Vaccinia virus D10 has broad decapping activity that is regulated by mRNA splicing

Vaccinia virus (VACV) encodes decapping enzyme D10 that suppresses gene expression by removing the protective 5' cap off mRNAs, rendering them susceptible to degradation by cellular exonucleases. Here, we use RNA-seq to profile the repertoire of transcripts targeted by D10 in isolation as well as in the context of VACV infection. We found that D10 is a broadly acting decapping enzyme and targets the vast majority of human transcripts. Notably, we found that the splicing architecture of a gene influences how robustly its corresponding transcript is targeted by D10, with transcripts derived from intronless genes being less susceptible to D10 activity. Since all viral genes are intronless, and some viral transcripts are uncapped, D10 preferentially targets host transcripts over viral transcripts. The disproportionate activity of D10 towards host transcripts may help the virus restrict host innate immune response and shift the translational resources towards viral protein synthesis. Overall design: RNA-seq of HEK293T cells with integrated doxycycline-inducible D10 gene and of HEK293T cells infected with different mutant strains of vaccinia virus. There were three biological replicates per condition, resulting in a total of 42 samples. We included untreated and mock samples as controls for doxycycline-treated cells and vaccinia-infected cells, respectively.