biostudies-literatureCui DConsejo Nacional de Ciencia y Tecnología, Paraguay (CONACYT)Georgia State University (GSU)NIAID NIH HHSHHS | NIH | National Institute of Allergy and Infectious DiseasesConsejo Nacional de Ciencia y Tecnología, ParaguayGeorgia State UniversityHHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)e0104021https://www.ebi.ac.uk/biostudies/studies/S-EPMC8549515biostudies-literatureUnknown95(22)We previously identified a subset of interferon-stimulated genes (ISGs) upregulated by West Nile virus (WNV) infection in wild-type mouse embryo fibroblasts (MEFs) after viral proteins had inhibited type I interferon (IFN)-mediated JAK-STAT signaling and also in WNV-infected RIG-I^-/-, MDA5^-/-, STAT1^-/-, STAT2^-/-, IFNAR^-/-, IRF3^-/-, IRF7^-/-, and IRF3/7^-/- MEFs. In this study, ISG upregulation by WNV infection in IFNAR^-/- MEFs was confirmed by transcriptome sequencing (RNA-seq). ISG upregulation by WNV infection was inhibited in RIG-I/MDA5^-/- MEFs. ISGs were upregulated in IRF1^-/- and IRF5^-/- MEFs but only minimally upregulated in IRF3/5/7^-/- MEFs, suggesting redundant IRF involvement. We previously showed that a single proximal interferon-stimulated response element (ISRE) in the <i>Oas1a</i> and <i>Oas1b</i> promoters bound the ISGF3 complex after type I IFN treatment. In this study, we used wild-type and mutant promoter luciferase reporter constructs to identify critical regions in the <i>Oas1b</i> and <i>Ifit1</i> promoters for gene activation in infected IFNAR^-/- MEFs. Two ISREs were required in both promoters. Mutation of these ISREs in an <i>Ifit1</i> promoter DNA probe reduced <i>in vitro</i> complex formation with infected nuclear extracts. An NF-κB inhibitor decreased <i>Ifit1</i> promoter activity in cells and <i>in vitro</i> complex formation. IRF3 and p50 promoter binding was detected by chromatin immunoprecipitation (ChIP) for upregulated ISGs with two proximal ISREs. The data indicate that ISREs function cooperatively to upregulate the expression of some ISGs when type I IFN signaling is absent, with the binding complex consisting of IRF3, IRF5, and/or IRF7 and an NF-κB component(s) as well as other, as-yet-unknown factors. <b>IMPORTANCE</b> Type I IFN signaling in mammalian cells induces formation of the ISGF3 transcription factor complex, which binds to interferon stimulated response elements (ISREs) in the promoters of interferon-stimulated genes (ISGs) in the cell nucleus. Flavivirus proteins counteract type I IFN signaling by preventing either the formation or nuclear localization of ISGF3. A subset of ISRE-regulated ISGs was still induced in West Nile virus (WNV)-infected mouse embryo fibroblasts (MEFs), indicating that cells have an alternative mechanism for activating these ISGs. In this study, cellular components involved in this ISG upregulation mechanism were identified using gene knockout MEFs and ChIP, and critical promoter regions for gene activation were mapped using reporter assays. The data indicate a cooperative function between two ISREs and required binding of IRF3, IRF5, and/or IRF7 and an NF-κB component(s). Moreover, type I IFN signaling-independent ISG activation requires different additional promoter activation regions than type I IFN-dependent activation.Journal of virologyTwo Interferon-Stimulated Response Elements Cooperatively Regulate Interferon-Stimulated Gene Expression in West Nile Virus-Infected IFNAR^-/- Mouse Embryo Fibroblasts.PMC8549515R21AI097851PRONII FellowshipR21 AI097851Molecular Basis of Disease FellowshipEspinola EEBrinton MAArora KCui DfalseTwo Interferon-Stimulated Response Elements Cooperatively Regulate Interferon-Stimulated Gene Expression in West Nile Virus-Infected IFNAR^-/- Mouse Embryo Fibroblasts.We previously identified a subset of interferon-stimulated genes (ISGs) upregulated by West Nile virus (WNV) infection in wild-type mouse embryo fibroblasts (MEFs) after viral proteins had inhibited type I interferon (IFN)-mediated JAK-STAT signaling and also in WNV-infected RIG-I^-/-, MDA5^-/-, STAT1^-/-, STAT2^-/-, IFNAR^-/-, IRF3^-/-, IRF7^-/-, and IRF3/7^-/- MEFs. In this study, ISG upregulation by WNV infection in IFNAR^-/- MEFs was confirmed by transcriptome sequencing (RNA-seq). ISG upregulation by WNV infection was inhibited in RIG-I/MDA5^-/- MEFs. ISGs were upregulated in IRF1^-/- and IRF5^-/- MEFs but only minimally upregulated in IRF3/5/7^-/- MEFs, suggesting redundant IRF involvement. We previously showed that a single proximal interferon-stimulated response element (ISRE) in the <i>Oas1a</i> and <i>Oas1b</i> promoters bound the ISGF3 complex after type I IFN treatment. In this study, we used wild-type and mutant promoter luciferase reporter constructs to identify critical regions in the <i>Oas1b</i> and <i>Ifit1</i> promoters for gene activation in infected IFNAR^-/- MEFs. Two ISREs were required in both promoters. Mutation of these ISREs in an <i>Ifit1</i> promoter DNA probe reduced <i>in vitro</i> complex formation with infected nuclear extracts. An NF-κB inhibitor decreased <i>Ifit1</i> promoter activity in cells and <i>in vitro</i> complex formation. IRF3 and p50 promoter binding was detected by chromatin immunoprecipitation (ChIP) for upregulated ISGs with two proximal ISREs. The data indicate that ISREs function cooperatively to upregulate the expression of some ISGs when type I IFN signaling is absent, with the binding complex consisting of IRF3, IRF5, and/or IRF7 and an NF-κB component(s) as well as other, as-yet-unknown factors. <b>IMPORTANCE</b> Type I IFN signaling in mammalian cells induces formation of the ISGF3 transcription factor complex, which binds to interferon stimulated response elements (ISREs) in the promoters of interferon-stimulated genes (ISGs) in the cell nucleus. Flavivirus proteins counteract type I IFN signaling by preventing either the formation or nuclear localization of ISGF3. A subset of ISRE-regulated ISGs was still induced in West Nile virus (WNV)-infected mouse embryo fibroblasts (MEFs), indicating that cells have an alternative mechanism for activating these ISGs. In this study, cellular components involved in this ISG upregulation mechanism were identified using gene knockout MEFs and ChIP, and critical promoter regions for gene activation were mapped using reporter assays. The data indicate a cooperative function between two ISREs and required binding of IRF3, IRF5, and/or IRF7 and an NF-κB component(s). Moreover, type I IFN signaling-independent ISG activation requires different additional promoter activation regions than type I IFN-dependent activation.2021-01-01T00:00:00Z2021 Oct2024-11-15T20:18:09.285Z2024-11-15T20:18:09.285ZS-EPMC85495153449569410.1128/JVI.01040-2110.1128/jvi.01040-21