SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome

We performed a transcriptomic analysis of H293T cells expressing individual SARS-CoV2 proteins. Overexpression of Nsp14, a protein known to be involved in viral RNA replication, provoked a dramatic remodeling of the transcriptome, altering the expression of ≈4000 RNAs (3'RNAseq). These transcriptome changes strongly resemble the ones observed following SARS-CoV-2 infection. We performed a timecourse 3'RNA seq experiment and detected genes related to NFkB activation as deregulated soon after the transfection. We showed that the effect does not depend by the presence of the co-factor Nsp10 (total RNA seq) or by the exonuclease activity of Nsp14 (3' RNA seq of Nsp14 D90A/G92A and Nsp14D273 mutants). Finally we saw that the effect are mediated by the cellular enzyme IMPDH2, since treatment with MPA partially rescued the effect induced by Nsp14OE (3'RNA seq). control cells were transfected with eGFP (pLVX-EF1alpha-eGFP-2xStrep-IRES-Puro Addgene 141395). The other samples were transfected with Nsp14 (pLXV-EF1alpha-2xStrep-SARS-CoV-2-nsp14-IRES-Puro Addgene 141380) or the indicated plasmid (pLVX-EF1alpha-SARS-CoV-2-proteins-2xStrep-IRES-Puro Gordon et al., 2020)