An efficient and rapid method to detect and verify natural antisense transcripts of animal genes

文献类型： 外文期刊

第一作者： Zhang Li

作者： Zhang Li;Zhao Rui;Xiao Mei;An Li-long;Lin Shu-dai;Li Bi-xiao;Qiu Feng-fang;Ma Jing-e;Zhang De-xiang;Nie Qing-hua;Zhang Xi-quan

作者机构：

关键词： natural antisense transcripts;transcription orientation;detection method;RNA sequencing;long non-coding RNA

期刊名称：JOURNAL OF INTEGRATIVE AGRICULTURE （ 影响因子：2.848； 五年影响因子：2.979 ）

ISSN： 2095-3119

年卷期： 2016 年 15 卷 9 期

页码：

收录情况： SCI

摘要： High-throughput sequencing has identified a large number of sense-antisense transcriptional pairs, which indicates that these genes were transcribed from both directions. Recent reports have demonstrated that many antisense RNAs, especially IncRNA (long non-coding RNA), can interact with the sense RNA by forming an RNA duplex. Many methods, such as RNA-sequencing, Northern blotting, RNase protection assays and strand-specific PCR, can be used to detect the anti sense transcript and gene transcriptional orientation. However, the applications of these methods have been constrained, to some extent, because of the high cost, difficult operation or inaccuracy, especially regarding the analysis of substantial amounts of data. Thus, we developed an easy method to detect and validate these complicated RNAs. We primarily took advantage of the strand specificity of RT-PCR and the single-strand specificity of S1 endonuclease to analyze sense and antisense transcripts. Four known genes, including mouse beta-actin and Tsix (Xist antisense RNA), chicken LXN (latexin) and GFM1 (G elongation factor, mitochondrial 1), were used to establish the method. These four genes were well studied and transcribed from positive strand, negative strand or both strands of DNA, respectively, which represented all possible cases. The results indicated that the method can easily distinguish sense, antisense and sense-antisense transcriptional pairs. In addition, it can be used to verify the results of high-throughput sequencing, as well as to analyze the regulatory mechanisms between RNAs. This method can improve the accuracy of detection and can be mainly used in analyzing single gene and was low cost.

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