Laboratory of Gene Expression and Cancer, GIGA-R (MBD), University of Liège, Liège, Belgium.
Department of Molecular Genetics & Microbiology, UF Health Cancer Center, University of Florida, Gainesville, FL, USA.
Cell Rep. 2019 Jun 25;27(13):3988-4002.e5. doi: 10.1016/j.celrep.2019.05.086.
The gammaherpesviruses, including Epstein-Barr virus (EBV), Kaposi's sarcoma-associated herpesvirus (KSHV), and murine gammaherpesvirus 68 (MHV68, MuHV-4, γHV68), are etiologic agents of a wide range of lymphomas and non-hematological malignancies. These viruses possess large and highly dense dsDNA genomes that feature >80 bidirectionally positioned open reading frames (ORFs). The abundance of overlapping transcripts and extensive splicing throughout these genomes have until now prohibited high throughput-based resolution of transcript structures. Here, we integrate the capabilities of long-read sequencing with the accuracy of short-read platforms to globally resolve MHV68 transcript structures using the transcript resolution through integration of multi-platform data (TRIMD) pipeline. This approach reveals highly complex features, including: (1) pervasive overlapping transcript structures; (2) transcripts containing intra-gene or trans-gene splices that yield chimeric ORFs; (3) antisense and intergenic transcripts containing ORFs; and (4) noncoding transcripts. This work sheds light on the underappreciated complexity of gammaherpesvirus transcription and provides an extensively revised annotation of the MHV68 transcriptome.
γ 疱疹病毒包括 EBV、卡波西肉瘤相关疱疹病毒（KSHV）和鼠 γ 疱疹病毒 68（MHV68、MuHV-4、γHV68），是多种淋巴瘤和非血液系统恶性肿瘤的病因。这些病毒具有大而高密度的双链 DNA 基因组，特征是 80 个以上双向定位的开放阅读框（ORF）。这些基因组中大量重叠的转录本和广泛的剪接，直到现在都妨碍了基于高通量的转录本结构解析。在这里，我们整合长读测序的能力和短读平台的准确性，使用转录本通过整合多平台数据（TRIMD）进行解析的方法，来全局解析 MHV68 的转录本结构。这种方法揭示了高度复杂的特征，包括：（1）普遍存在的重叠转录本结构；（2）包含基因内或基因间剪接的转录本，产生嵌合 ORF；（3）包含 ORF 的反义转录本和基因间转录本；（4）非编码转录本。这项工作揭示了 γ 疱疹病毒转录的被低估的复杂性，并提供了对 MHV68 转录组的广泛修订注释。
