{"doi":"10.1101/2023.04.14.536894","title":"Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors","abstract":"ABSTRACT Cooperativity and antagonism between transcription factors (TFs) can drastically modify their binding to regulatory DNA elements. While mapping these relationships between TFs is important for understanding their context-specific functions, existing approaches either rely on DNA binding motif predictions, interrogate one TF at a time, or study individual TFs in parallel. Here, we introduce paired yeast one-hybrid (pY1H) assays to detect cooperativity and antagonism across hundreds of TF-pairs at DNA regions of interest. We provide evidence that a wide variety of TFs are subject to modulation by other TFs in a DNA sequence-specific manner. We also demonstrate that TF-TF relationships are often affected by alternative isoform usage, and identify cooperativity and antagonism between human TFs and viral proteins. pY1H assays provide a broadly applicable framework to study how different functional relationships affect protein occupancy at regulatory DNA regions.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":406448,"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":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9568,"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":1065583,"name":"Ryan Lane","orcid":"0009-0009-0513-9849","position":1,"is_corresponding":false},{"id":630297,"name":"Luis F. Soto","orcid":"0000-0002-6348-6437","position":2,"is_corresponding":false},{"id":1065584,"name":"Mahir Patel","orcid":"0000-0002-3370-4595","position":3,"is_corresponding":false},{"id":1066150,"name":"Cosmin Ciausu","orcid":null,"position":4,"is_corresponding":false},{"id":69342,"name":"Zhaorong Li","orcid":"0000-0002-5268-6986","position":5,"is_corresponding":false},{"id":479617,"name":"Yilin Chen","orcid":"0009-0000-9552-5990","position":6,"is_corresponding":false},{"id":1065585,"name":"Sakshi Shah","orcid":"0000-0002-2075-6900","position":7,"is_corresponding":false},{"id":336753,"name":"Clarissa Santoso","orcid":"0000-0002-2743-7240","position":8,"is_corresponding":false},{"id":289952,"name":"Xing Liu","orcid":"0000-0002-3467-7103","position":9,"is_corresponding":false},{"id":106204,"name":"Kerstin Spirohn","orcid":"0000-0002-2071-1606","position":10,"is_corresponding":false},{"id":56379,"name":"Tong Hao","orcid":"0000-0001-7908-3256","position":11,"is_corresponding":false},{"id":56382,"name":"David E. Hill","orcid":"0000-0001-5192-0921","position":12,"is_corresponding":false},{"id":56381,"name":"Marc Vidal","orcid":"0000-0003-3391-5410","position":13,"is_corresponding":false},{"id":289954,"name":"Juan I. Fuxman Bass","orcid":"0000-0001-9457-1207","position":14,"is_corresponding":false},{"id":630298,"name":"Anna Berenson","orcid":"0000-0002-3782-6186","position":0,"is_corresponding":true}],"reference_count":66,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T01:21:03.432924Z","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":[]}