{
  "abstract": "Antiviral defense mechanisms are typically activated upon sensing virus-derived nucleic acids. During replication, viruses generate double-stranded RNA (dsRNA) intermediates that the innate immune system can sense, triggering several defense pathways. Conversely, mammalian cells avoid accumulating their own endogenous dsRNA to prevent activating these defense mechanisms. However, we demonstrate that mammalian embryonic stem cells (ESCs) accumulate endogenous dsRNA without activating these responses, as they lack all classical dsRNA-mediated antiviral pathways. To identify these endogenous dsRNAs, we have developed a two-step purification method that includes an antibody-based immunoprecipitation followed by RNase I treatment to remove single-stranded RNA regions that do not contribute to dsRNA formation. RNase I treatment results in an enrichment of overlapping sense/antisense transcripts containing A-to-I editing sites, suggesting successful purification of cellular dsRNA. Our refined protocol reveals that transposable elements (TEs), including evolutionary young elements from the LINE and LTR classes, are the predominant source of dsRNA in ESCs. This approach will be useful for investigating the role of dsRNA in disease settings, such as autoimmunity or cancer, where endogenous dsRNA accumulation has also been observed.",
  "abstract_shown": true,
  "affiliations": [
    "Institute of Immunology and Infection Research, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom",
    "GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada 18016, Spain",
    "Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, Granada 18071, Spain",
    "Department of Computer Languages and Systems, Universitat Jaume I, Castellon de la Plana 12071, Spain",
    "MRC Human Genetics Unit, Institute for Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 7,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Katharina J. Kases",
      "orcid": "0009-0008-3005-7688"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Pilar G. Marchante",
      "orcid": "0009-0000-8206-6860"
    },
    {
      "affs": [
        0
      ],
      "name": "Jeroen Witteveldt",
      "orcid": "0000-0001-8247-7010"
    },
    {
      "affs": [
        1,
        3
      ],
      "name": "Guillermo Peris",
      "orcid": "0000-0003-2010-7844"
    },
    {
      "affs": [
        4
      ],
      "name": "Grzegorz Kudla",
      "orcid": "0000-0002-7924-2744"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Sara R. Heras",
      "orcid": "0000-0003-1677-7685"
    },
    {
      "affs": [
        0
      ],
      "name": "Sara Macias",
      "orcid": "0000-0002-0643-3494"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/ba5yxj34t23e7.bib",
  "cited_by": 0,
  "doi": "10.1261/rna.081048.126",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13674447/",
  "id": "ba5yxj34t23e7",
  "issns": [
    "1355-8382",
    "1469-9001"
  ],
  "landing_url": "https://doi.org/10.1261/rna.081048.126",
  "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",
      "Report"
    ],
    [
      "openalex",
      "1312|RNA regulation and disease"
    ]
  ],
  "openalex": "W7154447361",
  "pdf_url": "http://rnajournal.cshlp.org/content/early/2026/08/28/rna.081048.126.full.pdf",
  "pmcid": "PMC13674447",
  "pmid": "42665368",
  "published": "2026-11-01",
  "publisher": "Cold Spring Harbor Laboratory Press",
  "ris": "https://research.draconitic.com/paper/ba5yxj34t23e7.ris",
  "sources": [
    {
      "first_seen": "2026-11-03T12:23:36Z",
      "native_id": "PMC13674447",
      "source": "pmc",
      "url": "https://doi.org/10.1261/rna.081048.126"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|RNA regulation and disease",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Identification of cellular double-stranded RNAs in mammalian embryonic stem cells",
  "title_text": "Identification of cellular double-stranded RNAs in mammalian embryonic stem cells",
  "type": "peer-reviewed",
  "updated_at": "2026-11-04T12:21:16Z",
  "url": "https://research.draconitic.com/paper/ba5yxj34t23e7",
  "venue": "RNA",
  "versions": []
}