A genome-wide investigation of expression characteristics of natural antisense transcripts in liver and muscle samples of pigs.
A genome-wide investigation of expression characteristics of natural antisense transcripts in liver and muscle samples of pigs.
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DOI：
10.1371/journal.pone.0052433
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Huang L
中科院分区：
文献类型：
--
作者：
Chen C;Wei R;Qiao R;Ren J;Yang H;Liu C;Huang L
天然反义转录物是与DNA的有义链互补的内源性转录物。这些转录本已在各种真核生物中被鉴定，并参与广泛的调控事件和生物过程。但其一般生物学功能、表达特征及调控机制尚不清楚。本研究从白色杜洛克×二花脸F2资源群体中采集了497份肝脏和586份肌肉样品。通过基于标签的RNA测序确定正义和反义转录物的表达谱。我们在肝脏和肌肉中分别发现33.7%和20.4%的转录本同时表达有义和反义转录本，12.5%和6.1%的转录本仅表达反义转录本。在geneimprint数据库中，超过32.2%的印迹或预测印迹基因被检测到有义和反义表达。在肝脏和肌肉中，正义-反义对中正义和反义表达之间的相关性是不同的，表现为正相关、负相关或不相关。反义表达增加基因表达变异性。更有趣的是，与正义转录本的eQTL定位相比，其中一个转录本被定位了一个以上的eQTL，每个反义转录本仅被鉴定出一个eQTL，并且反义eQTL中顺式eQTL的百分比高于正义eQTL。这表明反义转录本的表达倾向于由单个基因组位点顺式调节。据我们所知，本研究是第一个系统的研究反义转录在猪。这些发现提高了我们对猪转录组复杂性的理解。
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 F2 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.
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影响因子：
1.5
作者：
Gyoerffy, Andras;Surowiak, Pawel;Gyoerffy, Balazs
通讯作者：
Gyoerffy, Balazs
影响因子：
4.4
作者：
Braunschweig, MH;Van Laere, AS;Andersson, G
通讯作者：
Andersson, G
影响因子：
7
作者：
Morrissy, A. Sorana;Griffith, Malachi;Marra, Marco A.
通讯作者：
Marra, Marco A.
DOI：
10.1126/science.1163853
发表时间：
2008-12-19
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
He Y;Vogelstein B;Velculescu VE;Papadopoulos N;Kinzler KW
通讯作者：
Kinzler KW
影响因子：
56.9
作者：
Katayama, S;Tomaru, Y;Wahlestedt, C
通讯作者：
Wahlestedt, C