Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, 6720, Hungary.
Department of Genetics, School of Medicine, Stanford University, Stanford, California, 94305, USA.
Sci Rep. 2017 Nov 22;7(1):15989. doi: 10.1038/s41598-017-16262-z.
The human cytomegalovirus (HCMV) is a ubiquitous, human pathogenic herpesvirus. The complete viral genome is transcriptionally active during infection; however, a large part of its transcriptome has yet to be annotated. In this work, we applied the amplified isoform sequencing technique from Pacific Biosciences to characterize the lytic transcriptome of HCMV strain Towne varS. We developed a pipeline for transcript annotation using long-read sequencing data. We identified 248 transcriptional start sites, 116 transcriptional termination sites and 80 splicing events. Using this information, we have annotated 291 previously undescribed or only partially annotated transcript isoforms, including eight novel antisense transcripts and their isoforms, as well as a novel transcript (RS2) in the short repeat region, partially antisense to RS1. Similarly to other organisms, we discovered a high transcriptional diversity in HCMV, with many transcripts only slightly differing from one another. Comparing our transcriptome profiling results to an earlier ribosome footprint analysis, we have concluded that the majority of the transcripts contain multiple translationally active ORFs, and also that most isoforms contain unique combinations of ORFs. Based on these results, we propose that one important function of this transcriptional diversity may be to provide a regulatory mechanism at the level of translation.
人巨细胞病毒（HCMV）是一种普遍存在的、具有致病性的人类疱疹病毒。在感染过程中，完整的病毒基因组具有转录活性；然而，其转录组的很大一部分尚未被注释。在这项工作中，我们应用了太平洋生物科学公司的扩增异构体测序技术来描述 HCMV 株 Towne varS 的裂解转录组。我们开发了一个使用长读测序数据进行转录本注释的管道。我们确定了 248 个转录起始位点、116 个转录终止位点和 80 个剪接事件。利用这些信息，我们注释了 291 个以前未描述或仅部分注释的转录本异构体，包括 8 个新的反义转录本及其异构体，以及在短重复区的一个新的转录本（RS2），部分反义于 RS1。与其他生物一样，我们在 HCMV 中发现了很高的转录多样性，许多转录本彼此之间只有微小的差异。将我们的转录组分析结果与早期的核糖体足迹分析进行比较，我们得出结论，大多数转录本包含多个翻译活性的 ORF，并且大多数异构体包含独特的 ORF 组合。基于这些结果，我们提出这种转录多样性的一个重要功能可能是在翻译水平提供一种调节机制。
