{
  "abstract": "Regulatory evolution can alter phenotypes, but cis- and trans-regulatory mechanisms may also diverge extensively while total transcript abundance remains stable. Comparisons of parental expression with allele-specific expression in F1 hybrids provide a framework for separating cis- and trans-regulatory effects because both parental alleles are measured in a shared trans-regulatory environment. Here, we analyzed RNA sequencing data from Saccharomyces cerevisiae, S. paradoxus, and their F1 hybrid. Among the 4,164 genes with sufficient allele-specific support for strict classification, 2,134 (51.2%) showed detectable cis- and/or trans-regulatory divergence. However, hybrid expression remained largely conserved, with 81.5% of genes not significantly different from either parent. Compensatory cis–trans divergence predominated over reinforcing divergence; cross-replicate estimation reduced the apparent magnitude of this excess, but opposite-sign effects remained predominant in all 20 nonoverlapping replicate comparisons. To connect gene expression to genome sequence, we analyzed the strongly cis-diverged locus LYS2 and found species differences in promoter architecture, including an S. cerevisiae-specific AT-rich insertion, altered spacing among candidate regulatory features, and a promoter-proximal TATA-like element unique to S. cerevisiae. Sequence-based nucleosome prediction suggests that these differences create a broader promoter-proximal nucleosome-depleted region in S. cerevisiae than in S. paradoxus. We also quantified allele-resolved intron retention and found that it was broadly conserved, with only rare locus-specific hybrid-associated shifts. Together, these results show that regulatory divergence is widespread but often buffered in the hybrid, whereas intron-retention divergence is comparatively limited.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "name": "Danithza S Rojas",
      "orcid": "0009-0007-5834-3013"
    },
    {
      "name": "Gregory I Lang",
      "orcid": "0000-0002-7931-0428"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/8t9c1skv1syct.bib",
  "cited_by": 1,
  "doi": "10.1093/genetics/iyag233",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13732737/",
  "id": "8t9c1skv1syct",
  "issns": [
    "0016-6731",
    "1943-2631"
  ],
  "landing_url": "https://doi.org/10.1093/genetics/iyag233",
  "language": "en",
  "licence": "CC-BY-NC-ND-4.0",
  "licence_label": "CC BY-NC-ND 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "AcademicSubjects/SCI01140"
    ],
    [
      "heading",
      "AcademicSubjects/SCI01180"
    ],
    [
      "heading",
      "Investigation"
    ],
    [
      "openalex",
      "1312|Fungal and yeast genetics research"
    ]
  ],
  "openalex": "W7204838865",
  "pdf_url": "https://academic.oup.com/genetics/advance-article-pdf/doi/10.1093/genetics/iyag233/70878875/iyag233.pdf",
  "pmcid": "PMC13732737",
  "pmid": "42671011",
  "published": "2026-08-31",
  "publisher": "Oxford University Press",
  "ris": "https://research.draconitic.com/paper/8t9c1skv1syct.ris",
  "sources": [
    {
      "first_seen": "2026-11-08T12:22:40Z",
      "native_id": "PMC13732737",
      "source": "pmc",
      "url": "https://doi.org/10.1093/genetics/iyag233"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Fungal and yeast genetics research",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Gene expression is stable despite widespread cis and trans regulatory divergence in Saccharomyces yeasts",
  "title_text": "Gene expression is stable despite widespread cis and trans regulatory divergence in Saccharomyces yeasts",
  "type": "peer-reviewed",
  "updated_at": "2026-11-08T12:22:40Z",
  "url": "https://research.draconitic.com/paper/8t9c1skv1syct",
  "venue": "Genetics",
  "versions": []
}