{"doi":"10.7554/elife.68469","title":"Cis-regulatory variants affect gene expression dynamics in yeast","abstract":"Evolution of cis -regulatory sequences depends on how they affect gene expression and motivates both the identification and prediction of cis -regulatory variants responsible for expression differences within and between species. While much progress has been made in relating cis -regulatory variants to expression levels, the timing of gene activation and repression may also be important to the evolution of cis -regulatory sequences. We investigated allele-specific expression (ASE) dynamics within and between Saccharomyces species during the diauxic shift and found appreciable cis -acting variation in gene expression dynamics. Within-species ASE is associated with intergenic variants, and ASE dynamics are more strongly associated with insertions and deletions than ASE levels. To refine these associations, we used a high-throughput reporter assay to test promoter regions and individual variants. Within the subset of regions that recapitulated endogenous expression, we identified and characterized cis -regulatory variants that affect expression dynamics. Between species, chimeric promoter regions generate novel patterns and indicate constraints on the evolution of gene expression dynamics. We conclude that changes in cis -regulatory sequences can tune gene expression dynamics and that the interplay between expression dynamics and other aspects of expression is relevant to the evolution of cis -regulatory sequences.","journal":"eLife","year":2021,"id":187943,"datarank":0.7161304583661747,"base_score":2.8903717578961645,"endowment":2.8903717578961645,"self_citation_contribution":0.4335557636844247,"citation_network_contribution":0.28257469468174995,"self_endowment_contribution":0.4335557636844247,"citer_contribution":0.28257469468174995,"corpus_percentile":null,"corpus_rank":null,"citation_count":17,"citer_count":16,"citers_with_citation_signal":12,"citers_with_endowment":12,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9491,"is_data_producer":true,"deposit_databanks":{"GEO":["GSE165594"]},"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":378905,"name":"Justin C. Fay","orcid":"0000-0003-1893-877X","position":1,"is_corresponding":false},{"id":748197,"name":"Ching-Hua Shih","orcid":"0000-0002-6652-1197","position":0,"is_corresponding":true}],"reference_count":93,"raw_metadata":null,"created_at":"2026-07-18T23:49:05.976005Z","pmid":"34369376","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":[]}