.叶片和幼苗组织中环状RNA的全基因组发现
Genome-wide Discovery of Circular RNAs in the Leaf and Seedling Tissues of .
作者信息
Dou Yongchao, Li Shengjun, Yang Weilong, Liu Kan, Du Qian, Ren Guodong, Yu Bin, Zhang Chi
机构信息
School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA.
State Key Laboratory of Genetic Engineering, Institute of Plant Biology and Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai, China.
出版信息
Curr Genomics. 2017 Aug;18(4):360-365. doi: 10.2174/1389202918666170307161124.
BACKGROUND
Recently, identification and functional studies of circular RNAs, a type of non-coding RNAs arising from a ligation of 3' and 5' ends of a linear RNA molecule, were conducted in mammalian cells with the development of RNA-seq technology.
METHOD
Since compared with animals, studies on circular RNAs in plants are less thorough, a genome-wide identification of circular RNA candidates in Arabidopsis was conducted with our own developed bioinformatics tool to several existing RNA-seq datasets specifically for non-coding RNAs.
RESULTS
A total of 164 circular RNA candidates were identified from RNA-seq data, and 4 circular RNA transcripts, including both exonic and intronic circular RNAs, were experimentally validated. Interestingly, our results show that circular RNA transcripts are enriched in the photosynthesis system for the leaf tissue and correlated to the higher expression levels of their parent genes. Sixteen out of all 40 genes that have circular RNA candidates are related to the photosynthesis system, and out of the total 146 exonic circular RNA candidates, 63 are found in chloroplast.
背景
近年来，随着RNA测序技术的发展，在哺乳动物细胞中对环状RNA（一种由线性RNA分子的3'端和5'端连接产生的非编码RNA）进行了鉴定和功能研究。
方法
由于与动物相比，植物中环状RNA的研究不够深入，因此利用我们自己开发的生物信息学工具，对几个专门针对非编码RNA的现有RNA测序数据集进行了全基因组环状RNA候选物鉴定。
结果
从RNA测序数据中总共鉴定出164个环状RNA候选物，并通过实验验证了4个环状RNA转录本，包括外显子环状RNA和内含子环状RNA。有趣的是，我们的结果表明，环状RNA转录本在叶组织的光合作用系统中富集，并且与其亲本基因的高表达水平相关。所有40个有环状RNA候选物的基因中有16个与光合作用系统相关，在总共146个外显子环状RNA候选物中，有63个存在于叶绿体中。
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