, again with only 14% of 160,541 sites modified. Single-molecule analysis indicates that modification could be partial at any particular genomic site even with active restriction by DndF-H, with direct interaction of modification proteins with GAAC/GTTC sites demonstrated with oligonucleotides. These results point to highly unusual target selection by PT-modification proteins and rule out known R-M mechanisms.
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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.