Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People's Republic of China.
PLoS One. 2012;7(12):e52433. doi: 10.1371/journal.pone.0052433. Epub 2012 Dec 20.
Natural antisense transcripts are endogenous transcripts that are complementary to the sense-strand of DNA. These transcripts have been identified in various eukaryotic species and are involved in a broad range of regulatory events and biological processes. However, their general biological functions, expression characteristics and regulatory mechanisms are still unclear. In this study, 497 liver and 586 muscle samples were harvested from a White Duroc×Erhualian F(2) resource population. The expression profiles of sense and antisense transcripts were determined by tag-based RNA sequencing. We identified 33.7% and 20.4% of transcripts having both sense and antisense expression, and 12.5% and 6.1% of transcripts only expressing antisense transcripts in liver and muscle, respectively. More than 32.2% of imprinting or predicted imprinting genes in the geneimprint database were detected with both sense and antisense expression. The correlations between sense and antisense expression in sense-antisense pairs were diverse in both liver and muscle, showing positive, negative or absent correlation. Antisense expression increases gene expression variability. More interestingly, compared to eQTL mapping of sense transcripts in which more than one eQTL was mapped for a transcript, only one eQTL was identified for each antisense transcript, and the percentage of cis-eQTL in antisense eQTL was higher than that in sense eQTL. This suggests that the expressions of antisense transcripts tend to be cis-regulated by a single genomic locus. To our knowledge, this study is the first systematical investigation of antisense transcription in pigs. The findings improve our understanding of the complexity of porcine transcriptome.
天然反义转录本是与 DNA 正义链互补的内源性转录本。这些转录本已在各种真核生物中被鉴定出来，并参与了广泛的调节事件和生物过程。然而，它们的一般生物学功能、表达特征和调控机制尚不清楚。在这项研究中，我们从一个大白杜洛克×长白猪 F2 资源群体中采集了 497 份肝脏和 586 份肌肉样本。通过基于标签的 RNA 测序来确定正义和反义转录本的表达谱。我们分别在肝脏和肌肉中鉴定出 33.7%和 20.4%的转录本具有正反义表达，12.5%和 6.1%的转录本仅表达反义转录本。在基因印记数据库中，超过 32.2%的印记或预测的印记基因被检测到具有正反义表达。在肝脏和肌肉中，正、负或不存在相关性的情况都存在于正义和反义表达的相关性中。反义表达增加了基因表达的变异性。更有趣的是，与正义转录本的 eQTL 作图相比，在其中一个转录本上可以映射到多个 eQTL，而每个反义转录本只鉴定到一个 eQTL，反义 eQTL 中的顺式 eQTL 比例高于正义 eQTL。这表明反义转录本的表达倾向于由单个基因组座的顺式调控。据我们所知，这项研究是首次对猪的反义转录进行的系统研究。研究结果提高了我们对猪转录组复杂性的理解。
