The antiviral nuclear body protein SP140 represses Ifnb1 transcript stabilization by the novel regulator RESIST

Negative regulation of the antiviral cytokine IFN-I is critical to prevent host pathology, but is not fully understood. The highly conserved but understudied epigenetic reader and nuclear body protein SP140 represses IFN-I by an unknown mechanism. We describe the mechanism by which SP140 negatively regulates IFN-I, and include CUT&RUN data in this dataset. We performed anti-HA CUT&RUN on SP140KO macrophages transduced with HA-tagged or untagged SP140. We found that SP140 represses the expression of a novel positive regulator of IFN-I previously annotated as an annexin II receptor, which we rename RESIST (REgulated Stimulator of IFN-I via Stabilization of Transcript). RESIST promotes IFN-I mRNA stability by binding the CCR4-NOT mRNA deadenylase complex and blocking recruitment of the TTP family of RNA-binding proteins, which negatively regulate IFN-I mRNA stability, to CCR4-NOT. Mechanistically, RESIST uses N and C-terminal alpha-helices respectively to either dock to the CCR4-NOT complex or block TTP family binding. We also find SP140 does not bind the Ifnb1 gene itself. Consistent with previous results, SP140 binds genes involved in embryonic development. Our work reveals a new regulator of IFN-I and a new mechanism regulating IFN-I mRNA stability. We performed anti-HA CUT&RUN on 0.5e6 SP140 KO bone marrow derived macrophages (BMMs) transduced with untagged or HA-tagged SP140, treated with the STING agonist DMXAA at 100 ug/ml for 8 hours. We used triplicates (separate CUT&RUN reactions) for these conditions. We also performed CUT&RUN using an isotype control (rabbit) on 0.5e6 WT BMMs.