Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana.
Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana.
复制标题
拟南芥顺式天然反义转录本的全基因组预测和鉴定。
DOI：
10.1186/gb-2005-6-4-r30
复制
发表时间：
2005
期刊：
影响因子：
12.3
通讯作者：
Chua NH
中科院分区：
文献类型：
--
作者：
Wang XJ;Gaasterland T;Chua NH
一种新的计算方法用于预测拟南芥中顺式编码的自然反义转录本(NAT)，确定了1,340个潜在的NAT对。证实了957对NAT正义和反义转录本的表达，对MPSS数据的分析表明，对于大多数NAT对，两种转录本中的一种主要以组织特异性的方式表达。天然反义转录本(NAT)是一类与其他转录本具有序列互补性的内源性编码或非蛋白质编码的RNA。一些证据表明，顺式和反式NAT可能参与了广泛的基因调控事件。人类、小鼠和水稻中的顺式NAT的全基因组鉴定表明，它们广泛存在于真核生物中。然而，对模式植物拟南芥中的顺式NAT知之甚少。我们开发了一种新的计算方法来预测和识别拟南芥中顺式编码的NAT，并发现了1340个潜在的NAT对。利用拟南芥全长cDNA和公开的大规模并行签名测序(MPSS)数据证实了957个NAT对的正义和反义转录产物的表达。三个已知的或可能的拟南芥印迹基因都有顺式反义转录本。两个拟南芥NAT对的序列和基因组排列在水稻中是保守的。我们在NAT预测工作中结合了来自全长cDNA和拟南芥基因组注释的信息，并报告了仅使用两个数据集中的一个无法识别的顺式NAT对。对MPSS数据的分析表明，对于大多数拟南芥cis-NAT对，两个转录本中的一个以组织特异性的方式表达。
A new computational method for predicting cis-encoded natural antisense transcripts (NATs) in Arabidopsis identified 1,340 potential NAT pairs. The expression of both sense and antisense transcripts of 957 NAT pairs was confirmed, and analysis of MPSS data suggested that for most pairs one of the two transcripts is predominantly expressed in a tissue-specific manner. Natural antisense transcripts (NAT) are a class of endogenous coding or non-protein-coding RNAs with sequence complementarity to other transcripts. Several lines of evidence have shown that cis- and trans-NATs may participate in a broad range of gene regulatory events. Genome-wide identification of cis-NATs in human, mouse and rice has revealed their widespread occurrence in eukaryotes. However, little is known about cis-NATs in the model plant Arabidopsis thaliana. We developed a new computational method to predict and identify cis-encoded NATs in Arabidopsis and found 1,340 potential NAT pairs. The expression of both sense and antisense transcripts of 957 NAT pairs was confirmed using Arabidopsis full-length cDNAs and public massively parallel signature sequencing (MPSS) data. Three known or putative Arabidopsis imprinted genes have cis-antisense transcripts. Sequences and the genomic arrangement of two Arabidopsis NAT pairs are conserved in rice. We combined information from full-length cDNAs and Arabidopsis genome annotation in our NAT prediction work and reported cis-NAT pairs that could not otherwise be identified by using one of the two datasets only. Analysis of MPSS data suggested that for most Arabidopsis cis-NAT pairs, there is predominant expression of one of the two transcripts in a tissue-specific manner.