McNab, F., Mayer-Barber, K., Sher, A., Wack, A. & O’Garra, A. Type I interferons in infectious disease. Nat. Rev. Immunol. 15, 87–103 (2015).
Liu, S. et al. Phosphorylation of innate immune adaptor proteins MAVS, STING, and TRIF induces IRF3 activation. Science 347, aaa2630 (2015).
Long, L. et al. Recruitment of phosphatase PP2A by RACK1 adaptor protein deactivates transcription factor IRF3 and limits type I interferon signaling. Immunity 40, 515–529 (2014).
Yu, Y. & Hayward, G. S. The ubiquitin E3 ligase RAUL negatively regulates type I interferon through ubiquitination of the transcription factors IRF7 and IRF3. Immunity 33, 863–877 (2010).
Wang, P., Zhao, W., Zhao, K., Zhang, L. & Gao, C. TRIM26 negatively regulates interferon-β production and antiviral response through polyubiquitination and degradation of nuclear IRF3. PLoS Pathog. 11, e1004726 (2015).
Higgs, R. et al. The E3 ubiquitin ligase Ro52 negatively regulates IFN-β production post-pathogen recognition by polyubiquitin-mediated degradation of IRF3. J. Immunol. 181, 1780–1786 (2008).
Bibeau-Poirier, A. et al. Involvement of the IκB kinase (IKK)-related kinases tank-binding kinase 1/IKKi and Cullin-based ubiquitin ligases in IFN regulatory factor-3 degradation. J. Immunol. 177, 5059–5067 (2006).
Xie, W. et al. OTUD7B deubiquitinates SQSTM1/p62 and promotes IRF3 degradation to regulate antiviral immunity. Autophagy 18, 2288–2302 (2022).
Wu, Y. et al. Selective autophagy controls the stability of transcription factor IRF3 to balance type I interferon production and immune suppression. Autophagy 17, 1379–1392 (2021).
Kimura, T. et al. TRIM-mediated precision autophagy targets cytoplasmic regulators of innate immunity. J. Cell Biol. 210, 973–989 (2015).
Zhang, M. et al. Negative feedback regulation of cellular antiviral signaling by RBCK1-mediated degradation of IRF3. Cell Res. 18, 1096–1104 (2008).
Zhao, X. et al. c-Cbl-mediated ubiquitination of IRF3 negatively regulates IFN-β production and cellular antiviral response. Cell Signal. 28, 1683–1693 (2016).
Saitoh, T. et al. Negative regulation of interferon-regulatory factor 3-dependent innate antiviral response by the prolyl isomerase Pin1. Nat. Immunol. 7, 598–605 (2006).
Lei, C. Q. et al. FoxO1 negatively regulates cellular antiviral response by promoting degradation of IRF3. J. Biol. Chem. 288, 12596–12604 (2013).
Jiang, L. Q. et al. IFITM3 inhibits virus-triggered induction of type I interferon by mediating autophagosome-dependent degradation of IRF3. Cell Mol. Immunol. 15, 858–867 (2018).
Cadwell, K. Crosstalk between autophagy and inflammatory signalling pathways: balancing defence and homeostasis. Nat. Rev. Immunol. 16, 661–675 (2016).
Hedglin, M. & Benkovic, S. J. Regulation of Rad6/Rad18 activity during DNA damage tolerance. Annu. Rev. Biophys. 44, 207–228 (2015).
Huang, J. et al. RAD18 transmits DNA damage signalling to elicit homologous recombination repair. Nat. Cell Biol. 11, 592–603 (2009).
Panne, D., Maniatis, T. & Harrison, S. C. Crystal structure of ATF-2/c-Jun and IRF-3 bound to the interferon-β enhancer. EMBO J. 23, 4384–4393 (2004).
Zhu, M., Fang, T., Li, S., Meng, K. & Guo, D. Bipartite nuclear localization signal controls nuclear import and DNA-binding activity of IFN regulatory factor 3. J. Immunol. 195, 289–297 (2015).
Carty, M., Guy, C. & Bowie, A. G. Detection of viral infections by innate immunity. Biochem. Pharmacol. 183, 114316 (2021).
Yoneyama, M. et al. Direct triggering of the type I interferon system by virus infection: activation of a transcription factor complex containing IRF-3 and CBP/p300. EMBO J. 17, 1087–1095 (1998).
Yan, S. et al. IRF3 reduces adipose thermogenesis via ISG15-mediated reprogramming of glycolysis. J. Clin. Invest. 131, e144888 (2021).
Honda, K. & Taniguchi, T. IRFs: master regulators of signalling by Toll-like receptors and cytosolic pattern-recognition receptors. Nat. Rev. Immunol. 6, 644–658 (2006).
Ning, S., Huye, L. E. & Pagano, J. S. Regulation of the transcriptional activity of the IRF7 promoter by a pathway independent of interferon signaling. J. Biol. Chem. 280, 12262–12270 (2005).
Molle, C. et al. IL-27 synthesis induced by TLR ligation critically depends on IFN regulatory factor 3. J. Immunol. 178, 7607–7615 (2007).
Korzus, E. et al. Transcription factor-specific requirements for coactivators and their acetyltransferase functions. Science 279, 703–707 (1998).
Honda, K. et al. IRF-7 is the master regulator of type-I interferon-dependent immune responses. Nature 434, 772–777 (2005).
Yanai, H. et al. Role of IFN regulatory factor 5 transcription factor in antiviral immunity and tumor suppression. Proc. Natl Acad. Sci. USA 104, 3402–3407 (2007).
Zaffagnini, G. & Martens, S. Mechanisms of selective autophagy. J. Mol. Biol. 428, 1714–1724 (2016).
Hong, N. et al. Evaluation of ocular symptoms and tropism of SARS-CoV-2 in patients confirmed with COVID-19. Acta Ophthalmol. 98, e649–e655 (2020).
Wang, H (ed.). Diagnosis and treatment protocol for COVID-19 patients (tentative 9th version). Infect. Dis. Immun. 2, 135–144 (2022).
Hrecka, K. et al. VPX relieves inhibition of HIV-1 infection of macrophages mediated by the SAMHD1 protein. Nature 474, 658–661 (2011).
Yao, H. et al. Molecular architecture of the SARS-CoV-2 virus. Cell 183, 730–738 (2020).
Sormani, M. P. & De Stefano, N. Defining and scoring response to IFN-β in multiple sclerosis. Nat. Rev. Neurol. 9, 504–512 (2013).
Banchereau, J. & Pascual, V. Type I interferon in systemic lupus erythematosus and other autoimmune diseases. Immunity 25, 383–392 (2006).
Santana-de Anda, K. et al. Interferon regulatory factor 3 as key element of the interferon signature in plasmacytoid dendritic cells from systemic lupus erythematosus patients: novel genetic associations in the Mexican mestizo population. Clin. Exp. Immunol. 178, 428–437 (2014).
Smith, S. et al. Enhanced interferon regulatory factor 3 binding to the interleukin-23p19 promoter correlates with enhanced interleukin-23 expression in systemic lupus erythematosus. Arthritis Rheum. 64, 1601–1609 (2012).
Geng, F., Wenzel, S. & Tansey, W. P. Ubiquitin and proteasomes in transcription. Annu. Rev. Biochem. 81, 177–201 (2012).
Lipford, J. R. & Deshaies, R. J. Diverse roles for ubiquitin-dependent proteolysis in transcriptional activation. Nat. Cell Biol. 5, 845–850 (2003).
von der Lehr, N. et al. The F-box protein Skp2 participates in c-Myc proteosomal degradation and acts as a cofactor for c-Myc-regulated transcription. Mol. Cell 11, 1189–1200 (2003).
Reid, G. et al. Cyclic, proteasome-mediated turnover of unliganded and liganded ERα on responsive promoters is an integral feature of estrogen signaling. Mol. Cell 11, 695–707 (2003).
Venuprasad, K. et al. The E3 ubiquitin ligase Itch regulates expression of transcription factor Foxp3 and airway inflammation by enhancing the function of transcription factor TIEG1. Nat. Immunol. 9, 245–253 (2008).
Muratani, M. & Tansey, W. P. How the ubiquitin–proteasome system controls transcription. Nat. Rev. Mol. Cell Biol. 4, 192–201 (2003).
Wilcox, A. J. & Laney, J. D. A ubiquitin-selective AAA-ATPase mediates transcriptional switching by remodelling a repressor–promoter DNA complex. Nat. Cell Biol. 11, 1481–1486 (2009).
Han, J. H., Jang, K. W. & Myung, C. S. Garcinia cambogia attenuates adipogenesis by affecting CEBPB and SQSTM1/p62-mediated selective autophagic degradation of KLF3 through RPS6KA1 and STAT3 suppression. Autophagy 18, 518–539 (2022).
Shao, T. et al. Autophagy regulates differentiation of ovarian granulosa cells through degradation of WT1. Autophagy 18, 1864–1878 (2022).
Chang, C. P., Su, Y. C., Lee, P. H. & Lei, H. Y. Targeting NFκB by autophagy to polarize hepatoma-associated macrophage differentiation. Autophagy 9, 619–621 (2013).
Hochberg, M. C. Updating the American College of Rheumatology revised criteria for the classification of systemic lupus erythematosus. Arthritis Rheum. 40, 1725 (1997).
Uribe, A. G. The Systemic Lupus Activity Measure-revised, the Mexican Systemic Lupus Erythematosus Disease Activity Index (SLEDAI), and a modified SLEDAI-2K are adequate instruments to measure disease activity in systemic lupus erythematosus. J. Rheumatol. 31, 1934–1940 (2004).
Huang, J. et al. Autophagy facilitates age—related cell apoptosis-a new insight from senile cataract. Cell Death Dis. 13, 37 (2022).
