The conserved HDAC Rpd3 drives transcriptional quiescence in S. cerevisiae.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26697386", "kind": "science-record", "revision": 4, "content_hash": "sha256:6ec33f6a0b7cefd484aca6b8fa27297b55ed25b87de609a8c310a600607e6849", "created_at": "2026-11-01T15:40:15Z", "updated_at": "2026-11-01T21:20:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The conserved HDAC Rpd3 drives transcriptional quiescence in S. cerevisiae.", "doi": "10.1016/j.gdata.2015.10.008", "pmid": "26697386", "authors": ["Jeffrey N McKnight", "Toshio Tsukiyama"], "journal": "Genomics data", "year": 2015, "abstract": "Quiescence is a ubiquitous cell cycle stage conserved from microbes through humans and is essential to normal cellular function and response to changing environmental conditions. We recently reported a massive repressive event associated with quiescence in Saccharomyces cerevisiae, where Rpd3 establishes repressive chromatin structure that drives transcriptional shutoff [6]. Here, we describe in detail the experimental procedures, data collection, and data analysis related to our characterization of transcriptional quiescence in budding yeast (GEO: GSE67151). Our results provide a bona fide molecular event driven by widespread changes in chromatin structure through action of Rpd3 that distinguishes quiescence as a unique cell cycle stage in S. cerevisiae.", "claims": [{"id": "claim-method", "statement": "Difference in transcription, H3, acetylation, or Rpd3 binding was determined for different growth conditions and Pearson correlations between relevant variables were determined using R software.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697386", "locator": "sections[9] \"Data analysis\" paragraph 2", "quote": "Difference in transcription, H3, acetylation, or Rpd3 binding was determined for different growth conditions and Pearson correlations between relevant variables were determined using R software."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Direct link to deposited data\nStrand-specific RNA sequencing for wild type and Δrpd3 yeast entering quiescence [RNA-seq].\nhttp://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67149.\nGenome-wide maps of nucleosome positions in purified quiescent S. cerevisiae cells [MNase-seq].\nhttp://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67148.\nCharacterization of H3 density, H3 or H4 acetylation, Rpd3 binding, TFIIB binding, and Rpb3(pol II) binding in wild type and rpd3 cells as they transition from logarithmic growth to diauxid shift to quiescence (ChIP-seq).\nhttp://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67150.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697386", "locator": "sections[2] \"Direct link to deposited data\" paragraphs 1-7", "quote": "Direct link to deposited data\nStrand-specific RNA sequencing for wild type and Δrpd3 yeast entering quiescence [RNA-seq].\nhttp://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67149.\nGenome-wide maps of nucleosome positions in purified quiescent S. cerevisiae cells [MNase-seq].\nhttp://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67148.\nCharacterization of H3 density, H3 or H4 acetylation, Rpd3 binding, TFIIB binding, and Rpb3(pol II) binding in wild type and rpd3 cells as they transition from logarithmic growth to diauxid shift to quiescence (ChIP-seq).\nhttp://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67150."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:26697386"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE67148"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE67148"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26697386", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.10.008", "sha256": 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H4 acetylation, Rpd3 binding, TFIIB binding, and Rpb3(pol II) binding in wild type and rpd3 cells as they transition from logarithmic growth to diauxid shift to quiescence (ChIP-seq).\nhttp://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67150.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1640253", "GSM1640254", "GSM1640255", "GSM1640256"], "sample_count": 4, "group_sizes": null, "group_sizes_basis": null, "platform": "9134", "taxon": "Saccharomyces cerevisiae", "title": "Genome-wide maps of nucleosome positions in purified quiescent S. cerevisiae cells [MNase-Seq]", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE67149", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67149", "sha256": null, 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“diauxic shift cells”), or after Percoll separation of quiescent cells from 7-day stationary phase cultures (“Q” or “quiescent”) [1]. 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