Status lab-led for Schmid 2010 and Schmid 2014, co-led with the Maniatis laboratory for Ng 2011, and training period for tenOever 2007, which was carried out with the Maniatis and García-Sastre laboratories and is not the independent program's work Areas Innate Immune Signaling and the Interferon Response
The interferon response had been described as a switch in which detection yields interferon, interferon signals, and a few hundred interferon-stimulated genes come on. That account cannot explain why the induced set differs between infections, cell types and host genotypes, and it treats a gene annotated as interferon-stimulated as though its induction required interferon. The training-period observation that framed the problem is that mice lacking IKKepsilon made normal interferon beta yet failed to induce roughly a third of interferon-stimulated genes, that the defect persisted when interferon was supplied from outside the cell, and that the substrate separating responsive from unresponsive promoters was STAT1 Ser708 (tenOever 2007).
Two mechanisms of allocation were then established. Ng 2011 placed Ser708 in the homodimer interface of the published tyrosine-phosphorylated STAT1 structure and showed that phosphorylation there blocks the activated homodimer while leaving the STAT1 and STAT2 interaction intact, so a limiting STAT1 pool is driven into ISGF3 and away from GAF. Loss of IKKepsilon lowered ISGF3 assembly and element binding while raising GAF assembly, and adenoviral IKKepsilon produced the mirror-image shift. Schmid 2014 found the same logic among the interferon regulatory factors, where the IRF7-selective kinase MAP3K8 drives phosphorylation in the proline-rich hinge of IRF3 and redirects it from homodimers into IRF3 and IRF7 heterodimers, with fibroblasts lacking MAP3K8 supporting more vesicular stomatitis virus and failing to induce roughly seventy genes.
The DNA side supplied the other half. Mice lacking both the type I and type III interferon receptors still induced a large block of interferon-stimulated genes after infection with an NS1-deficient influenza A virus, so those genes do not require interferon signalling, and systematic mutagenesis of the ISG15 element separated positions conferring IRF7 specificity, ISGF3 specificity or both, with ISGF3 requiring contacts beyond the consensus core and IRF7 tolerating more variation (Schmid 2010). Activating IRF7 in interferon-unresponsive cells reproduced about eighty percent of the set induced in infected knockout lung, and individual promoters sorted as predicted, with MxA restricted to ISGF3 and CXCL10 to IRF7.
What is now known is that the interferon-stimulated gene set is a structured and divisible output, that a large part of it is inducible with no interferon signalling at all, and that composition is set by which complex assembles and which element it can read. The reading that one design principle appears twice, a kinase acting at or near a dimer interface to allocate a shared subunit, is synthesis across Ng 2011 and Schmid 2014 and is asserted by neither. The structural chemistry is unresolved, since Ng 2011 states that the consequences of Ser708 phosphorylation within ISGF3 are unknown and Schmid 2014 does not establish MAP3K8 as a direct kinase for IRF3 or identify the modified hinge residues. The consensus sequences in Schmid 2010 are generalisations from derivatives of one element, and the thread did not continue as a mechanistic program after 2014.
Substantiated by - Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, training-period work dividing interferon-stimulated response elements into kinase-dependent and kinase-independent classes and naming STAT1 Ser708 - IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses, explains that phosphosite as a block on STAT1 homodimerisation that reallocates a shared subunit between two complexes - Transcription Factor Redundancy Ensures Induction of the Antiviral State, shows that much of the antiviral transcriptome is inducible without interferon and gives sequence criteria sorting promoters by the factor that reads them - Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, identifies a feedback kinase that changes which IRF dimer forms and therefore which promoters the response reaches
Sustained IRF7 activity induces the kinase MAP3K8, which phosphorylates the proline-rich hinge of IRF3 and redirects it from homodimers into IRF3 and IRF7 heterodimers, broadening the antiviral transcriptome and scaling the cellular response to the persistence of the viral threat.
Phosphorylation of STAT1 serine 708 by IKKε blocks formation of the STAT1 homodimer that constitutes GAF while leaving the STAT1 and STAT2 heterodimer of ISGF3 intact, biasing the shared STAT1 pool and the interferon-stimulated transcriptome toward the type I response.
IRF7 and ISGF3 engage overlapping interferon-stimulated response elements and drive largely overlapping antiviral transcriptomes, so that a substantial interferon-like gene program is still induced when type I and type III interferon signaling are both absent.
Mice lacking IKKε produce normal interferon-β but fail to induce roughly a third of interferon-stimulated genes, because interferon activates IKKε, which phosphorylates STAT1 at Ser708 and thereby determines whether ISGF3 occupies a subset of response elements.