RNA: DNA hybrids are a novel molecular pattern sensed by TLR9

Rachel E. Rigby, Lauren M. Webb, Karen J. Mackenzie, Yue Li, Andrea Leitch, Martin A M Reijns, Rachel J. Lundie, Ailsa Revuelta, Donald J. Davidson, Sandra Diebold, Yorgo Modis, Andrew S. MacDonald, Andrew P Jackson

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The sensing of nucleic acids by receptors of the innate immune system is a key component of antimicrobial immunity. RNA:DNA hybrids, as essential intracellular replication intermediates generated during infection, could therefore represent a class of previously uncharacterised pathogen-associated molecular patterns sensed by pattern recognition receptors. Here we establish that RNA:DNA hybrids containing viral-derived sequences efficiently induce pro-inflammatory cytokine and antiviral type I interferon production in dendritic cells. We demonstrate that MyD88-dependent signalling is essential for this cytokine response and identify TLR9 as a specific sensor of RNA:DNA hybrids. Hybrids therefore represent a novel molecular pattern sensed by the innate immune system and so could play an important role in host response to viruses and the pathogenesis of autoimmune disease. Synopsis Nucleic acids are potent ligands for the pattern recognition receptors of the innate immune system. In this work, RNA:DNA hybrids are established to be a novel class of immunostimulatory nucleic acid, binding and activating intracellular TLR9 in dendritic cells. TLR9 may therefore have a wider role in host response to microbial infection, including the sensing of RNA:DNA hybrid replication intermediates. RNA:DNA hybrids are a novel class of pattern recognition receptor ligand. RNA:DNA hybrids are detectable in cytoplasmic and endosomal fractions during retroviral infection. TLR9 is an intracellular sensor of RNA:DNA hybrids, binding with high affinity. As TLR9 senses both RNA:DNA hybrids and DNA, PRRs are not always restricted to detecting one type of nucleic acid. TLR9, classically known as cytokine-inducing sensor of bacterial DNA, gains an additional role in detecting RNA:DNA hybrids containing virus-derived sequences, making them a novel type of pathogen-associated molecular pattern.

Original languageEnglish
Pages (from-to)542-558
Number of pages17
JournalThe EMBO Journal
Issue number6
Publication statusPublished - 18 Mar 2014
Externally publishedYes


  • innate immune signalling
  • pathogen-associated molecular pattern
  • RNA:DNA hybrid
  • TLR9

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