Integrative analysis of Arabidopsis thaliana transcriptomics reveals intuitive splicing mechanism for circular RNA.
A new regulatory class of small endogenous RNAs called circular RNAs (circRNAs) has been described as miRNA sponges in animals. Using 16 Arabidopsis thaliana RNA-Seq data sets, we identified 803 circRNAs in RNase R-/non-RNase R-treated samples. The results revealed the following features: Canonical and noncanonical splicing can generate circRNAs; chloroplasts are a hotspot for circRNA generation; furthermore, limited complementary sequences exist not only in introns, but also in the sequences flanking splice sites. The latter finding suggests that multiple combinations between complementary sequences may facilitate the formation of the circular structure. Our results contribute to a better understanding of this novel class of plant circRNAs.
Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China. johnsunx1@yahoo.com, johnsunx1@126.com.
Xiaoyong
X
Sun
Department of Plant Pathology, Nanjing Agricultural University, China.
Lin
L
Wang
Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China.
Jiechao
J
Ding
Department of Plant Pathology, Nanjing Agricultural University, China.
Yanru
Y
Wang
Department of Plant Pathology, Nanjing Agricultural University, China.
Jiansheng
J
Wang
Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China.
Xiaoyang
X
Zhang
Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China.
Yulei
Y
Che
Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China.
Ziwei
Z
Liu
Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China.
Xinran
X
Zhang
Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China.
Jiazhen
J
Ye
Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China.
Jie
J
Wang
Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney, Broadway, NSW, Australia.
Gaurav
G
Sablok
State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
Zhiping
Z
Deng
Department of Plant Pathology, Nanjing Agricultural University, China. hzhao@njau.edu.cn.
Hongwei
H
Zhao
D017360:Arabidopsis / Q000235:genetics*; D002736:Chloroplasts / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D012313:RNA / Q000235:genetics*; D012326:RNA Splicing; D000079962:RNA, Circular; D018749:RNA, Plant / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*
D000079962:RNA, Circular; D018749:RNA, Plant; D012336:RNA, Ribosomal, 16S; D012313:RNA
alternative splicing; back-splicing; chloroplast; complementary sequences