{"doi":"10.1186/gb-2012-13-4-r27","title":"Genome-wide identification and characterization of replication origins by deep sequencing","abstract":"<h4>Background</h4>DNA replication initiates at distinct origins in eukaryotic genomes, but the genomic features that define these sites are not well understood.<h4>Results</h4>We have taken a combined experimental and bioinformatic approach to identify and characterize origins of replication in three distantly related fission yeasts: Schizosaccharomyces pombe, Schizosaccharomyces octosporus and Schizosaccharomyces japonicus. Using single-molecule deep sequencing to construct amplification-free high-resolution replication profiles, we located origins and identified sequence motifs that predict origin function. We then mapped nucleosome occupancy by deep sequencing of mononucleosomal DNA from the corresponding species, finding that origins tend to occupy nucleosome-depleted regions.<h4>Conclusions</h4>The sequences that specify origins are evolutionarily plastic, with low complexity nucleosome-excluding sequences functioning in S. pombe and S. octosporus, and binding sites for trans-acting nucleosome-excluding proteins functioning in S. japonicus. Furthermore, chromosome-scale variation in replication timing is conserved independently of origin location and via a mechanism distinct from known heterochromatic effects on origin function. These results are consistent with a model in which origins are simply the nucleosome-depleted regions of the genome with the highest affinity for the origin recognition complex. This approach provides a general strategy for understanding the mechanisms that define DNA replication origins in eukaryotes.","journal":"Genome Biology","year":2012,"id":3985,"datarank":3.9373434725447405,"base_score":4.61512051684126,"endowment":4.61512051684126,"self_citation_contribution":0.692268077526189,"citation_network_contribution":3.2450753950185516,"self_endowment_contribution":0.692268077526189,"citer_contribution":3.2450753950185516,"corpus_percentile":null,"corpus_rank":null,"citation_count":100,"citer_count":92,"citers_with_citation_signal":76,"citers_with_endowment":76,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.084,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2012-04-24","fair_score":12.5,"fair_percentile":0.15391380826737028,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":37163,"name":"Yoshimi Yanagisawa","orcid":null,"position":1,"is_corresponding":false},{"id":12171,"name":"Alexander M. 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Milos","orcid":null,"position":17,"is_corresponding":false},{"id":34450,"name":"Nick Rhind","orcid":"0000-0003-1758-7736","position":18,"is_corresponding":false},{"id":39978,"name":"Jia Xu","orcid":"0000-0003-3921-018X","position":0,"is_corresponding":true}],"reference_count":55,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","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":20.0,"fair_a":30.0,"fair_i":0.0,"fair_r":0.0,"fair_zscore":-2.9589,"fair_rationale":{"fair_score":12.5,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":20.0,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"datacite=0, pmcid=False, pmid=False","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null},{"key":"f_metadata_richness","label":"Rich, machine-readable metadata","kind":"llm","weight":1.0,"fraction":0.0,"signal":null,"rationale":"No mention of machine-readable metadata, data formats, or metadata standards."}]},"A":{"name":"Accessible","score":30.0,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"Open Access","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"0 OA location(s)","rationale":null},{"key":"a_access_protocol","label":"Clear data/code access protocol","kind":"llm","weight":1.0,"fraction":0.0,"signal":null,"rationale":"No protocol for accessing data or code is provided; no repository or download link is stated."}]},"I":{"name":"Interoperable","score":0.0,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":0.0,"signal":null,"rationale":"No use of standard formats, vocabularies, or persistent identifiers is described."}]},"R":{"name":"Reusable","score":0.0,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"not a dataset","rationale":null},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":0.0,"signal":null,"rationale":"No data-availability statement, license, or reproducibility details are given."}]}},"suggestions":["Deposit raw and processed sequencing data in a public repository (e.g., GEO, SRA) and cite the accession numbers.","Provide analysis scripts and software used in a public code repository (e.g., GitHub) with a clear license.","Include a data availability statement in the paper specifying where data and code can be accessed.","Use standard file formats (e.g., BAM, BED, FASTA) and controlled vocabularies (e.g., SO, GO) for interoperability.","Assign persistent identifiers (e.g., DOIs) to datasets and code, and reference them in the paper."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v1","fulltext_source":"abstract_only"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v1","fair_fulltext_source":"abstract_only","fair_has_llm":true,"fair_computed_at":"2026-06-14T20:28:58.528115Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}