Central to innate immunity is the sensing of pathogen-associated molecular patterns by cytosolic and membrane-associated receptors1,2,3,4. In particular, DNA is a potent activator of immune responses during infection or tissue damage5,6,7, and evidence indicates that, in addition to the membrane-associated Toll-like receptor 9, an unidentified cytosolic DNA sensor(s) can activate type I interferon (IFN) and other immune responses8,9,10. Here we report on a candidate DNA sensor, previously named DLM-1 (also called Z-DNA binding protein 1 (ZBP1))11, for which biological function had remained unknown; we now propose the alternative name DAI (DNA-dependent activator of IFN-regulatory factors12). The artificial expression of otherwise IFN-inducible DAI (DLM-1/ZBP1) in mouse fibroblasts selectively enhances the DNA-mediated induction of type I IFN and other genes involved in innate immunity. On the other hand, RNA interference of messenger RNA for DAI (DLM-1/ZBP1) in cells inhibits this gene induction programme upon stimulation by DNA from various sources. Moreover, DAI (DLM-1/ZBP1) binds to double-stranded DNA and, by doing so, enhances its association with the IRF3 transcription factor and the TBK1 serine/threonine kinase. These observations underscore an integral role of DAI (DLM-1/ZBP1) in the DNA-mediated activation of innate immune responses, and may offer new insight into the signalling mechanisms underlying DNA-associated antimicrobial immunity and autoimmune disorders.
Subscribe to Journal
Get full journal access for 1 year
only $3.90 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Janeway, C. A. & Medzhitov, R. Innate immune recognition. Annu. Rev. Immunol. 20, 197–216 (2002)
Takeda, K., Kaisho, T. & Akira, S. Toll-like receptors. Annu. Rev. Immunol. 21, 335–376 (2003)
Meylan, E., Tschopp, J. & Karin, M. Intracellular pattern recognition receptors in the host response. Nature 442, 39–44 (2006)
Creagh, E. M. & O’Neill, L. A. TLRs, NLRs and RLRs: a trinity of pathogen sensors that co-operate in innate immunity. Trends Immunol. 27, 352–357 (2006)
Krieg, A. M. et al. CpG motifs in bacterial DNA trigger direct B-cell activation. Nature 374, 546–549 (1995)
Tokunaga, T., Yamamoto, T. & Yamamoto, S. How BCG led to the discovery of immunostimulatory DNA. Jpn. J. Infect. Dis. 52, 1–11 (1999)
Ishii, K. J. & Akira, S. Innate immune recognition of, and regulation by, DNA. Trends Immunol. 27, 525–532 (2006)
Hochrein, H. et al. Herpes simplex virus type-1 induces IFN-α production via Toll-like receptor 9-dependent and -independent pathways. Proc. Natl Acad. Sci. USA 101, 11416–11421 (2004)
Ishii, K. J. et al. A Toll-like receptor-independent antiviral response induced by double-stranded B-form DNA. Nature Immunol. 7, 40–48 (2006)
Stetson, D. B. & Medzhitov, R. Recognition of cytosolic DNA activates an IRF3-dependent innate immune response. Immunity 24, 93–103 (2006)
Fu, Y. et al. Cloning of DLM-1, a novel gene that is up-regulated in activated macrophages, using RNA differential display. Gene 240, 157–163 (1999)
Honda, K. & Taniguchi, T. IRFs: master regulators of signalling by Toll-like receptors and cytosolic pattern-recognition receptors. Nature Rev. Immunol. 6, 644–658 (2006)
Napirei, M. et al. Features of systemic lupus erythematosus in Dnase1-deficient mice. Nature Genet. 25, 177–181 (2000)
Yoshida, H., Okabe, Y., Kawane, K., Fukuyama, H. & Nagata, S. Lethal anemia caused by interferon-β produced in mouse embryos carrying undigested DNA. Nature Immunol. 6, 49–56 (2005)
Yoneyama, M. et al. The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses. Nature Immunol. 5, 730–737 (2004)
Kato, H. et al. Differential roles of MDA5 and RIG-I helicases in the recognition of RNA viruses. Nature 441, 101–105 (2006)
Alexopoulou, L., Holt, A. C., Medzhitov, R. & Flavell, R. A. Recognition of double-stranded RNA and activation of NF-κB by Toll-like receptor 3. Nature 413, 732–738 (2001)
Hornung, V. et al. 5′-Triphosphate RNA is the ligand for RIG-I. Science 314, 994–997 (2006)
Pichlmair, A. et al. RIG-I-mediated antiviral responses to single-stranded RNA bearing 5′-phosphates. Science 314, 997–1001 (2006)
Verthelyi, D. & Zeuner, R. A. Differential signaling by CpG DNA in DCs and B cells: not just TLR9. Trends Immunol. 24, 519–522 (2003)
Ha, S. C. et al. Biochemical characterization and preliminary X-ray crystallographic study of the domains of human ZBP1 bound to left-handed Z-DNA. Biochim. Biophys. Acta 1764, 320–323 (2006)
Schwartz, T., Behlke, J., Lowenhaupt, K., Heinemann, U. & Rich, A. Structure of the DLM-1–Z-DNA complex reveals a conserved family of Z-DNA-binding proteins. Nature Struct. Biol. 8, 761–765 (2001)
Rich, A. & Zhang, S. Timeline: Z-DNA: the long road to biological function. Nature Rev. Genet. 4, 566–572 (2003)
Sato, M. et al. Distinct and essential roles of transcription factors IRF-3 and IRF-7 in response to viruses for IFN-α/β gene induction. Immunity 13, 539–548 (2000)
Honda, K. et al. IRF-7 is the master regulator of type-I interferon-dependent immune responses. Nature 434, 772–777 (2005)
Takaoka, A. et al. Integral role of IRF-5 in the gene induction programme activated by Toll-like receptors. Nature 434, 243–249 (2005)
Deigendesch, N., Koch-Nolte, F. & Rothenburg, S. ZBP1 subcellular localization and association with stress granules is controlled by its Z-DNA binding domains. Nucleic Acids Res. 34, 5007–5020 (2006)
Pham, H. T., Park, M. Y., Kim, K. K., Kim, Y. G. & Ahn, J. H. Intracellular localization of human ZBP1: Differential regulation by the Z-DNA binding domain, Zα, in splice variants. Biochem. Biophys. Res. Commun. 348, 145–152 (2006)
Suggs, J. W. & Wagner, R. W. Nuclease recognition of an alternating structure in a d(AT)14 plasmid insert. Nucleic Acids Res. 14, 3703–3716 (1986)
Braun, C. S. et al. The structure of DNA within cationic lipid/DNA complexes. Biophys. J. 84, 1114–1123 (2003)
We thank A. Katoh and M. Kidokoro for the vaccinia virus (MO) genome for ligand stimulation; T. Fujita and M. Yoneyama for RIG-I cDNA; J. Miyazaki for pCAGGS; A. Miyawaki for Venus; R. Kuroda for her support for CD spectrometry; Toray Industries for murine IFN-β; J. V. Ravetch for advice; Y. Fujita, R. Takeda and M. Shishido for technical assistance; and D. Savitsky for critical reading of the manuscript. This work was supported in part by a grant for Advanced Research on Cancer and a Grant-In-Aid for Scientific Research on Priority Areas, and for Scientific Research, from the Ministry of Education, Culture, Sports, Science, and Technology of Japan. Z.W. and H.N. are research fellows of the Japan Society for the Promotion of Science. M.K.C. is a research fellow of the Korea Science and Engineering Foundation.
Author Contributions A.T., Z.W., M.K.C., H.Y., H.N., T.B., Y.L. and T.T. conceived the research, planned experiments and analyses, and largely conducted experiments. K.H. and M.M. helped to design RNAi experimental protocols. T.K. performed microarray experiments and data analysis. Fluorescence microscopy and FRET analysis were conducted by Y.O. T.T. oversaw the entire project.
Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.
About this article
Cite this article
Takaoka, A., Wang, Z., Choi, M. et al. DAI (DLM-1/ZBP1) is a cytosolic DNA sensor and an activator of innate immune response. Nature 448, 501–505 (2007). https://doi.org/10.1038/nature06013
International Journal of Biological Macromolecules (2021)
European Journal of Medicinal Chemistry (2021)
Frontiers in Immunology (2021)