RNase L activation in the cytoplasm induces aberrant processing of mRNAs in the nucleus

The antiviral endoribonuclease, RNase L, is activated by the mammalian innate immune response to destroy host and viral RNA to ultimately reduce viral gene expression. Herein, we show that RNase L and RNase L-mediated mRNA decay are primarily localized to the cytoplasm. Consequently, RNA-binding proteins (RBPs) translocate from the cytoplasm to the nucleus upon RNase L activation due to the presence of intact nuclear RNA. The re-localization of RBPs to the nucleus coincides with global alterations to RNA processing in the nucleus. While affecting many host mRNAs, these alterations are pronounced in mRNAs encoding type I and type III interferons and correlate with their retention in the nucleus and reduction in interferon protein production. Similar RNA processing defects also occur during infection with either dengue virus or SARS-CoV-2 when RNase L is activated. These findings reveal that the distribution of RBPs between the nucleus and cytosol is dictated by the availability of RNA in each compartment. Thus, viral infections that trigger RNase L-mediated cytoplasmic RNA in the cytoplasm also alter RNA processing in the nucleus, resulting in an ingenious multi-step immune block to protein biogenesis. Author summary Ribonuclease L (RNase L) initiates rapid and widespread degradation of cellular mRNAs in response to double-stranded RNA or viral infection. How the mass degradation of mRNAs affects cellular functions is unknown. Herein, we show that RNase L-mediated mRNA decay is predominately localized to the cytoplasm. Consequently, RNA-binding proteins re-localize from the cytoplasm to the nucleus upon RNase L activation. Coinciding with the influx of RNA-binding proteins into the nucleus, we also observe perturbation of nuclear processing of mRNAs, and these processing defects down-regulate key antiviral cytokines, such as type I interferons. Importantly, we observe these processes occurring during dengue virus and SARS-CoV-2 infection, revealing previously unknown aspects of antiviral gene regulation during pathogenic viral infections. Combined, these findings uncover novel mechanisms by which RNase L regulates host gene expression and expand the potential means by which RNase L blocks protein synthesis.

Automated summary

RNase L-mediated mRNA decay occurs primarily in the cytoplasm and leads to the re-localization of RNA-binding proteins from the cytoplasm to the nucleus. This re-localization coincides with altered RNA processing in the nucleus, particularly affecting mRNAs encoding interferons. Similar RNA processing defects are observed during dengue virus and SARS-CoV-2 infection. These findings uncover novel mechanisms by which RNase L regulates host gene expression and blocks protein synthesis.