Integrative analysis of circRNAs acting as ceRNAs involved in ethylene pathway in tomato

Abstract

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.

Systematic identification and analysis of heat‐stress‐responsive lncRNAs, circRNAs and miRNAs with associated co‐expression and ceRNA networks in cucumber (Cucumis sativus L.)

“…These three mRNAs are pivotal genes in the plant hormone signal transduction pathway according to KEGG analysis. et al 2013, Hansen et al 2013a, 2013b, Wang et al 2017b. Expression profiles of some plant circRNAs showed a positive correlation with their parental genes (Ye et al 2015, Pan et al 2018.…”

“…Reports have indicated that circRNAs play important roles in miRNA‐mediated posttranscriptional regulation of gene expression by acting as ceRNAs (Sebastian et al , Hansen et al , , Wang et al ). Expression profiles of some plant circRNAs showed a positive correlation with their parental genes (Ye et al , Pan et al ).…”

“…In addition to participating in biotic and abiotic stresses, circRNAs are also involved in a series of physiological and biochemical metabolic pathways during plant growth and development. Recently, Wang et al () used ‘Zhongcai No. 4’ and LeERF1 transgenic tomato plants to verify the possible role of circRNA in regulating ethylene metabolism‐related pathways in tomato fruits.…”

“…For example, two circRNAs, ciRs‐7/CDR1 and Sry, have been reported to be miRNA sponges in humans (Sebastian et al , Hansen et al , ). In addition, circRNAs, as ceRNAs, are involved in the complex regulation of ethylene in tomato fruits (Wang et al ). Competition of lncRNAs with other miRNA sponges has an important role in plants and animals (Franco‐Zorrilla et al , Sumazin et al , Wang et al , Wu et al , Zhang et al ).…”

Identification and Characterization of circRNAs Responsive to Methyl Jasmonate in Arabidopsis thaliana

“…Furthermore, although most circRNAs are considered to be noncoding RNAs, some circRNAs undergo cap-free translation under certain conditions [14]. Recently, increasing numbers of circRNAs have been detected in Arabidopsis thaliana [15][16][17], maize [18][19][20], rice [15,21], tomato [22][23][24], wheat [25][26][27], and grape [28], indicating that circRNAs are widespread in plants. Plant circRNAs are as conserved and tissue specific as animal circRNAs, but their flanking introns do not contain as many repetitive elements and reverse complementary sequences as those in animals [15,16,19,29].…”