The Transcriptome of the Baculovirus Autographa californica Multiple Nucleopolyhedrovirus in Trichoplusia ni Cells
The Transcriptome of the Baculovirus Autographa californica Multiple Nucleopolyhedrovirus in Trichoplusia ni Cells
复制标题
DOI：
10.1128/jvi.00194-13
复制
发表时间：
2013-06-01
影响因子：
5.4
通讯作者：
Blissard, Gary W.
中科院分区：
文献类型：
--
作者：
Chen, Yun-Ru;Zhong, Silin;Blissard, Gary W.
杆状病毒是重要的昆虫病原体，已被开发为昆虫细胞中的蛋白质表达载体和哺乳动物细胞的转导载体。它们具有包含大约156个紧密间隔的基因的大的双链DNA基因组，并且它们对转录组分析提出了重大挑战。在这项研究中，我们报告了AcMNPV在粉纹夜蛾细胞中感染过程中转录的第一次全面分析，通过链特异性RNA测序（RNA-Seq）和5'加帽转录起始位点和3'多聚腺苷酸化位点的深度测序的组合。我们确定了四个集群的基因与独特的模式，通过AcMNPV感染周期的mRNA积累。共定位了218个转录起始位点（TSS）和120个多聚腺苷酸化位点（PAS）。只有29个TSS与典型的TATA盒相关，14个起始于先前确定的CAGT起始基序内或附近。大多数病毒转录物（126）在杆状病毒晚期启动子基序（TAAG）内起始，并且晚期转录物精确地在基序的第二位置起始。对3'端的分析表明，92个（77%）的3' PAS位于共有终止信号（AAUAAA或AUUAAA）下游30个核苷酸（nt）内。58个转录本的PAS下游约2 ~ 10 nt处存在一个保守的富U区。12个剪接事件和一个意想不到的大量的反义RNA被确定，揭示了新的细节可能的调控机制控制AcMNPV基因的表达。结合起来，这些数据提供了一个新兴的全球图片的组织和调节AcMNPV转录通过感染周期。
Baculoviruses are important insect pathogens that have been developed as protein expression vectors in insect cells and as transduction vectors for mammalian cells. They have large double-stranded DNA genomes containing approximately 156 tightly spaced genes, and they present significant challenges for transcriptome analysis. In this study, we report the first comprehensive analysis of AcMNPV transcription over the course of infection in Trichoplusia ni cells, by a combination of strand-specific RNA sequencing (RNA-Seq) and deep sequencing of 5' capped transcription start sites and 3' polyadenylation sites. We identified four clusters of genes associated with distinctive patterns of mRNA accumulation through the AcMNPV infection cycle. A total of 218 transcription start sites (TSS) and 120 polyadenylation sites (PAS) were mapped. Only 29 TSS were associated with a canonical TATA box, and 14 initiated within or near the previously identified CAGT initiator motif. The majority of viral transcripts (126) initiated within the baculovirus late promoter motif (TAAG), and late transcripts initiated precisely at the second position of the motif. Analysis of 3' ends showed that 92 (77%) of the 3' PAS were located within 30 nucleotides (nt) downstream of a consensus termination signal (AAUAAA or AUUAAA). A conserved U-rich region was found approximately 2 to 10 nt downstream of the PAS for 58 transcripts. Twelve splicing events and an unexpectedly large number of antisense RNAs were identified, revealing new details of possible regulatory mechanisms controlling AcMNPV gene expression. Combined, these data provide an emerging global picture of the organization and regulation of AcMNPV transcription through the infection cycle.