Skip to content
DraconiticResearch
Search Sources API
197,768 studies31 sourcesUpdated 12 min ago
Peer-reviewedCC BY 4.0RNA

Identification of cellular double-stranded RNAs in mammalian embryonic stem cells

  • Katharina J. Kases1
  • Pilar G. Marchante2,3
  • Jeroen Witteveldt1
  • Guillermo Peris2,4
  • Grzegorz Kudla5
  • Sara R. Heras2,3
  • Sara Macias1
5 affiliations
  1. 1Institute of Immunology and Infection Research, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
  2. 2GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada 18016, Spain
  3. 3Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, Granada 18071, Spain
  4. 4Department of Computer Languages and Systems, Universitat Jaume I, Castellon de la Plana 12071, Spain
  5. 5MRC Human Genetics Unit, Institute for Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
Read full textPDFDOICite

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.

Related

  1. RNA self-association limits the removal of double-stranded RNA by affinity chromatography
    N. E. Clark, H. Mallory, C. J. Ndong +10
    bioRxivPreprintAll rights reservedFull textMolecular biology & gene regulationbioRxiv
  2. Enhancing double-duplex invasion by using multiple parallel-stranded peptide nucleic acids
    Masanari Shibata, Kota Ito, Osami Shoji +1
    ChemRxivPreprintCC BYFull textMolecular biology & gene regulationChemRxiv
  3. AI-driven structural informatics reveals diverse glycosylation machinery across double-stranded DNA viruses
    Lan Na
    arXivPreprintCC BY 4.0Full textBiophysicsarXiv
  4. Double-Stranded RNA Profiling with Mass Photometry
    M. J. Ranaghan, N. E. Clark, K. Fay +4
    bioRxivPreprintCC BYFull textBiophysicsbioRxiv
  5. A superfamily 1 helicase translocates on double-stranded DNA
    S. Pangeni, A. M. Nakara, O. Yang +3
    bioRxivPreprintCC BY-NCFull textBiophysicsbioRxiv

Cite

BibTeXRIS
BibTeX
@article{kases2026identification,
  title = {{Identification of cellular double-stranded RNAs in mammalian embryonic stem cells}},
  author = {Katharina J. Kases and Pilar G. Marchante and Jeroen Witteveldt and Guillermo Peris and Grzegorz Kudla and Sara R. Heras and Sara Macias},
  journal = {RNA},
  year = {2026},
  month = nov,
  doi = {10.1261/rna.081048.126},
  url = {https://doi.org/10.1261/rna.081048.126},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Identification of cellular double-stranded RNAs in mammalian embryonic stem cells
AU  - Katharina J. Kases
AU  - Pilar G. Marchante
AU  - Jeroen Witteveldt
AU  - Guillermo Peris
AU  - Grzegorz Kudla
AU  - Sara R. Heras
AU  - Sara Macias
PY  - 2026
DA  - 2026/11/01
JO  - RNA
DO  - 10.1261/rna.081048.126
UR  - https://doi.org/10.1261/rna.081048.126
AB  - 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.
SN  - 1355-8382
SN  - 1469-9001
ER  -