Viral-induced alternative splicing of host genes promotes influenza replication

Abstract

Viral infection induces the expression of numerous host genes that impact the outcome of infection. Here we show that infection of human lung epithelial cells with Influenza A virus (IAV) also induces a broad program of alternative splicing of host genes. While these splicing-regulated genes are not enriched for canonical regulators of viral infection, we find that many of these genes do impact replication of IAV. Moreover, in several cases, specific inhibition of the IAV-induced splicing pattern also attenuates viral infection. We further show that approximately a quarter of the IAV-induced splicing events are regulated by hnRNP K, a host protein required for efficient splicing of the IAV M transcript in nuclear speckles. Finally, we find an increase in hnRNP K in nuclear speckles upon IAV infection, which may alter accessibility of hnRNP K for host transcripts thereby leading to a program of host splicing changes that promote IAV replication.

Global transcriptomics reveals specialized roles for splicing regulatory proteins in the macrophage innate immune response

“…A similar hyper-restriction phenotype was recently reported for hnRNP K knockdown A549 cell lines infected with influenza virus by Thompson et al [52]. These results argue strongly for splicing factors contributing to innate immune and infection outcomes in important ways and suggest that some of these factors may work in a cooperative fashion.…”

“…Remarkably, we observed almost no replication of VSV in either hnRNP knockdown cell line at any time point. A similar hyper-restriction phenotype was recently reported for hnRNP K knockdown A549 cell lines infected with influenza virus by Thompson et al[51]. These results argue strongly for splicing factors contributing to innate immune and infection outcomes in important ways and suggest that some of these factors may work in a cooperative fashion.DISCUSSIONWhile the involvement of splicing factors in regulating steady state gene expression in macrophages should in some ways be a foregone conclusion, our discoveries regarding the diversity of genes impacted by individual splicing factors and the dramatic reliance of some innate immune genes versus others on SR/hnRNPs for establishing or maintaining proper steady state levels, are surprising.…”

“…The copyright holder for this preprint this version posted December 7, 2020. ; https://doi.org/10.1101/2020.12.06.413690 doi: bioRxiv preprint Earlier studies also found a lack of overlap between transcriptome changes and alternative splicing events in Salmonella-infected human monocytes [15] and influenza virus-infected A549 cells [52]. Together these data suggest that changes to constitutive intron removal and/or alternative splicing of an upstream master regulator are more likely explanations for how loss of SR/hnRNPs influences steady state RNA expression levels in cells.…”

“…For example, dephosphorylation of SRSF10 by the phosphatase PP1 represses splicing and limits gene expression in HeLa cells following heat shock [19,69,70] and arginine methylation of hnRNPA1/B2 triggers its export to the cytoplasm where it activates TBK1/IRF3 signaling following infection with a DNA virus [71]. Very recent work from the Lynch lab showed that hnRNP K is redistributed in the nucleus during influenza infection, becoming enriched in nuclear speckles [51]. Indeed, subcellular redistribution is a common trait of SR/hnRNPs during infection [72,73] Workbench to be the number of exons/introns based on the mRNA annotations of the reference genome.…”

Interplay Between CMGC Kinases Targeting SR Proteins and Viral Replication: Splicing and Beyond

“…Indeed, several studies have documented that viral infections, caused by DNA or RNA viruses, can modulate splicing of cellular RNAs ( Boudreault et al, 2019 ; Chauhan et al, 2019 ). Notably, a recent study on IAV indicates that the set of genes regulated by splicing following infection is different from those regulated at the transcriptional level ( Thompson et al, 2020 ). While some of these splicing modulations may arise as a consequence of host response to infection, others may be due to a virus-directed effect on splicing kinases, in particular those targeting SR proteins.…”