RNA-Seq Identifies Circular RNAs in Arabidopsis

Leaf growth and senescence are controlled by tight genetic factors involved regulation at multiple levels. Circular RNAs (circRNAs) have recently been reported as the microRNA sponge to accomplish corresponding regulatory roles. This study aims to explore the expression profile and functional role of circRNAs in Arabidopsis leaf growth and senescence. Researchers at East China Normal University used publically available RNA-seq data of Arabidopsis leaves to identify the circular RNA expression profile and used quantitative real-time PCR to validate their identified circRNAs. The functions of circRNAs were explored using distinct bioinformatics methods including analysis of network, gene ontology and KEGG pathway. The researchers identified 168 circRNAs, including 40 novel circRNAs, in Arabidopsis thaliana leaves, with 158 (94.1%) circRNAs arising from the exons of genes. Real-time PCRs were used to verify 4 highly expressed circRNAs and they all showed consistent expression patterns with the RNA-seq results. Interestingly, 6 and 35 circRNAs were differentially expressed at G- to -M stage and M- to -S stage, respectively. The circRNAs display an upregulation trend during the lifespan of Arabidopsis leaves. Moreover, the expression of circRNAs during senescence is independent of host gene expression to a certain degree. The gene ontology (GO) and KEGG pathway analysis of the targeted mRNA of circRNA-miRNA-mRNA network showed that the circRNAs may be involved in plant hormone signal transduction, Porphyrin and chlorophyll metabolism during leaves senescence. This comprehensive analysis of the expression profile of circRNAs and their potential functions during leaf growth and senescence suggest that circRNAs may function as new post-transcriptional regulators in the senescence of Arabidopsis leaves.

The distribution of circRNAs during the lifespan of leaves and expression pattern of DE-circRNAs

rna-seq

(A) Numbers of circRNAs at G- to -M and M- to -S. (B) Numbers of DE-circRNAs at G- to -M and M- to -S. (C) Heat maps showing the expression patterns of 38 DE-circRNAs during leaf growth, maturation and senescence.

Liu T, Zhang L, Chen G, Shi T. (2017) Identifying and Characterizing the Circular RNAs during the Lifespan of Arabidopsis Leaves. Front Plant Sci 8:1278. [article]

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