Full-Length Isoform Sequencing Reveals Novel Transcripts and Substantial Transcriptional Overlaps in a Herpesvirus.
Full-Length Isoform Sequencing Reveals Novel Transcripts and Substantial Transcriptional Overlaps in a Herpesvirus.
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DOI：
10.1371/journal.pone.0162868
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Boldogkői Z
中科院分区：
文献类型：
--
作者：
Tombácz D;Csabai Z;Oláh P;Balázs Z;Likó I;Zsigmond L;Sharon D;Snyder M;Boldogkői Z
全转录组研究对于理解遗传调控的复杂性至关重要。然而，传统应用的短读测序平台不能可靠地区分许多转录异构体。太平洋生物科学（PacBio） RS II平台能够在单次测序运行中读取长核酸延伸。伪狂犬病毒（PRV）是研究疱疹病毒基因表达和转录单位之间潜在相互作用的良好系统。在这项工作中，使用非扩增和扩增的同种异构体测序方案来表征PRV裂解转录组的poly（A+）部分，目的是对病毒基因进行完整的转录注释。分析揭示了以前未被认识到的PRV转录组的复杂性，包括发现新的蛋白质编码和非编码基因，新的单反反子和多反反子转录单位，以及邻近和远端基因之间广泛的转录重叠。本研究发现了重叠PRV所有三个复制起点的非编码转录本，这可能在控制DNA合成中起作用。我们还建立了基因产物的相对表达水平。我们的研究表明，整个PRV基因组都被用于转录，包括所有编码区域和基因间区域的DNA链。转录物重叠在全基因组范围内的发生表明，基因之间通过相互作用的转录机制形成的网络进行串扰，该网络具有控制基因表达的潜在功能。
Whole transcriptome studies have become essential for understanding the complexity of genetic regulation. However, the conventionally applied short-read sequencing platforms cannot be used to reliably distinguish between many transcript isoforms. The Pacific Biosciences (PacBio) RS II platform is capable of reading long nucleic acid stretches in a single sequencing run. The pseudorabies virus (PRV) is an excellent system to study herpesvirus gene expression and potential interactions between the transcriptional units. In this work, non-amplified and amplified isoform sequencing protocols were used to characterize the poly(A+) fraction of the lytic transcriptome of PRV, with the aim of a complete transcriptional annotation of the viral genes. The analyses revealed a previously unrecognized complexity of the PRV transcriptome including the discovery of novel protein-coding and non-coding genes, novel mono- and polycistronic transcription units, as well as extensive transcriptional overlaps between neighboring and distal genes. This study identified non-coding transcripts overlapping all three replication origins of the PRV, which might play a role in the control of DNA synthesis. We additionally established the relative expression levels of gene products. Our investigations revealed that the whole PRV genome is utilized for transcription, including both DNA strands in all coding and intergenic regions. The genome-wide occurrence of transcript overlaps suggests a crosstalk between genes through a network formed by interacting transcriptional machineries with a potential function in the control of gene expression.
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影响因子：
3.7
作者：
Boldogköi Z
通讯作者：
Boldogköi Z
Biopython：用于计算分子生物学和生物信息学的免费 Python 工具。
DOI：
10.1093/bioinformatics/btp163
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cock PJ;Antao T;Chang JT;Chapman BA;Cox CJ;Dalke A;Friedberg I;Hamelryck T;Kauff F;Wilczynski B;de Hoon MJ
通讯作者：
de Hoon MJ
影响因子：
56.9
作者：
Bertone, P;Stolc, V;Snyder, M
通讯作者：
Snyder, M
影响因子：
3.8
作者：
Camacho, A;Tabares, E
通讯作者：
Tabares, E
影响因子：
56.9
作者：
Katayama, S;Tomaru, Y;Wahlestedt, C
通讯作者：
Wahlestedt, C