{
  "abstract": "Cell-cycle remodeling is fundamental to pluripotency and lineage commitment, yet whether its transcriptional and post-transcriptional architecture is conserved across species and developmental states has remained unresolved. Here we introduce Ciclopes, a biology-informed deep-learning framework that resolves continuous cell-cycle phase and phase-dependent mRNA transcription and degradation directly from single-cell RNA sequencing. Applying Ciclopes across six mouse and human pluripotent stem-cell systems spanning naive and primed states, we uncover striking divergence in transcriptional complexity and oscillatory control: mouse systems sustain elevated baseline expression of core cell-cycle regulators, while human systems trade higher baseline expression for larger oscillatory amplitude. Strikingly, mRNA degradation timing remain far more conserved across systems than transcription timing, exposing post-transcriptional regulation as a stable evolutionary backbone. As human iPSCs differentiate into definitive endoderm, cells progressively exit the cell cycle, cell-cycle-coupled gene networks contract, and surviving regulators oscillate with larger amplitude. Ciclopes establishes a general framework for dissecting how pluripotent cells tune proliferation across evolutionary and developmental transitions.",
  "abstract_shown": true,
  "affiliations": [
    "Institut de Genetique et de Biologie Moleculaire et Cellulaire"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 8,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "M. K. Nariya"
    },
    {
      "name": "D. Santiago-Algarra"
    },
    {
      "name": "G. Zanardelli"
    },
    {
      "name": "I. K. Boudjelthia"
    },
    {
      "name": "T. Ye"
    },
    {
      "name": "C. Thibault-Carpentier"
    },
    {
      "name": "S. Jarriault"
    },
    {
      "name": "N. Molina"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/5pxhg7vr8xyk3.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.14.751360",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.14.751360v1.full",
  "id": "5pxhg7vr8xyk3",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.14.751360v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "systems biology"
    ],
    [
      "openalex",
      "1312|Pluripotent Stem Cells Research"
    ]
  ],
  "openalex": "W7212876340",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.14.751360v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-14",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/5pxhg7vr8xyk3.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:22:37Z",
      "native_id": "10.64898/2026.09.14.751360",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.14.751360v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:systems biology",
      "subfield": "systems-synthetic"
    }
  ],
  "title": "Comparison of cell-cycle gene expression dynamics and mRNA kinetics across mouse and human pluripotent systems",
  "title_text": "Comparison of cell-cycle gene expression dynamics and mRNA kinetics across mouse and human pluripotent systems",
  "type": "preprint",
  "updated_at": "2026-10-30T12:22:37Z",
  "url": "https://research.draconitic.com/paper/5pxhg7vr8xyk3",
  "venue": "bioRxiv",
  "versions": []
}