{"doi":"10.1101/2020.07.04.187286","title":"Evolution of DNA Replication Origin Specification and Gene Silencing Mechanisms","abstract":"Abstract DNA replication in eukaryotic cells initiates from chromosomal locations, called replication origins, that bind the Origin Recognition Complex (ORC) prior to S phase. Origin establishment is guided by well-defined DNA sequence motifs in Saccharomyces cerevisiae and some other budding yeasts, but most eukaryotes lack sequence-specific origins. At present, the mechanistic and evolutionary reasons for this difference are unclear. A 3.9 Å structure of S. cerevisiae ORC-Cdc6-Cdt1-Mcm2-7 (OCCM) bound to origin DNA revealed, among other things, that a loop within Orc2 inserts into a DNA minor groove and an α-helix within Orc4 inserts into a DNA major groove 1 . We show that this Orc4 α-helix mediates the sequence-specificity of origins in S. cerevisiae . Specifically, mutations were identified within this α-helix that alter the sequence-dependent activity of individual origins as well as change global genomic origin firing patterns. This was accomplished using a massively parallel origin selection assay analyzed using a custom mutual-information-based modeling approach and a separate analysis of whole-genome replication profiling and statistics. Interestingly, the sequence specificity of DNA replication initiation, as mediated by the Orc4 α-helix, has evolved in close conjunction with the gain of ORC-Sir4-mediated gene silencing and the loss of RNA interference.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":121657,"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":6,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9478,"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":335871,"name":"Ammar Tareen","orcid":null,"position":1,"is_corresponding":false},{"id":335004,"name":"Yi-Jun Sheu","orcid":"0000-0003-1612-5708","position":2,"is_corresponding":false},{"id":300814,"name":"William T. Ireland","orcid":"0000-0003-0971-2904","position":3,"is_corresponding":false},{"id":335005,"name":"Christian Speck","orcid":"0000-0001-6646-1692","position":4,"is_corresponding":false},{"id":236568,"name":"Huilin Li","orcid":"0000-0001-8085-8928","position":5,"is_corresponding":false},{"id":335006,"name":"Leemor Joshua‐Tor","orcid":"0000-0001-8185-8049","position":6,"is_corresponding":false},{"id":16804,"name":"Justin B. Kinney","orcid":"0000-0003-1897-3778","position":7,"is_corresponding":false},{"id":335007,"name":"Bruce Stillman","orcid":"0000-0002-9453-4091","position":8,"is_corresponding":false},{"id":335003,"name":"Yixin Hu","orcid":"0000-0001-9392-8016","position":0,"is_corresponding":true}],"reference_count":53,"raw_metadata":null,"created_at":"2026-07-18T23:14:46.979435Z","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":[]}