{"doi":"10.1101/2023.07.14.549009","title":"GAGA zinc finger transcription factor searches chromatin by 1D-3D facilitated diffusion","abstract":"To elucidate how eukaryotic sequence-specific transcription factors (TFs) search for gene targets on chromatin, we used multi-color smFRET and single-particle imaging to track the diffusion of purified GAGA-Associated Factor (GAF) on DNA and nucleosomes. Monomeric GAF DNA-binding domain (DBD) bearing one zinc finger finds its cognate site by 1D or 3D diffusion on bare DNA and rapidly slides back-and-forth between naturally clustered motifs for seconds before escape. Multimeric, full-length GAF also finds clustered motifs on DNA by 1D-3D diffusion, but remains locked on target for longer periods. Nucleosome architecture effectively blocks GAF-DBD 1D-sliding into the histone core but favors retention of GAF-DBD when targeting solvent-exposed sites by 3D-diffusion. Despite the occlusive power of nucleosomes, 1D-3D facilitated diffusion enables GAF to effectively search for clustered cognate motifs in chromatin, providing a mechanism for navigation to nucleosome and nucleosome-free sites by a member of the largest TF family.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":394843,"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":3,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9605,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":340385,"name":"Maryam Yamadi","orcid":"0000-0001-7080-5566","position":1,"is_corresponding":false},{"id":326918,"name":"Yiben Fu","orcid":"0000-0002-6043-5183","position":2,"is_corresponding":false},{"id":1170219,"name":"Kaitlin M. Ness","orcid":null,"position":3,"is_corresponding":false},{"id":868433,"name":"Celina Liu","orcid":"0009-0005-3138-5200","position":4,"is_corresponding":false},{"id":891825,"name":"Ishtiyaq Ahmed","orcid":"0000-0001-8816-1375","position":5,"is_corresponding":false},{"id":479538,"name":"Gregory D. Bowman","orcid":"0000-0001-8025-4315","position":6,"is_corresponding":false},{"id":326921,"name":"Margaret E. Johnson","orcid":"0000-0001-9881-291X","position":7,"is_corresponding":false},{"id":22168,"name":"Taekjip Ha","orcid":"0000-0003-2195-6258","position":8,"is_corresponding":false},{"id":52465,"name":"Carl Wu","orcid":"0000-0001-6933-5763","position":9,"is_corresponding":false},{"id":677971,"name":"Xinyu A. Feng","orcid":"0000-0001-5862-1983","position":0,"is_corresponding":true}],"reference_count":81,"raw_metadata":null,"created_at":"2026-07-19T01:19:18.686170Z","pmid":"37502885","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":[]}