Identification and characterization of CircRNAs involved in the regulation of wheat root length

Abstract

Background Recent studies indicate that circular RNAs (circRNAs) may play important roles in the regulation of plant growth and development. Plant roots are the main organs of nutrient and water uptake. However, whether circRNAs involved in the regulation of plant root growth remains to be elucidated. Methods LH9, XN979 and YN29 are three Chinese wheat varieties with contrasting root lengths. Here, the root circRNA expression profiles of LH9, XN979 and YN29 were examined by using high-throughput sequencing technology. Results Thirty-three and twenty-two differentially expressed circRNAs (DECs) were identified in the YN29-LH9 comparison and YN29-XN979 comparison, respectively. Among them, ten DECs coexisted in both comparisons. As the roots of both LH9 and XN979 were significantly larger and deeper than YN29, the ten DECs coexisting in the two comparisons were highly likely to be involved in the regulation of wheat root length. Moreover, three of the ten DECs have potential miRNA binding sites. Real-time PCR analysis showed that the expression levels of the potential binding miRNAs exhibited significant differences between the long root plants and the short root plants. Conclusions The expression levels of some circRNAs exhibited significant differences in wheat varieties with contrasting root phenotypes. Ten DECs involved in the regulation of wheat root length were successfully identified in which three of them have potential miRNAs binding sites. The expression levels of putative circRNA-binding miRNAs were correlated with their corresponding circRNAs. Our results provide new clues for studying the potential roles of circRNAs in the regulation of wheat root length. Electronic supplementary material The online version of this article (10.1186/s40659-019-0228-5) contains supplementary material, which is available to authorized users.

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

“…To reveal whether DEcircRNAs can target miRNAs and participate in the transcriptional regulation of genes, we identified 385 DEcircRNAs predicted to contain miRNA decoy sites. As expected, 36 of the 385 DEcircRNAs were predicted to have one to nine miRNA decoy sites, which is consistent with other studies in plants [26,27,57]. For instance, circRNA Chr4:12480688|12481259 has nine miRNA decoy sites, indicating that it might regulate various processes through different miRNAs.…”

“…Recently, with the development of high-throughput sequencing technology, increasing numbers of circRNAs have been detected in plants and animals. In plants, circRNAs are closely related to plant development and stress responses, including biotic and abiotic stresses [20,[22][23][24][25][26][27][28]30,53]. However, whether circRNAs participate in the pathways of plant responses to hormones is unclear.…”

“…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].…”

Systematic identification and characterization of circular RNAs involved in flag leaf senescence of rice

“…Accumulating evidences have demonstrated that circRNAs play important functions in various biological processes including stress, growth and development (Barrett and Salzman 2016 ). With the rapid development of high-throughput sequencing and bioinformatics technology, a vast number of circRNAs have been identified in plants, such as trifoliate orange (Zeng et al 2018 ), cucumber (Zhu et al 2019 ), wheat (Xu et al 2019 ), Arabidopsis (Chen et al 2017b ) and maize (Han et al 2020 ), revealing their important roles in multiple different biological process. Some plant development related circRNAs were also identified.…”

Transcriptomic Analysis Reveals the Contribution of QMrl-7B to Wheat Root Growth and Development

“…Overexpression of the transcription factor (TF)-encoding genes TaNAC2-5A [21], TaNFYA-B1 [22], TaNAC69-1 [23] and TaWRKY51 [24] resulted in enhanced root growth, while the TF-encoding gene TabZIP60 [25] had the opposite effects, implying a complex genetic basis of the formation of root traits. In addition, circular RNAs have been shown to participate in root length regulation [26].…”