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Abstract：
In this study, we used the amplified isoform sequencing technique from Pacific Biosciences to characterize the poly(A)+ fraction of the lytic transcriptome of the herpes simplex virus type 1 (HSV-1). Our analysis detected 34 formerly unidentified protein-coding genes, 10 non-coding RNAs, as well as 17 polycistronic and complex transcripts. This work also led us to identify many transcript isoforms, including 13 splice and 68 transcript end variants, as well as several transcript overlaps. Additionally, we determined previously unascertained transcriptional start and polyadenylation sites. We analyzed the transcriptional activity from the complementary DNA strand in five convergent HSV gene pairs with quantitative RT-PCR and detected antisense RNAs in each gene. This part of the study revealed an inverse correlation between the expressions of convergent partners. Our work adds new insights for understanding the complexity of the pervasive transcriptional overlaps by suggesting that there is a crosstalk between adjacent and distal genes through interaction between their transcription apparatuses. We also identified transcripts overlapping the HSV replication origins, which may indicate an interplay between the transcription and replication machineries. The relative abundance of HSV-1 transcripts has also been established by using a novel method based on the calculation of sequencing reads for the analysis.
摘要：
在这项研究中,我们使用PacificBiosciences的扩增同工型测序技术来表征1型单纯疱疹病毒(HSV-1)裂解转录组的poly(A)+部分.我们的分析检测到34个以前未识别的蛋白质编码基因，10个非编码RNA，以及17个多顺反子和复杂转录本。这项工作还使我们确定了许多转录同工型，包括13个剪接和68个转录末端变体，以及几个成绩单重叠。此外,我们确定了以前未确定的转录起始和多聚腺苷酸化位点。我们使用定量RT-PCR分析了五个会聚的HSV基因对中互补DNA链的转录活性，并检测了每个基因中的反义RNA。研究的这一部分揭示了收敛伙伴的表达之间的负相关。我们的工作通过暗示相邻和远端基因之间通过其转录装置之间的相互作用而存在串扰，为理解普遍转录重叠的复杂性增加了新的见解。我们还确定了与HSV复制起点重叠的转录本，这可能表明转录和复制机制之间的相互作用。HSV-1转录物的相对丰度也已经通过使用基于用于分析的测序读段的计算的新方法来建立。
