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 > T/G > A-compatible class, whereas C > A/G > 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 > C/A > G and T > A/A > 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.

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Preťo O, Iaparov B, Freund F, Karhanek M, Stolc V

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