{"doi":"10.1101/2025.09.04.674194","title":"A scheduler for rhythmic gene expression","abstract":"molting clock as a model, we investigate how oscillators can schedule the orderly expression of thousands of genes. Single cell RNA sequencing reveals a broad peak phase dispersion in individual issues, mirrored by rhythmic changes in chromatin accessibility at thousands of regulatory elements identified by time-resolved ATAC-seq. We develop a linear model to predict chromatin dynamics based on the binding of >200 transcription factors. This identifies nine key regulators acting additively to determine the peak phase and amplitude of each regulatory element. Strikingly, these factors can also generate constitutive, non-rhythmic activity through destructive interference. Validating its power, the model accurately predicts the impact of GRH-1/Grainyhead perturbation on both chromatin and transcript dynamics. This work provides a conceptual framework for understanding how combinatorial, non-cooperative transcription factor binding schedules complex gene expression patterns in development and other dynamic biological processes.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":574269,"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":0.9467,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1481710,"name":"Maike Graf-Landua","orcid":"0000-0003-2723-2015","position":1,"is_corresponding":false},{"id":551822,"name":"Stephen P. Methot","orcid":"0000-0003-2854-2226","position":2,"is_corresponding":false},{"id":1482061,"name":"Michaela Woelk","orcid":null,"position":3,"is_corresponding":false},{"id":642626,"name":"Giovanna Brancati","orcid":"0000-0002-8589-3463","position":4,"is_corresponding":false},{"id":1221469,"name":"Yannick P. Hauser","orcid":"0000-0003-1357-9712","position":5,"is_corresponding":false},{"id":1481711,"name":"Milou W.M. Meeuse","orcid":"0000-0001-6382-6449","position":6,"is_corresponding":false},{"id":909235,"name":"Smita Nahar","orcid":"0000-0001-7449-9324","position":7,"is_corresponding":false},{"id":568755,"name":"Kathrin Braun","orcid":"0000-0003-1576-0486","position":8,"is_corresponding":false},{"id":1424974,"name":"Marit van der Does","orcid":"0000-0002-2476-158X","position":9,"is_corresponding":false},{"id":1482062,"name":"Sirisha Aluri","orcid":null,"position":10,"is_corresponding":false},{"id":642627,"name":"Hubertus Kohler","orcid":"0000-0003-4395-7630","position":11,"is_corresponding":false},{"id":636503,"name":"Sébastien A. Smallwood","orcid":"0009-0006-8466-2459","position":12,"is_corresponding":false},{"id":372024,"name":"Helge Großhans","orcid":"0000-0002-8169-6905","position":13,"is_corresponding":false},{"id":339437,"name":"Dimos Gaidatzis","orcid":"0000-0003-4294-4504","position":0,"is_corresponding":true}],"reference_count":46,"raw_metadata":null,"created_at":"2026-07-19T02:57:40.686992Z","pmid":"40950051","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":[]}