Dremel Sarah E, Koparde Vishal N, Arbuckle Jesse H, Hogan Chad H, Kristie Thomas M, Krug Laurie T, Conrad Nicholas K, Ziegelbauer Joseph M
HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA.
Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908, USA.
EMBO J. 2025 Apr;44(8):2323-2352. doi: 10.1038/s44318-025-00398-0. Epub 2025 Mar 3.
Herpesviruses require the host transcriptional machinery, inducing significant changes in gene expression to prioritize viral transcripts. We examined alpha- and gamma-herpesvirus alterations to a type of alternative splicing, namely circular RNA (circRNA) synthesis. We developed "Circrnas in Host And viRuses anaLysis pIpEline" (CHARLIE) to facilitate viral profiling. This method identified thousands of back-splicing variants, including circRNA common to lytic and latent phases of infection. Ours is the first report of Herpes Simplex Virus-1 circRNAs, including species derived from ICP0 and the latency-associated transcript. We characterized back-splicing cis- and trans-elements, and found viral circRNAs resistant to spliceosome perturbation and lacking canonical splice donor-acceptors. Subsequent loss-of-function studies of host RNA ligases (RTCB, RLIG1) revealed instances of decreased viral back splicing. Using eCLIP and 4sU-Sequencing, we determined that the KSHV RNA-binding protein, ORF57, enhanced synthesis for a subset of viral and host circRNAs. Our work explores unique splicing mechanisms driven by lytic infection, and identifies a class of transcripts with the potential to function in replication, persistence, or tumorigenesis.
疱疹病毒需要宿主转录机制，诱导基因表达发生显著变化以优先产生病毒转录本。我们研究了α和γ疱疹病毒对一种可变剪接类型，即环状RNA（circRNA）合成的影响。我们开发了“宿主和病毒中环状RNA分析管道”（CHARLIE）以促进病毒分析。该方法鉴定出数千种反向剪接变体，包括感染裂解期和潜伏期共有的circRNA。我们首次报道了单纯疱疹病毒1型circRNA，包括源自ICP0和潜伏期相关转录本的种类。我们对反向剪接的顺式和反式元件进行了表征，发现病毒circRNA对剪接体扰动具有抗性且缺乏典型的剪接供体-受体。随后对宿主RNA连接酶（RTCB、RLIG1）的功能丧失研究揭示了病毒反向剪接减少的情况。使用eCLIP和4sU测序，我们确定卡波西肉瘤相关疱疹病毒RNA结合蛋白ORF57增强了一部分病毒和宿主circRNA的合成。我们的工作探索了由裂解感染驱动的独特剪接机制，并鉴定出一类在复制、持续存在或肿瘤发生中具有潜在功能的转录本。
