{"doi":"10.17615/gzna-2b89","title":"Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization","abstract":"Eukaryotic transcription occurs within a chromatin environment, whose organization plays an important regulatory role and is partly encoded in cis by the DNA sequence itself1-6. Here, we examine whether evolutionary changes in gene expression are linked to changes in the DNA-encoded nucleosome organization of promoters. We find that in aerobic yeast species, where cellular respiration genes are active under typical growth conditions, the promoter sequences of these genes encode a relatively open (nucleosome-depleted) chromatin organization. This nucleosome-depleted organization requires only DNA sequence information, is independent of any co-factors and of transcription, and is a general property of growth-related genes. In contrast, in anaerobic yeast species, where cellular respiration genes are inactive under typical growth conditions, respiration gene promoters encode relatively closed (nucleosome-occupied) chromatin organizations. Thus, our results suggest a previously unidentified genetic mechanism underlying phenotypic diversity, consisting of DNA sequence changes that directly alter the DNA-encoded nucleosome organization of promoters.","journal":"UNC Libraries","year":2020,"id":135889,"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":0.9545,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":17128,"name":"Jonathan Widom","orcid":null,"position":1,"is_corresponding":false},{"id":17125,"name":"Yair Field","orcid":"0000-0002-5327-1678","position":2,"is_corresponding":false},{"id":11673,"name":"Jason D. Lieb","orcid":null,"position":3,"is_corresponding":false},{"id":24,"name":"Eran Segal","orcid":"0000-0002-6859-1164","position":4,"is_corresponding":false},{"id":17129,"name":"Yvonne Fondufe‐Mittendorf","orcid":"0000-0002-2551-9920","position":5,"is_corresponding":false},{"id":593409,"name":"N. Kaplan","orcid":"0000-0001-9940-1987","position":6,"is_corresponding":false},{"id":349831,"name":"Yaniv Lubling","orcid":"0000-0003-3461-9621","position":7,"is_corresponding":false},{"id":17126,"name":"Irene K. Moore","orcid":null,"position":8,"is_corresponding":false},{"id":13808,"name":"Piotr A. Mieczkowski","orcid":"0000-0003-2418-0096","position":0,"is_corresponding":true}],"reference_count":0,"raw_metadata":null,"created_at":"2026-07-18T23:16:35.237665Z","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":[]}