文献类型：期刊文献

中文题名：An efficient and rapid method to detect and verify natural antisense transcripts of animal genes

英文题名：An efficient and rapid method to detect and verify natural antisense transcripts of animal genes

作者：Zhang Li[1];Zhao Rui[1];Xiao Mei[1];Lin Shu-dai[2];Li Bi-xiao[2];Qiu Feng-fang[2];Ma Jing-e[2];Zhang De-xiang[2];Nie Qing-hua[2];An Li-long[1];Zhang Xi-quan[2]

机构：[1]Guangdong Ocean Univ, Coll Agr, Zhanjiang 524088, Peoples R China;[2]South China Agr Univ, Guangdong Prov Key Lab Agroanim Genom & Mol Breed, Key Lab Chicken Genet Breeding & Reprod, Minist Agr, Guangzhou 510642, Guangdong, Peoples R China

年份：2016

卷号：15

期号：9

起止页码：2070

中文期刊名：Journal of Integrative Agriculture

外文期刊名：JOURNAL OF INTEGRATIVE AGRICULTURE

收录：SCI-EXPANDED(收录号：WOS:000383411900014)、CSTPCD、、CSCD2015_2016、Scopus(收录号：2-s2.0-84998772080)、WOS、CSCD

基金：This work was supported by the National Natural Science Foundation of China (31301958) and the Chinese Postdoctoral Science Foundation (2013T60808).

语种：英文

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

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

中文摘要：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 lnc RNA（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 antisense 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 β-actin and Tsix（Xist antisense RNA）, chicken LXN（latexin） and GFM1（Gelongation 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.

外文摘要：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.