Identification of New Viral Genes and Transcript Isoforms during Epstein-Barr Virus Reactivation using RNA-Seq
Identification of New Viral Genes and Transcript Isoforms during Epstein-Barr Virus Reactivation using RNA-Seq
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DOI：
10.1128/jvi.06537-11
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发表时间：
2012-02-01
影响因子：
5.4
通讯作者：
Flemington, Erik K.
中科院分区：
文献类型：
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作者：
Concha, Monica;Wang, Xia;Flemington, Erik K.
使用增强的RNA-Seq管道来分析EB病毒（EBV）转录组，我们研究了B细胞受体介导的再激活后Akata细胞系中的病毒和细胞基因表达。观察到EBV基因表达的稳健诱导，其中大多数病毒基因被诱导> 200倍，并且EBV转录物占细胞内所有映射读数的7%。诱导后，使用连接映射器TopHat检测到数百个候选剪接事件，包括在gp 350/gp 220位点的一个新的非生产性剪接事件和在LMP 2位点的几个选择性剪接事件。对裂解性LMP 2转录物的更详细分析显示，总体上缺乏原型III型潜伏期剪接事件。细胞核与细胞质RNA-Seq数据的分析显示，LMP 2、EBNA-2、EBNA-LP和EBNA-3A、-3B和-3C的裂解形式具有比大多数裂解基因（包括经典晚期基因）更高的细胞核与细胞质积累比率。这些数据提出的可能性，至少有一些裂解转录来自这些潜伏基因位点可能有独特的，非编码核功能在重新激活。我们的分析还确定了两个以前未知的基因，BCLT 1和BCRT 2，映射到EBV基因组的BamHI C区。B细胞受体活化后细胞基因表达变化的途径分析确定炎症反应为最高预测功能，ILK和TREM 1为最高预测经典途径。
Using an enhanced RNA-Seq pipeline to analyze Epstein-Barr virus (EBV) transcriptomes, we investigated viral and cellular gene expression in the Akata cell line following B-cell-receptor-mediated reactivation. Robust induction of EBV gene expression was observed, with most viral genes induced > 200-fold and with EBV transcripts accounting for 7% of all mapped reads within the cell. After induction, hundreds of candidate splicing events were detected using the junction mapper TopHat, including a novel nonproductive splicing event at the gp350/gp220 locus and several alternative splicing events at the LMP2 locus. A more detailed analysis of lytic LMP2 transcripts showed an overall lack of the prototypical type III latency splicing events. Analysis of nuclear versus cytoplasmic RNA-Seq data showed that the lytic forms of LMP2, EBNA-2, EBNA-LP, and EBNA-3A, -3B, and -3C have higher nuclear-to-cytoplasmic accumulation ratios than most lytic genes, including classic late genes. These data raise the possibility that at least some lytic transcripts derived from these latency gene loci may have unique, noncoding nuclear functions during reactivation. Our analysis also identified two previously unknown genes, BCLT1 and BCRT2, that map to the BamHI C-region of the EBV genome. Pathway analysis of cellular gene expression changes following B-cell receptor activation identified an inflammatory response as the top predicted function and ILK and TREM1 as the top predicted canonical pathways.