title: Herpes simplex virus ICP27 regulates alternative pre-mRNA polyadenylation and splicing in a sequence-dependent manner.
abstract: The herpes simplex virus (HSV) infected cell culture polypeptide 27 (ICP27) protein is essential for virus infection of cells. Recent studies suggested that ICP27 inhibits splicing in a gene-specific manner via an unknown mechanism. Here, RNA-sequencing revealed that ICP27 not only inhibits splicing of certain introns in <1% of cellular genes, but also can promote use of alternative 5' splice sites. In addition, ICP27 induced expression of pre-mRNAs prematurely cleaved and polyadenylated from cryptic polyadenylation signals (PAS) located in intron 1 or 2 of ∼1% of cellular genes. These previously undescribed prematurely cleaved and polyadenylated pre-mRNAs, some of which contain novel ORFs, were typically intronless, <2 Kb in length, expressed early during viral infection, and efficiently exported to cytoplasm. Sequence analysis revealed that ICP27-targeted genes are GC-rich (as are HSV genes), contain cytosine-rich sequences near the 5' splice site, and have suboptimal splice sites in the impacted intron, suggesting that a common mechanism is shared between ICP27-mediated alternative polyadenylation and splicing. Optimization of splice site sequences or mutation of nearby cytosines eliminated ICP27-mediated splicing inhibition, and introduction of C-rich sequences to an ICP27-insensitive splicing reporter conferred this phenotype, supporting the inference that specific gene sequences confer susceptibility to ICP27. Although HSV is the first virus and ICP27 is the first viral protein shown to activate cryptic PASs in introns, we suspect that other viruses and cellular genes also encode this function.
authors: Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993 philip.krause@fda.hhs.gov shuang.tang@fda.hhs.gov.
authors: Shuang
authors: S
authors: Tang
authors: Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993.
authors: Amita
authors: A
authors: Patel
authors: Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993 philip.krause@fda.hhs.gov shuang.tang@fda.hhs.gov.
authors: Philip R
authors: 0000-0002-1045-7536
authors: PR
authors: Krause
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D000818:Animals; D002460:Cell Line; D002522:Chlorocebus aethiops; D006801:Humans; D017874:Immediate-Early Proteins / Q000235:genetics*; D007438:Introns / Q000235:genetics; D026723:Polyadenylation / Q000235:genetics; D012322:RNA Precursors / Q000235:genetics; D022821:RNA Splice Sites / Q000235:genetics; D020871:RNA Stability / Q000235:genetics; D018139:Simplexvirus / Q000235:genetics*
chemical_list: C057120:ICP27 protein, human herpesvirus 1; D017874:Immediate-Early Proteins; D012322:RNA Precursors; D022821:RNA Splice Sites
keywords: DNA viruses; RNA 3′ polyadenylation signals; alternative splicing; host–pathogen interactions; polyadenylation