Taslim Tommy Henry, Finkelberg Joseph Alexander, Kales Susan, Soto-Ugaldi Luis, D'Elia Benedetta, Engin Berkay, Muñoz-Esquivel George, Morara Elvis, Purinton Jacob, Chandok Harshpreet, Rottenberg Jaice Theodore, Castro Rodrigo, Martinez-Cuesta Lucia, Paz Matias Alejandro, Tewhey Ryan, Bass Juan Ignacio Fuxman
Molecular Biology, Cell Biology and Biochemistry Program, Boston University, Boston, MA 02215, USA.
Bioinformatics Program, Boston University, Boston, MA 02215, USA.
bioRxiv. 2025 Jul 20:2025.07.20.665756. doi: 10.1101/2025.07.20.665756.
Most double-stranded DNA (dsDNA) viruses use the host transcriptional machinery to express viral genes for replication and immune evasion. This is mediated by viral cis-regulatory elements (CREs) regulated by host and viral transcription factors (TFs). Although some viral CREs and their regulatory mechanisms have been determined, most remain unidentified. Here, we used massively parallel reporter assays to identify ~2,000 CREs across 27 dsDNA viruses from the Adenovirus, Herpesvirus, Polyomavirus and Papillomavirus families. Viral genomes have a higher CRE density than the human genome, with most viral CREs having promoter-like features and overlapping protein coding sequences. Using saturation mutagenesis and machine learning models, we report viral CRE regulators, including SP, ETS, bZIPs, and TFs acting downstream of signal-activated pathways. Altogether, we present a comprehensive functional CRE map of human-infecting dsDNA viruses that serves as a blueprint for further studies in viral regulation, reactivation, evolution, and viral vector design.
大多数双链DNA（dsDNA）病毒利用宿主转录机制来表达用于复制和免疫逃避的病毒基因。这由宿主和病毒转录因子（TFs）调控的病毒顺式调控元件（CREs）介导。尽管一些病毒CREs及其调控机制已被确定，但大多数仍未被识别。在此，我们使用大规模平行报告基因检测，从腺病毒、疱疹病毒、多瘤病毒和乳头瘤病毒家族的27种dsDNA病毒中鉴定出约2000个CREs。病毒基因组的CRE密度高于人类基因组，大多数病毒CREs具有启动子样特征并与蛋白质编码序列重叠。通过饱和诱变和机器学习模型，我们报告了病毒CRE调控因子，包括SP、ETS、bZIPs以及在信号激活途径下游起作用的TFs。总之，我们展示了人类感染性dsDNA病毒的全面功能性CRE图谱，为病毒调控、激活、进化及病毒载体设计的进一步研究提供了蓝图。
