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Integrative analysis of circRNAs acting as ceRNAs involved in ethylene pathway in tomato
Author(s) -
Wang Yunxiang,
Wang Qing,
Gao Lipu,
Zhu Benzhong,
Luo Yunbo,
Deng Zhiping,
Zuo Jinhua
Publication year - 2017
Publication title -
physiologia plantarum
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.351
H-Index - 146
eISSN - 1399-3054
pISSN - 0031-9317
DOI - 10.1111/ppl.12600
Subject(s) - competing endogenous rna , biology , microrna , gene , computational biology , transgene , ethylene , rna , genetics , microbiology and biotechnology , long non coding rna , biochemistry , catalysis
Circular RNAs (circRNAs) are a large class of non‐coding endogenous RNAs that could act as competing endogenous RNAs (ceRNAs) to terminate the mRNA targets' suppression of miRNAs. To elucidate the intricate regulatory roles of circRNAs in the ethylene pathway in tomato fruit, deep sequencing and bioinformatics methods were performed. After strict screening, a total of 318 circRNAs were identified. Among these circRNAs, 282 were significantly differentially expressed among wild‐type and sense‐/antisense‐ LeERF1 transgenic tomato fruits. Besides, 1254 target genes were identified and a large amount of them were found to be involved in ethylene pathway. In addition, a sophisticated regulatory model consisting of circRNAs, target genes and ethylene was set up. Importantly, 61 circRNAs were found to be potential ceRNAs to combine with miRNAs and some of the miRNAs had been revealed to participate in the ethylene signaling pathway. This research further raised the possibility that the ethylene pathway in tomato fruit may be under the regulation of various circRNAs and provided a new perspective of the roles of circRNAs.