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Genome-wide Discovery of Circular RNAs in the Leaf and Seedling Tissues of Arabidopsis Thaliana

[ Vol. 18 , Issue. 4 ]

Author(s):

Yongchao Dou, Shengjun Li, Weilong Yang, Kan Liu, Qian Du, Guodong Ren, Bin Yu and Chi Zhang   Pages 360 - 365 ( 6 )

Abstract:


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.

Keywords:

Circular RNAs, Non-coding RNAs, RNA-seq, Bioinformatics of non-coding RNA identification, Next-generation sequencing data analysis.

Affiliation:

School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, State Key Laboratory of Genetic Engineering, Institute of Plant Biology and Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska

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