Natural antisense transcripts and long non-coding RNA in Neurospora crassa.
Natural antisense transcripts and long non-coding RNA in Neurospora crassa.
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DOI：
10.1371/journal.pone.0091353
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Crosthwaite SK
中科院分区：
文献类型：
--
作者：
Arthanari Y;Heintzen C;Griffiths-Jones S;Crosthwaite SK
长链非编码RNA（lncRNA）和天然反义转录物（NAT）在多种生物体中普遍存在。虽然尚未就其全球重要性达成共识，但越来越多的例子已被证明是功能性的，在转录和转录后水平上调节基因表达。在这里，我们使用ABI SOLiD平台的RNA测序数据来鉴定从不同光照和温度条件下生长的丝状真菌粗糙脉孢菌样品中获得的lncRNA和NAT。我们鉴定了939个新的lncRNA，其中477个与注释基因反义。在整个数据集中，有义和反义转录本之间的重叠程度很大：371个有义/反义转录本互补超过500 nt或更多，236个重叠超过1000 nt。最常见的是会聚转录的正义/反义对之间的3′端重叠，但也存在发散转录对和嵌套转录物的例子。我们通过qPCR确认了有义/反义转录物对的子集的表达。我们检查的大小，类型的重叠和表达水平在不同的环境刺激下的光和温度，并确定11 lncRNA的上调响应光。我们还发现，在转录长度和内含子的位置之间的差异，有反义表达的蛋白质编码转录本和转录本没有反义表达。这些结果证明了N. crassa lncRNA和NAT受不同环境刺激的调节，并为进一步研究NAT的功能提供了范围。
The prevalence of long non-coding RNAs (lncRNA) and natural antisense transcripts (NATs) has been reported in a variety of organisms. While a consensus has yet to be reached on their global importance, an increasing number of examples have been shown to be functional, regulating gene expression at the transcriptional and post-transcriptional level. Here, we use RNA sequencing data from the ABI SOLiD platform to identify lncRNA and NATs obtained from samples of the filamentous fungus Neurospora crassa grown under different light and temperature conditions. We identify 939 novel lncRNAs, of which 477 are antisense to annotated genes. Across the whole dataset, the extent of overlap between sense and antisense transcripts is large: 371 sense/antisense transcripts are complementary over 500 nts or more and 236 overlap by more than 1000 nts. Most prevalent are 3′ end overlaps between convergently transcribed sense/antisense pairs, but examples of divergently transcribed pairs and nested transcripts are also present. We confirm the expression of a subset of sense/antisense transcript pairs by qPCR. We examine the size, types of overlap and expression levels under the different environmental stimuli of light and temperature, and identify 11 lncRNAs that are up-regulated in response to light. We also find differences in transcript length and the position of introns between protein-coding transcripts that have antisense expression and transcripts with no antisense expression. These results demonstrate the ability of N. crassa lncRNAs and NATs to be regulated by different environmental stimuli and provide the scope for further investigation into the function of NATs.
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影响因子：
56.9
作者：
Carninci, P;Kasukawa, T;Hayashizaki, Y
通讯作者：
Hayashizaki, Y
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影响因子：
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Lipovich, Leonard
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作者：
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通讯作者：
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影响因子：
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作者：
Lee HC;Li L;Gu W;Xue Z;Crosthwaite SK;Pertsemlidis A;Lewis ZA;Freitag M;Selker EU;Mello CC;Liu Y
通讯作者：
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