Journal article
Genome-wide protein-DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase
Nature microbiology, Vol.7(6), pp.844-855
06/2022
DOI: 10.1038/s41564-022-01133-9
PMCID: PMC9159945
PMID: 35650286
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.
Details
- Title: Subtitle
- Genome-wide protein-DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase
- Creators
- Larry A Gallagher - University of WashingtonElena Velazquez - Systems Biology Department, National Center of Biotechnology CSIC, Madrid, SpainS Brook Peterson - University of WashingtonJames C Charity - Boston Children's HospitalMatthew C Radey - University of WashingtonMichael J Gebhardt - Boston Children's HospitalFoSheng Hsu - University of WashingtonLauren M Shull - University of WashingtonKevin J Cutler - University of WashingtonKeven Macareno - Boston Children's HospitalMarcos H de Moraes - University of WashingtonKelsi M Penewit - University of WashingtonJennifer Kim - University of WashingtonPia A Andrade - University of WashingtonThomas LaFramboise - Case Western Reserve UniversityStephen J Salipante - University of WashingtonMichelle L Reniere - University of WashingtonVictor de Lorenzo - Systems Biology Department, National Center of Biotechnology CSIC, Madrid, SpainPaul A Wiggins - University of WashingtonSimon L Dove - Boston Children's HospitalJoseph D Mougous - University of Washington
- Resource Type
- Journal article
- Publication Details
- Nature microbiology, Vol.7(6), pp.844-855
- DOI
- 10.1038/s41564-022-01133-9
- PMID
- 35650286
- PMCID
- PMC9159945
- NLM abbreviation
- Nat Microbiol
- ISSN
- 2058-5276
- eISSN
- 2058-5276
- Grant note
- GM128191 / U.S. Department of Health & Human Services | National Institutes of Health (NIH) AI143771 / U.S. Department of Health & Human Services | National Institutes of Health (NIH) DK089507 / U.S. Department of Health & Human Services | National Institutes of Health (NIH) AI080609 / U.S. Department of Health & Human Services | National Institutes of Health (NIH) postdoctoral fellowship / Cystic Fibrosis Foundation (CF Foundation) SINGH19R0 / Cystic Fibrosis Foundation (CF Foundation) n/a / Howard Hughes Medical Institute (HHMI)
- Language
- English
- Date published
- 06/2022
- Academic Unit
- Microbiology and Immunology
- Record Identifier
- 9984297316902771
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