Transcriptional and chromatin regulation in interferon and innate antiviral gene expression

Abstract

In response to virus infections, a cell-autonomous, transcription-based antiviral program is engaged to create resistance, impair pathogen replication, and alert professional cells in innate and adaptive immunity. This dual phase antiviral program consists of type I interferon (IFN) production followed by the response to IFN signaling. Pathogen recognition leads to activation of IRF and NFκB factors that function independently and together to recruit cellular coactivators that remodel chromatin, modify histones and activate RNA polymerase II (Pol II) at target gene loci, including the well-characterized IFNβ enhanceosome. In the subsequent response to IFN, a receptor-mediated JAK-STAT signaling cascade directs the assembly of the IRF9-STAT1-STAT2 transcription factor complex called ISGF3, which recruits its own cohort of remodelers, coactivators, and Pol II machinery to activate transcription of a wide range of IFN-stimulated genes. Regulation of the IFN and antiviral gene regulatory networks is not only important for driving innate immune responses to infections, but also may inform treatment of a growing list of chronic diseases that are characterized by hyperactive and constitutive IFN and IFN-stimulated gene (ISG) expression. Here, gene-specific and genome-wide investigations of the chromatin landscape at IFN and ISGs is discussed in parallel with IRF- and STAT- dependent regulation of Pol II transcription.

Keywords: Antiviral; Chromatin; IRF; Interferon; NFκB; STAT; Transcription.

Figure 1.. Antiviral signaling and activation of IFNβ transcription.

Illustrations of the cell during steady state (left) and following RNA virus infection (right). Prior to virus infection (left), transcription factors IRF3 and NFκB are in their latent state, with NFκB bound to its inhibitor, IκB. Inside the nucleus (dotted line), the IFNβ promoter region is depicted with a −1 and +1 nucleosome flanking a nucleosome-free positive regulatory domain (PRD) depicting response elements PRDI-PRDIV. The +1 nucleosome obscures the transcriptional start site. Generic IRF3 and NFκB-driven targets are illustrated below. Following virus infection (right), viral-origin non-self nucleic acids are detected by RIG-I-like and Toll-like pattern recognition receptors resulting in IRF3 and NFκB activation and nuclear translocation. IRF3 homodimer and NFκB bind to their respective PRD sites along with ATF2/cJun to form the enhanceosome. Enhanceosome-mediated recruitment of chromatin modifying factors leads to eviction of the +1 nucleosome, revealing the IFN transcription start site and enabling Pol II assembly and IFNβ transcription. Individual IRF3 and NFκB target genes feature either recruited Pol II or paused Pol II, respectively.

Figure 2.. IFN-JAK-STAT signaling pathway

Illustrations of the canonical ISGF3 signaling system at steady state (left) and following type I IFN-stimulation (right). Prior to IFN stimulation, transmembrane IFNAR1/2 receptor chains are associated with TYK2 and JAK1 kinases, and latent factors STAT1 and STAT2 are present in the cytoplasm. IRF9 associates with STAT2 in the cytoplasm and also shuttles into the nucleus. Histones H2A.Z and H3.3 occupy transcriptionally silent ISG promoters. IFN binding to the receptor complex (right) induces oligomerization and phosphorylation of the receptor chains, generating docking sites for the latent STAT proteins’ SH2 domains, resulting in phosphorylation of STAT2 Y690 and STAT1 Y701. Phosphorylated STAT1 and STAT2 undergo SH2-mediated dimerization and along with IRF9 form the ISGF3 complex. ISGF3 translocates into the nucleus, where it binds to the ISRE at ISG promoters and recruits coactivators relevant to histone modification, chromatin remodeling, and Pol II activation, including GCN5 and BRD2 that remodel the H2A.Z-containing nucleosome, MED14 to recruit Pol II for activating ISG transcription, and histone H3.3 is deposited at ISG gene bodies. The roles for essential co-activators RVB1, RVB2, CBP, BRG1, and HDACs are poorly understood.

Figure 3.. IRFs and STATs drive the IFN antiviral response.

Depiction of the two-phase antiviral response following virus infection (left), leading to IFN-mediated JAK-STAT signaling (right). The networks of both primary response genes activated by IRF3 and NFκB and IFN target genes activated by ISGF3, combine to produce a potent and coordinated response to infection. The ability of IRF proteins to recognize common core response elements leads to overlapping patterns of target gene expression, as exemplified by genes like ISG15 that are activated by IRF3 during virus infection and ISGF3 following IFN stimulation. In addition to the canonical IRF and ISGF3 factors, non-canonical STAT complexes are present both prior to and following IFN stimulation.