{"doi":"10.1016/j.molcel.2023.04.002","title":"Complementary strategies for directing in vivo transcription factor binding through DNA binding domains and intrinsically disordered regions","abstract":null,"journal":"Molecular Cell","year":2023,"id":637425,"datarank":0.62147020895873,"base_score":4.143134726391533,"endowment":4.143134726391533,"self_citation_contribution":0.62147020895873,"citation_network_contribution":0.0,"self_endowment_contribution":0.62147020895873,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":62,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1655122,"name":"Felix Jonas","orcid":null,"position":1,"is_corresponding":false},{"id":1655124,"name":"Tamar Jana","orcid":null,"position":2,"is_corresponding":false},{"id":1655125,"name":"Sagie Brodsky","orcid":null,"position":3,"is_corresponding":false},{"id":1655126,"name":"Miri Carmi","orcid":null,"position":4,"is_corresponding":false},{"id":86292,"name":"Naama Barkai","orcid":"0000-0002-2444-6061","position":5,"is_corresponding":false},{"id":1655121,"name":"Divya Krishna Kumar","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Complementary strategies for directing in vivo transcription factor binding through DNA binding domains and intrinsically disordered regions","abstract":"DNA binding domains (DBDs) of transcription factors (TFs) recognize DNA sequence motifs that are highly abundant in genomes. Within cells, TFs bind a subset of motif-containing sites as directed by either their DBDs or DBD-external (nonDBD) sequences. To define the relative roles of DBDs and nonDBDs in directing binding preferences, we compared the genome-wide binding of 48 (∼30%) budding yeast TFs with their DBD-only, nonDBD-truncated, and nonDBD-only mutants. With a few exceptions, binding locations differed between DBDs and TFs, resulting from the cumulative action of multiple determinants mapped mostly to disordered nonDBD regions. Furthermore, TFs' preferences for promoters of the fuzzy nucleosome architecture were lost in DBD-only mutants, whose binding spread across promoters, implicating nonDBDs' preferences in this hallmark of budding yeast regulatory design. We conclude that DBDs and nonDBDs employ complementary DNA-targeting strategies, whose balance defines TF binding specificity along genomes.","is_dataset_classified":null,"base_score":4.143134726391533,"endowment":4.143134726391533,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"37116493","pmcid":null,"openalex_id":"https://openalex.org/W4367325962","authors":[],"funders":[{"funder_name":"HORIZON EUROPE Framework Programme","grant_id":"","title":null},{"funder_name":"European Research Council","grant_id":"","title":null},{"funder_name":"Israel Science Foundation","grant_id":"","title":null},{"funder_name":"Minerva Foundation","grant_id":"","title":null}],"total_grants":4,"fwci":5.7184,"citation_percentile":0.9738873,"influential_citations":0,"citation_trend":[{"year":2022,"count":1},{"year":2023,"count":9},{"year":2024,"count":23},{"year":2025,"count":21},{"year":2026,"count":8}],"oa_status":"closed","license":"http://www.elsevier.com/open-access/userlicense/1.0/","oa_locations":[{"url":"https://api.elsevier.com/content/article/PII:S1097276523002460?httpAccept=text/xml","host_type":"publisher"},{"url":"https://api.elsevier.com/content/article/PII:S1097276523002460?httpAccept=text/plain","host_type":"publisher"},{"url":"https://doi.org/10.1016/j.molcel.2023.04.002","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/37116493","host_type":"repository"}],"fields_of_study":["Genomics and Chromatin Dynamics","RNA Research and Splicing","RNA and protein synthesis mechanisms"],"mesh_terms":["Binding Sites","DNA","Protein Binding","4-Acetamido-4'-isothiocyanatostilbene-2,2'-disulfonic Acid","Transcription Factors"],"keywords":["Biology","Transcription factor","Promoter","Genetics","Genome","Binding site","DNA","DNA binding site","DNA-binding protein","Nucleosome","Consensus sequence","Budding yeast","DNA-binding domain","Yeast","Saccharomyces cerevisiae","Gene","Histone","Gene expression","Base sequence","Transcription factors","Genome organization","Gene Regulatory Network","Intrinsically Disordered Regions","Genome-wide Binding Specificity"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life in Land"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-06T18:55:04.023768Z","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":[]}