{
  "abstract": "Chimeric RNAs are a class of molecules defined as RNA transcripts containing genetic information for multiple genes. While their expression patterns across tissue types and disease states have been well documented, the biological function of these transcripts remains poorly understood. In this study, we developed an integrative prediction pipeline to establish an atlas of 569,640 chimeric RNAs across 1019 cancer cell lines. Leveraging this resource, we performed a systematic functional dependency screen by integrating our predictions with perturbation datasets from The Cancer Dependency Map project. This approach moves beyond prediction to identifying high-confidence functional chimeric RNAs essential for cellular processes, including a subset of recurrent chimeric transcripts generated by cis-splicing of adjacent genes. We demonstrate that depletion of selected candidate chimeras disrupts cell cycle progression and cellular fitness and that these transcripts are frequently dysregulated in primary breast tumors. Together, these results demonstrate that chimeric RNAs constitute a previously underappreciated layer of gene expression, expanding the functional genome beyond conventional genetics.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.",
    "Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA.",
    "Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China.",
    "State Key Laboratory of Metabolic Dysregulation & Prevention and Treatment of Esophageal Cancer, Tianjian Laboratory of Advanced Biomedical Sciences, School of Convergence Medicine, Zhengzhou University, Zhengzhou 450052, China.",
    "Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA.",
    "Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA.",
    "Center for RNA Science and Medicine, University of Virginia, Charlottesville, VA 22908, USA."
  ],
  "article_type": "Research Article",
  "arxiv": null,
  "author_total": 14,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Samir Lalani",
      "orcid": "0000-0002-4122-7055"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Samuel Haddox"
    },
    {
      "affs": [
        0
      ],
      "name": "Kendall Bromley"
    },
    {
      "affs": [
        1
      ],
      "name": "Shafaque Zahra",
      "orcid": "0000-0002-3697-8065"
    },
    {
      "affs": [
        1
      ],
      "name": "Marina Wang",
      "orcid": "0009-0009-8823-332X"
    },
    {
      "affs": [
        1
      ],
      "name": "Mason Ingram"
    },
    {
      "affs": [
        1
      ],
      "name": "Sehajroop Gadh"
    },
    {
      "affs": [
        1
      ],
      "name": "Shriya Gunalan",
      "orcid": "0009-0005-5361-6620"
    },
    {
      "affs": [
        2
      ],
      "name": "Sulun Ke",
      "orcid": "0009-0000-2630-3462"
    },
    {
      "affs": [
        2
      ],
      "name": "Qiong Wang",
      "orcid": "0000-0003-2564-7778"
    },
    {
      "affs": [
        3
      ],
      "name": "Fujun Qin",
      "orcid": "0000-0003-2337-7137"
    },
    {
      "affs": [
        4
      ],
      "name": "Eric Hendrickson"
    },
    {
      "affs": [
        0
      ],
      "name": "Anja Bielinsky",
      "orcid": "0000-0003-1783-619X"
    },
    {
      "affs": [
        0,
        1,
        5,
        6
      ],
      "name": "Hui Li",
      "orcid": "0000-0002-7879-1792"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/1r0zvgxr198zm.bib",
  "cited_by": 0,
  "doi": "10.1126/sciadv.aei0901",
  "fulltext_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13721984/?tool=EBI",
  "id": "1r0zvgxr198zm",
  "issns": [
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  "landing_url": "https://www.science.org/doi/abs/10.1126/sciadv.aei0901",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Biomedicine and Life Sciences"
    ],
    [
      "heading",
      "Cancer"
    ],
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      "heading",
      "Molecular Biology"
    ],
    [
      "heading",
      "Research Article"
    ],
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      "heading",
      "SciAdv r-articles"
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  "openalex": null,
  "pdf_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13721984/pdf/?tool=EBI",
  "pmcid": "PMC13721984",
  "pmid": "42962001",
  "published": "2026-10-30",
  "publisher": "American Association for the Advancement of Science (AAAS)",
  "ris": "https://research.draconitic.com/paper/1r0zvgxr198zm.ris",
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  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "heading:Molecular Biology",
      "subfield": "molecular-biology"
    },
    {
      "field": "medicine",
      "origin": "heading:Cancer",
      "subfield": "oncology"
    }
  ],
  "title": "Integrative discovery and functional dependency mapping uncover essential chimeric RNAs in the active transcriptome",
  "title_text": "Integrative discovery and functional dependency mapping uncover essential chimeric RNAs in the active transcriptome",
  "type": "peer-reviewed",
  "updated_at": "2026-11-03T12:22:34Z",
  "url": "https://research.draconitic.com/paper/1r0zvgxr198zm",
  "venue": "Science Advances",
  "versions": []
}