دورية أكاديمية
أعرض في EDS

Genome-wide protein-DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase.

التفاصيل البيبلوغرافية
العنوان: Genome-wide protein-DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase.
المؤلفون: Gallagher LA; Department of Microbiology, University of Washington, Seattle, WA, USA., Velazquez E; Department of Microbiology, University of Washington, Seattle, WA, USA.; Systems Biology Department, National Center of Biotechnology CSIC, Madrid, Spain., Peterson SB; Department of Microbiology, University of Washington, Seattle, WA, USA., Charity JC; Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA., Radey MC; Department of Microbiology, University of Washington, Seattle, WA, USA., Gebhardt MJ; Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA., Hsu F; Department of Microbiology, University of Washington, Seattle, WA, USA., Shull LM; Department of Microbiology, University of Washington, Seattle, WA, USA., Cutler KJ; Department of Physics, University of Washington, Seattle, WA, USA., Macareno K; Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA., de Moraes MH; Department of Microbiology, University of Washington, Seattle, WA, USA., Penewit KM; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA., Kim J; Department of Microbiology, University of Washington, Seattle, WA, USA., Andrade PA; Department of Microbiology, University of Washington, Seattle, WA, USA., LaFramboise T; Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA., Salipante SJ; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA., Reniere ML; Department of Microbiology, University of Washington, Seattle, WA, USA., de Lorenzo V; Systems Biology Department, National Center of Biotechnology CSIC, Madrid, Spain., Wiggins PA; Department of Microbiology, University of Washington, Seattle, WA, USA.; Department of Physics, University of Washington, Seattle, WA, USA.; Department of Bioengineering, University of Washington, Seattle, WA, USA., Dove SL; Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA. simon.dove@childrens.harvard.edu., Mougous JD; Department of Microbiology, University of Washington, Seattle, WA, USA. mougous@uw.edu.; Department of Biochemistry, University of Washington School of Medicine, Seattle, WA, USA. mougous@uw.edu.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA. mougous@uw.edu.
المصدر: Nature microbiology [Nat Microbiol] 2022 Jun; Vol. 7 (6), pp. 844-855. Date of Electronic Publication: 2022 Jun 01.
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101674869 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2058-5276 (Electronic) Linking ISSN: 20585276 NLM ISO Abbreviation: Nat Microbiol Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : Nature Publishing Group, [2016]-
مواضيع طبية MeSH: Cytosine Deaminase* , Genome*, Bacteria/metabolism ; DNA/metabolism ; Protein Interaction Mapping
مستخلص: 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.
(© 2022. The Author(s).)
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معلومات مُعتمدة: P30 DK089507 United States DK NIDDK NIH HHS; United States HHMI Howard Hughes Medical Institute; R01 AI143771 United States AI NIAID NIH HHS; R01 GM128191 United States GM NIGMS NIH HHS; R01 AI080609 United States AI NIAID NIH HHS; T32 GM008268 United States GM NIGMS NIH HHS
المشرفين على المادة: 9007-49-2 (DNA)
EC 3.5.4.1 (Cytosine Deaminase)
تواريخ الأحداث: Date Created: 20220601 Date Completed: 20220603 Latest Revision: 20240607
رمز التحديث: 20240607
مُعرف محوري في PubMed: PMC9159945
DOI: 10.1038/s41564-022-01133-9
PMID: 35650286
قاعدة البيانات: MEDLINE
الوصف
تدمد:2058-5276
DOI:10.1038/s41564-022-01133-9