{"doi":"10.1101/2021.08.01.454665","title":"Genome-wide protein-DNA interaction site mapping using a double strand DNA-specific cytosine deaminase","abstract":"DNA–protein interactions (DPIs) are central to such fundamental cellular processes as transcription and chromosome maintenance and organization. The spatiotemporal dynamics of these interactions dictate their functional consequences; therefore, there is great interest in facile methods for defining the sites of DPI within cells. Here, we present a general method for mapping DPI sites in vivo using the double stranded DNA-specific cytosine deaminase toxin DddA. Our approach, which we term DddA-sequencing (3D-seq), entails generating a translational fusion of DddA to a DNA binding protein of interest, inactivating uracil DNA glycosylase, modulating DddA activity via its natural inhibitor protein, and DNA sequencing for genome-wide DPI detection. We successfully applied this method to three Pseudomonas aeruginosa transcription factors that represent divergent protein families and bind variable numbers of chromosomal locations. 3D-seq offers several advantages over existing technologies including ease of implementation and the possibility to measure DPIs at single-cell resolution.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2021,"id":221399,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9603,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":821427,"name":"Elena Velázquez","orcid":"0000-0001-6648-1634","position":1,"is_corresponding":false},{"id":253493,"name":"S. Brook Peterson","orcid":"0000-0003-2648-0965","position":2,"is_corresponding":false},{"id":821979,"name":"James C. Charity","orcid":null,"position":3,"is_corresponding":false},{"id":577539,"name":"FoSheng Hsu","orcid":"0000-0001-8486-7311","position":4,"is_corresponding":false},{"id":296701,"name":"Matthew C. Radey","orcid":null,"position":5,"is_corresponding":false},{"id":417864,"name":"Michael J. Gebhardt","orcid":"0000-0002-1213-8408","position":6,"is_corresponding":false},{"id":577538,"name":"Marcos H. de Moraes","orcid":"0000-0003-3096-9384","position":7,"is_corresponding":false},{"id":424554,"name":"Kelsi Penewit","orcid":"0000-0003-1454-6381","position":8,"is_corresponding":false},{"id":821428,"name":"Jennifer Kim","orcid":"0000-0003-2922-1010","position":9,"is_corresponding":false},{"id":821980,"name":"Pia A. Andrade","orcid":null,"position":10,"is_corresponding":false},{"id":336354,"name":"Thomas LaFramboise","orcid":"0000-0003-1793-4777","position":11,"is_corresponding":false},{"id":424556,"name":"Stephen J. Salipante","orcid":"0000-0001-8355-6992","position":12,"is_corresponding":false},{"id":294932,"name":"Vı́ctor de Lorenzo","orcid":"0000-0002-6041-2731","position":13,"is_corresponding":false},{"id":96742,"name":"Paul A. Wiggins","orcid":"0000-0002-8316-4339","position":14,"is_corresponding":false},{"id":474945,"name":"Simon L. Dove","orcid":"0000-0002-3758-608X","position":15,"is_corresponding":false},{"id":253495,"name":"Joseph D. Mougous","orcid":"0000-0002-5417-4861","position":16,"is_corresponding":false},{"id":353211,"name":"Larry A. Gallagher","orcid":"0000-0002-1517-4236","position":0,"is_corresponding":true}],"reference_count":50,"raw_metadata":null,"created_at":"2026-07-18T23:53:55.215284Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}