High-resolution analysis of immune-activated alternative splicing

An infecting virus can replicate within a fraction of the time required for the host cell to divide. Vertebrate hosts evolved a dynamic antiviral program, the interferon response, that counters virus replication. Recognition of viral motifs triggers a transcriptional program that rapidly alters expression of cellular genes to combat infection and hinder virus spread. Gene expression profiling following viral infection identified approximately 1,000 genes that are regulated by interferon. However, a shortcoming of this transcriptome profiling approach is ignorance of alternative splicing, leaving a large gap in our understanding that we will fill with long-read sequencing. Previously we demonstrated that splice isoform variance controls influenza virus. ANP32A, a key activator hijacked by the influenza virus polymerase, has alternatively spliced transcripts. Across influenza hosts, the prevalence of the most active isoform of ANP32A tracks with the ability for a species to support viral infection (Baker et al. 2018, Cell Reports). We also used Illumina-based sequencing to map host transcriptional changes during interferon stimulation or influenza infection (2x150 paired end reads, 35-55 million reads/sample) (Baker et al. 2022, PLoS Biology; BioProject PRJNA667475). These data uncovered hundreds of potentially alternatively spliced exons. This dataset uses the same RNA samples to generate Iso-Seq scaffolds of the alternative transcriptome. We can then leverage our short-read sequencing data to quantitatively test genome-wide variance in antiviral alternative splicing. This will help uncover the extent and role of alternative splicing in antiviral responses, a currently understudied and important facet of the dynamic host-virus interface.