ArticleNature microbiology2022
Genome-wide protein-DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase.
Article in Nature microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 30 citations in OpenAlex.
- Genome-wide profiling of histone modifications and transcription factor binding at single-cell resolution by DeChIC-seq.Cell research · 2026Article
- Mechanism of persister formation in response to nitrogen starvation.Nature communications · 2026Article
- RGTBind: RBF-gate graph transformer with spatially biased attention for protein-DNA binding-site prediction.Journal of molecular modeling · 2026Article
- Predicting protein-nucleic acid interactions via protein language models with biophysical and evolutionary priors.iScience · 2026Article
- Structural basis for double-stranded DNA cytosine deamination by BaDTF3 and its application in mitochondrial genome editing.Nature communications · 2026Article
- A default silencing mechanism restrains stress-induced genes inbioRxiv : the preprint server for biology · 2025Article
- Coupling CRISPR scanning with targeted chromatin accessibility profiling using a double-stranded DNA deaminase.Nature methods · 2025Article
- MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model.Briefings in bioinformatics · 2025Article
- A universal and wide-range cytosine base editor via domain-inlaid and fidelity-optimized CRISPR-FrCas9.Nature communications · 2025Article
- iProtDNA-SMOTE: Enhancing protein-DNA binding sites prediction through imbalanced graph neural networks.PloS one · 2025Article
- EGPDI: identifying protein-DNA binding sites based on multi-view graph embedding fusion.Briefings in bioinformatics · 2024Article
- A comparison between full-length 16S rRNA Oxford nanopore sequencing and Illumina V3-V4 16S rRNA sequencing in head and neck cancer tissues.Archives of microbiology · 2024Article
- Article
- ULDNA: integrating unsupervised multi-source language models with LSTM-attention network for high-accuracy protein-DNA binding site prediction.Briefings in bioinformatics · 2024Article
- Modeling genotype-protein interaction and correlation for Alzheimer's disease: a multi-omics imaging genetics study.Briefings in bioinformatics · 2024Article
- Harnessing regulatory networks in Actinobacteria for natural product discovery.Journal of industrial microbiology & biotechnology · 2024Review
- Structures of theProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Mechanisms and biotechnological applications of transcription factors.Synthetic and systems biotechnology · 2023Review
- Developing mitochondrial base editors with diverse context compatibility and high fidelity via saturated spacer library.Nature communications · 2023Article
- Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA.Nature structural & molecular biology · 2023Article
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Authors and funding
21 authors at 5 institutions in 2 countries.
Funding
Abstract
DNA-protein interactions are central to fundamental cellular processes, yet widely implemented technologies for measuring these interactions on a genome scale in bacteria are laborious and capture only a snapshot of binding events. We devised a facile method for mapping DNA-protein interaction sites in vivo using the double-stranded DNA-specific cytosine deaminase toxin DddA. In 3D-seq (DddA-sequencing), strains containing DddA fused to a DNA-binding protein of interest accumulate characteristic mutations in DNA sequence adjacent to sites occupied by the DNA-bound fusion protein. High-depth sequencing enables detection of sites of increased mutation frequency in these strains, yielding genome-wide maps of DNA-protein interaction sites. We validated 3D-seq for four transcription regulators in two bacterial species, Pseudomonas aeruginosa and Escherichia coli. We show that 3D-seq offers ease of implementation, the ability to record binding event signatures over time and the capacity for single-cell resolution.
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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.