{
  "abstract": "Understanding how T. gondii builds an invasion-competent cell has been limited by its rapid, asynchronous division cycle, incomplete gene function annotation, and studies that have examined one regulator or complex at a time. Here, we placed acute perturbation of 21 transcriptional and epigenetic factors, promoter occupancy, chromatin accessibility, and molecular validation on a common single-cell clock. The resulting consensus map links the lytic-cycle programs to candidate activating and repressive inputs, organizes genes into 108 co-regulated communities, and nominates regulatory partnerships that would not have emerged from any single data type. The work bridges three longstanding gaps: it resolves perturbation responses in cell-cycle time, distinguishes promoter occupancy from perturbation-linked regulation, and turns a large multidimensional dataset into an experimentally navigable map. We indeed confirmed known factor interactions such as MORC/HDAC3 and recovered combinations such as the Cdc5/SNIP1 and DMAP1/EPL1 as coregulatory nodes (that in other systems have been described to cooperate). Furthermore, we discovered a novel apicomplexan specific combination of AAF1/AP2XI-5 that provides mechanistic insights of the unique AP2 transcription factor family.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 18,
  "authors": [
    {
      "name": "Yihan Wu",
      "orcid": "0009-0005-0155-8887"
    },
    {
      "name": "Argenis A. Arriojas",
      "orcid": "0000-0002-0479-1300"
    },
    {
      "name": "Nachiket Shankar",
      "orcid": "0009-0004-9785-3997"
    },
    {
      "name": "Shalini Aggarwal",
      "orcid": "0000-0002-5951-2102"
    },
    {
      "name": "Jingjing Lou",
      "orcid": "0000-0002-3304-454X"
    },
    {
      "name": "Prarthana Prathap"
    },
    {
      "name": "Shreya Dua",
      "orcid": "0009-0006-1801-3805"
    },
    {
      "name": "Gretchen M. Diffendall",
      "orcid": "0000-0002-0783-517X"
    },
    {
      "name": "Jiahong Li",
      "orcid": "0000-0002-9687-0101"
    },
    {
      "name": "Pamodya Pamunuwa",
      "orcid": "0000-0002-1045-3308"
    },
    {
      "name": "Prince Oppong",
      "orcid": "0009-0009-4147-1611"
    },
    {
      "name": "Omar Graia",
      "orcid": "0009-0004-8115-1501"
    },
    {
      "name": "Lee Sarah Izhaki-Tavor",
      "orcid": "0000-0002-7520-7984"
    },
    {
      "name": "Eranthie Weerapana",
      "orcid": "0000-0002-0835-8301"
    },
    {
      "name": "Mélissa Léger-Abraham",
      "orcid": "0000-0001-9374-0718"
    },
    {
      "name": "Manoj T. Duraisingh",
      "orcid": "0000-0001-8534-5515"
    },
    {
      "name": "Kourosh Zarringhalam",
      "orcid": "0000-0002-5108-8108"
    },
    {
      "name": "Marc-Jan Gubbels",
      "orcid": "0000-0002-2769-8600"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/d50q8f5m9t84j.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.29.762658",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.29.762658v1.full",
  "id": "d50q8f5m9t84j",
  "issns": [
    "2692-8205"
  ],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.29.762658v1",
  "language": "en",
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "microbiology"
    ],
    [
      "heading",
      "Article"
    ]
  ],
  "openalex": null,
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.29.762658v1.full.pdf",
  "pmcid": "PMC13734140",
  "pmid": "42990604",
  "published": "2026-10-29",
  "publisher": "Cold Spring Harbor Laboratory Preprints",
  "ris": "https://research.draconitic.com/paper/d50q8f5m9t84j.ris",
  "sources": [
    {
      "first_seen": "2026-10-31T00:21:20Z",
      "native_id": "10.64898/2026.10.29.762658",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.29.762658v1"
    },
    {
      "first_seen": "2026-11-08T12:23:46Z",
      "native_id": "PMC13734140",
      "source": "pmc",
      "url": "https://doi.org/10.64898/2026.10.29.762658"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:microbiology",
      "subfield": "microbiology"
    }
  ],
  "title": "A MultiOmics time-resolved systems map of gene regulation in Toxoplasma gondii",
  "title_text": "A MultiOmics time-resolved systems map of gene regulation in Toxoplasma gondii",
  "type": "preprint",
  "updated_at": "2026-11-08T12:23:46Z",
  "url": "https://research.draconitic.com/paper/d50q8f5m9t84j",
  "venue": "bioRxiv",
  "versions": []
}