{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T11:11:58Z","timestamp":1785409918241,"version":"3.56.0"},"reference-count":47,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T00:00:00Z","timestamp":1784764800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon Europe research and innovation program through the A4L_BRIDGE project","award":["101136453"],"award-info":[{"award-number":["101136453"]}]},{"name":"Biomedical Research Center, Slovak Academy of Sciences"},{"id":[{"id":"https:\/\/ror.org\/03h7qq074","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antioxidants"],"abstract":"<jats:p>The yeast metabolic cycle (YMC) in Saccharomyces cerevisiae provides a tractable model for examining how mitochondrial respiration, redox timing, and metabolic phase shape transcriptome abundance and fidelity. Ribosomal-RNA-depleted whole-transcriptome RNA sequencing (WRS) and RNA-seq-derived mismatch analyses were performed across low-dissolved-oxygen (Low-DO)\/high-respiration and high-dissolved-oxygen (High-DO)\/lower-respiration phases. Among 1505 phase-differentially expressed genes, Low DO was enriched for ribosome biogenesis, rRNA processing, translation, sulfur metabolism, and protein synthesis, whereas High DO was enriched for oxidant detoxification, oxidoreductase activity, and redox-buffering-related pathways. Generalized linear mixed models identified a substitution-class-dependent Low-DO-associated RNA-seq mismatch response. The strongest mismatch-level increase occurred in the collapsed C &gt; T\/G &gt; A-compatible class, whereas C &gt; A\/G &gt; T did not increase. This pattern was not consistent with a simple single-lesion model and instead supported a mixed Low-DO-associated RNA-seq sequence-discordance landscape. Variant-rate modeling additionally detected T &gt; C\/A &gt; G and T &gt; A\/A &gt; T increases, indicating that multiple biological and technical processes may contribute to the observed spectrum. Recurrence analysis showed that most called variants were sample-specific, supporting a transient RNA-seq mismatch landscape rather than stable DNA mutation. These findings establish the YMC as a reductionist eukaryotic framework for studying how metabolic phase and redox state shape transcriptome fidelity.<\/jats:p>","DOI":"10.3390\/antiox15080914","type":"journal-article","created":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T09:11:26Z","timestamp":1784797886000},"page":"914","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The Yeast Metabolic Cycle as a Tractable Cellular Framework for Redox Timing, Redox Buffering, and Transcriptome Fidelity"],"prefix":"10.3390","volume":"15","author":[{"given":"Ondrej","family":"Pre\u0165o","sequence":"first","affiliation":[{"name":"Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3398-2093","authenticated-orcid":false,"given":"Bogdan","family":"Iaparov","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Friedemann","family":"Freund","sequence":"additional","affiliation":[{"name":"SETI Institute, Mountain View, CA 94043, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8310-681X","authenticated-orcid":false,"given":"Miloslav","family":"Karhanek","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Viktor","family":"Stolc","sequence":"additional","affiliation":[{"name":"SETI Institute, Mountain View, CA 94043, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1007\/s42764-020-00021-y","article-title":"The impact of transcription-mediated replication stress on genome instability and human disease","volume":"1","author":"Gnan","year":"2020","journal-title":"Genome Instab. 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