KSHV 2.0: a comprehensive annotation of the Kaposi's sarcoma-associated herpesvirus genome using next-generation sequencing reveals novel genomic and functional features.
KSHV 2.0: a comprehensive annotation of the Kaposi's sarcoma-associated herpesvirus genome using next-generation sequencing reveals novel genomic and functional features.
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DOI：
10.1371/journal.ppat.1003847
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发表时间：
2014-01
期刊：
影响因子：
6.7
通讯作者：
Ganem D
中科院分区：
文献类型：
--
作者：
Arias C;Weisburd B;Stern-Ginossar N;Mercier A;Madrid AS;Bellare P;Holdorf M;Weissman JS;Ganem D
生产性疱疹病毒感染需要对病毒转录组和蛋白质组进行深刻的、时间控制的重塑。为了深入了解卡波西肉瘤相关疱疹病毒（KSHV）的基因组结构和基因表达控制，我们对病毒在整个裂解周期中的转录和翻译活性进行了系统的全基因组调查。通过mrna测序和核糖体分析，我们发现编码裂解基因的转录本在裂解再激活时被核糖体迅速结合，这表明它们的调控主要是转录的。我们的方法还发现了新的基因组特征，如病毒非编码rna的核糖体占用，许多上游和小开放阅读框（orf），以及扩展病毒编码库的不寻常策略，包括选择性剪接，动态病毒mRNA编辑和使用替代翻译起始密码子。此外，我们提供了KSHV基因组空间中已知和新的病毒特征的转录起始位点、聚腺苷化位点、剪接连接和起始/终止密码子的精炼和扩展注释，我们将其称为KSHV 2.0。我们的研究结果代表了裂解性KSHV感染过程中基因调控的全面基因组尺度图像，大大扩展了我们对病毒基因组结构和编码能力的理解。卡波西肉瘤相关疱疹病毒（KSHV）是免疫功能低下患者的致癌物，可在其宿主中建立长期感染。最初于1994年被描述并被广泛研究，KSHV分子生物学在大致上被理解，但许多细节问题仍有待解决。近二十年后，有关KSHV基因组组织的具体方面以及感染生产阶段病毒转录本的命运仍未被探索。在这里，我们使用系统的全基因组方法来研究在被称为裂解周期的感染生产阶段基因和蛋白质表达的变化。我们发现病毒基因组具有很大的编码能力，能够产生至少45%以上的产物，比最初的生物信息学分析预测的多，并且它使用多种策略来扩大其编码能力，远远超出仅由其基因组的DNA序列决定的能力。我们还提供了KSHV中已知和新的基因组特征的扩展和高度详细的注释。我们将这个新的体系结构和功能注释命名为KSHV 2.0。我们的研究结果表明，病毒基因组比预期的更复杂，并且它们受到严格的调节机制以确保正确的基因表达。
Productive herpesvirus infection requires a profound, time-controlled remodeling of the viral transcriptome and proteome. To gain insights into the genomic architecture and gene expression control in Kaposi's sarcoma-associated herpesvirus (KSHV), we performed a systematic genome-wide survey of viral transcriptional and translational activity throughout the lytic cycle. Using mRNA-sequencing and ribosome profiling, we found that transcripts encoding lytic genes are promptly bound by ribosomes upon lytic reactivation, suggesting their regulation is mainly transcriptional. Our approach also uncovered new genomic features such as ribosome occupancy of viral non-coding RNAs, numerous upstream and small open reading frames (ORFs), and unusual strategies to expand the virus coding repertoire that include alternative splicing, dynamic viral mRNA editing, and the use of alternative translation initiation codons. Furthermore, we provide a refined and expanded annotation of transcription start sites, polyadenylation sites, splice junctions, and initiation/termination codons of known and new viral features in the KSHV genomic space which we have termed KSHV 2.0. Our results represent a comprehensive genome-scale image of gene regulation during lytic KSHV infection that substantially expands our understanding of the genomic architecture and coding capacity of the virus. Kaposi's sarcoma-associated herpesvirus (KSHV) is a cancer-causing agent in immunocompromised patients that establishes long-lasting infections in its hosts. Initially described in 1994 and extensively studied ever since, KSHV molecular biology is understood in broad outline, but many detailed questions are still to be resolved. After almost two decades, specific aspects pertaining to the organization of the KSHV genome as well as the fate of the viral transcripts during the productive stages of infection remain unexplored. Here we use a systematic genome-wide approach to investigate changes in gene and protein expression during the productive stage of infection known as the lytic cycle. We found that the viral genome has a large coding capacity, capable of generating at least 45% more products than initially anticipated by bioinformatic analyses alone, and that it uses multiple strategies to expand its coding capacity well beyond what is determined solely by the DNA sequence of its genome. We also provide an expanded and highly detailed annotation of known and new genomic features in KSHV. We have termed this new architectural and functional annotation KSHV 2.0. Our results indicate that viral genomes are more complex than anticipated, and that they are subject to tight mechanisms of regulation to ensure correct gene expression.
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