Influenza A virus RNA Polymerase targets the chromatin of innate immune response genes

KEY POINTSO_LIFluPol is linked to RNAs in gene body and 3-downstream regions C_LIO_LIFluPol Chromatin-targets are involved in the cell defense C_LIO_LICap-snatching could occur everywhere during transcription elongation C_LI The influenza A virus (IAV) RNA polymerase (FluPol) primes the viral transcription by using capped 5-ends << snatched >> from host nascent RNAs. However, the exact localization of the FluPol on the genome or the timing of its snatching activity remains poorly characterized. Here, we have monitored IAV infection from the perspective of the FluPol interaction with the host chromatin template. Quantification of chromatin-bound RNAs shows a significant perturbation in host transcription that correlates with a relocalization of RNA polymerase II (RNAPII) from the gene bodies to downstream intergenic regions. This extended transcription leading to the production of RNA downstream of genes (DoGs) was previously linked to the NS1-mediated inhibition of the transcriptional termination. However, immunoprecipitation of FluPol-bound RNA in the chromatin fraction revealed that FluPol remains linked to nascent host transcripts during phases of transcriptional elongation and termination, thereby extending the window of opportunity in which cap-snatching may occur. In addition, chromatin-associated FluPol was enriched at transcription termination sites, suggesting that it may participate in the virus-induced termination defects. Finally, we observed that, rather than targeting just highly expressed genes, the FluPol was preferentially recruited to promoters activated by the viral infection and enhancers. Together, these observations suggest the FluPol uses the early immune response to target regulatory elements of defense-related genes at which it interferes with the fate of the transcripts, and possibly also limits RNAPII re-initiation by impairing the termination process. Author SummaryThe influenza A virus (IAV) exploits the transcriptional machinery of the infected cells to generate its own RNAs with the viral polymerase (FluPol) hijacking cap structures from host mRNAs. This "cap snatching" requires an interaction between FluPol and the cellular RNA polymerase (RNAPII) accumulating at transcription start sites (TSS) of genes. In parallel, another IAV factor interferes the termination of gene transcription, resulting in frequent transcription downstream of genes and reduced recycling of the RNAPII. Here, employing genome-wide ChIP assays, we show that FluPol selectively targets the TSS of infection-activated genes often associated with cellular defense mechanisms, and thereby contributing to their downregulation. In addition, we show that FluPol is not only recruited to promoters and enhancers, but also within genes, where it interacts with nascent RNAs during transcription and splicing. It is further detected beyond the 3 end of the genes, suggesting that FluPol exerts a broad influence on host transcription by affecting both transcription initiation through cap-snatching and transcription re-initiation via its involvement in the virus-induced transcription-termination defect at the end of genes.