{
  "abstract": "Eukaryotic mRNA 3' UTRs encode regulatory information that shapes post-transcriptional control, RNA fate and gene expression. However, a 3' UTR-specific foundation model that spans broad eukaryotic sequence diversity while supporting both functional prediction and sequence design is lacking. Here we present EukaUTR, a 3' UTR-specific foundation model trained on a large-scale eukaryotic 3' UTR sequence corpus spanning diverse evolutionary lineages. Across 13 prediction tasks spanning post-transcriptional regulation, RNA fate and expression output, EukaUTR models matched or exceeded the strongest external baselines on nearly all tasks, with relative improvements of up to 27.45%. EukaUTR also generated de novo 3' UTRs with natural-like sequence and regulatory properties. EukaUTR-Guide further derived stability-associated signals from small sequence sets to guide editing towards enhanced predicted stability. Together, EukaUTR provides a sequence-to-function-to-design framework for transferable 3' UTR modelling and design.",
  "abstract_shown": true,
  "affiliations": [
    "Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 9,
  "authors": [
    {
      "name": "M. lang"
    },
    {
      "name": "X. Fang"
    },
    {
      "name": "M. Chen"
    },
    {
      "name": "Z. Wang"
    },
    {
      "name": "Z. Cheng"
    },
    {
      "name": "X. Zhu"
    },
    {
      "name": "K. Y. Tam"
    },
    {
      "name": "J. Zhang"
    },
    {
      "affs": [
        0
      ],
      "name": "X. Li"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/03efefc895b6v.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.07.749809",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.07.749809v1.full",
  "id": "03efefc895b6v",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.07.749809v1",
  "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",
      "bioinformatics"
    ],
    [
      "openalex",
      "1312|RNA Research and Splicing"
    ]
  ],
  "openalex": "W7212074799",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.07.749809v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-07",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/03efefc895b6v.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:20:25Z",
      "native_id": "10.64898/2026.09.07.749809",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.07.749809v2"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "EukaUTR: a foundation model for functional modelling and design of eukaryotic 3' UTRs",
  "title_text": "EukaUTR: a foundation model for functional modelling and design of eukaryotic 3' UTRs",
  "type": "preprint",
  "updated_at": "2026-10-30T12:21:10Z",
  "url": "https://research.draconitic.com/paper/03efefc895b6v",
  "venue": "bioRxiv",
  "versions": []
}