{
  "abstract": "Coronaviruses employ discontinuous transcription to produce canonical subgenomic RNAs (sgRNAs) essential for gene expression. Although TRS-dependent template switching mechanism has been proposed, its structural basis remains poorly defined, and the functional significance of abundant non-canonical sgRNAs persists as a critical gap since the discovery of discontinuous RNA synthesis. Here, we help bridge this gap through the first cross-genus integrated analysis of coronavirus transcriptomes and RNA interactomes. We show that canonical sgRNA formation is associated with same-direction RNA-RNA interactions. In contrast, non-canonical sgRNAs form through distinct architectural mechanisms: short-range junctions mediated by stem-loop structures overlapping genomic deletion hotspots, and conserved long-range ORF1a-N interactions generating sgRNAs encoding immune-modulatory ORFs — a function not previously attributed to non-canonical transcription. These findings suggest architecturally programmed discontinuous RNA synthesis and highlight a potential link between non-canonical sgRNAs, genomic plasticity, and immune modulation, which may have implications for coronavirus adaptation.",
  "abstract_shown": true,
  "affiliations": [
    "National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070 China",
    "Hubei Hongshan Laboratory, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, Hubei 430070 China",
    "College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070 China",
    "Yazhou Bay National Laboratory, Sanya, Hainan 572024 China",
    "National Reference Laboratory of Veterinary Drug Residues (HZAU) and National Safety Laboratory of Veterinary Drug (HZAU), MOA Key Laboratory for Detection of Veterinary Drug Residues, MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, Hubei 430070 China",
    "National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, Hubei 430079 China",
    "Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, Hubei 430070 China",
    "Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000 China",
    "Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000 China"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 13,
  "authors": [
    {
      "affs": [
        0,
        1,
        2,
        3
      ],
      "name": "Zi Wen",
      "orcid": "0000-0001-7600-4399"
    },
    {
      "affs": [
        0,
        1,
        4
      ],
      "name": "Lei Chen"
    },
    {
      "affs": [
        0,
        1,
        4
      ],
      "name": "Dehua Luo"
    },
    {
      "affs": [
        0,
        1,
        4
      ],
      "name": "Ju Sun"
    },
    {
      "affs": [
        0,
        1,
        4
      ],
      "name": "Liangrong Guo"
    },
    {
      "affs": [
        0,
        1,
        4
      ],
      "name": "Yingxiang Deng"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Zhiyuan Huang"
    },
    {
      "affs": [
        0,
        1,
        4
      ],
      "name": "Yuxiang Wang"
    },
    {
      "affs": [
        0,
        1,
        4
      ],
      "name": "Ke Pan"
    },
    {
      "affs": [
        5
      ],
      "name": "Fan Wang",
      "orcid": "0000-0003-2664-9214"
    },
    {
      "affs": [
        0
      ],
      "name": "Shaobo Xiao",
      "orcid": "0000-0003-0023-9188"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Li Li",
      "orcid": "0000-0002-9594-8341"
    },
    {
      "affs": [
        0,
        1,
        4,
        6,
        7,
        8
      ],
      "name": "Dengguo Wei",
      "orcid": "0000-0001-9923-789X"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/7db0y36wb31em.bib",
  "cited_by": 0,
  "doi": "10.1038/s44320-026-00239-0",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13728164/",
  "id": "7db0y36wb31em",
  "issns": [
    "1744-4292"
  ],
  "landing_url": "https://doi.org/10.1038/s44320-026-00239-0",
  "language": "en",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Article"
    ],
    [
      "openalex",
      "2725|SARS-CoV-2 and COVID-19 Research"
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  "openalex": "W7171871958",
  "pdf_url": "https://link.springer.com/content/pdf/10.1038/s44320-026-00239-0.pdf",
  "pmcid": "PMC13728164",
  "pmid": "42533184",
  "published": "2026-07-30",
  "publisher": "Nature Publishing Group",
  "ris": "https://research.draconitic.com/paper/7db0y36wb31em.ris",
  "sources": [
    {
      "first_seen": "2026-11-06T12:23:54Z",
      "native_id": "PMC13728164",
      "source": "pmc",
      "url": "https://doi.org/10.1038/s44320-026-00239-0"
    }
  ],
  "subjects": [
    {
      "field": "medicine",
      "origin": "openalex:2725|SARS-CoV-2 and COVID-19 Research",
      "subfield": "infectious-disease"
    }
  ],
  "title": "Cross-genus analysis reveals architecturally programmed sgRNA synthesis patterns in coronaviruses",
  "title_text": "Cross-genus analysis reveals architecturally programmed sgRNA synthesis patterns in coronaviruses",
  "type": "peer-reviewed",
  "updated_at": "2026-11-07T12:21:12Z",
  "url": "https://research.draconitic.com/paper/7db0y36wb31em",
  "venue": "Molecular Systems Biology",
  "versions": []
}