Identification of circular RNAs and their targets during tomato fruit ripening

Yin, Junliang; Liu, Mengyu; Ma, Dongfang; Wu, Jiawen; Li, Shenglan; Zhu, Yong‐Guan; Han, Bin

doi:10.1016/j.postharvbio.2017.10.013

Cited by 71 publications

(78 citation statements)

References 55 publications

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“…It has been reported that 53 differentially expressed circRNAs were predicted as the corresponding nine miRNAs sponges and play a role in the sea buckthorn fruit ripening process (Zhang et al 2019a(Zhang et al , 2019b. Similar research found that circRNAs play an important role in the regulation and control of tomato fruits (Yin et al 2018). CircRNA is widely distributed in plants and has been identified in several plants such as Arabidopsis, rice, tomato and soybean using deep RNA-seq and bioinformatic tools (Lu et al 2015, Chen et al 2017, Conn et al 2017, Tan et al 2017, Zhao et al 2017, Zhou et al 2018.…”

Section: Introductionmentioning

confidence: 91%

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

Guo

Wang

et al. 2019

Physiologia Plantarum

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Researchers have shown that long non‐coding RNAs (lncRNAs) and circular RNAs (circRNAs) act as competitive endogenous RNAs (ceRNAs) and are mutually regulated by competition for binding to common microRNA response elements (MREs). However, a comprehensive identification and analysis of lncRNAs and circRNAs as ceRNAs have not yet been completed in cucumber (Cucumis sativus L.) exposed to high‐temperature stress. In our study, 32 663 coding transcripts, 2085 lncRNAs, 2477 circRNAs and 348 differentially expressed miRNAs were identified using RNA sequencing. In addition, six heat‐stress‐responsive miRNAs (five known and one novel miRNAs) and eight lncRNAs were selected for qPCR to confirm their expression profiles. By analyzing the cis effects of lncRNAs, we constructed a lncRNA‐mRNA co‐expression network. Based on the results, the corresponding lncRNAs play a regulatory role in the stress response in cucumber plants. In our study, the PatMatch software was used to predict the potential function of lncRNAs and circRNAs as ceRNAs. A total of 18 lncRNAs and seven circRNAs were predicted to bind to 114 differentially expressed miRNAs and compete with 359 mRNAs for miRNA binding sites. These mRNAs are predicted to be involved in various pathways, such as plant hormone signal transduction, plant–pathogen interaction and glutathione metabolism. Among them, TCONS_00031790, TCONS_00014332, TCONS_00014717, TCONS_00005674, novel_circ_001543 and novel_circ_000876 may interact with miR9748 by plant hormone signal transduction pathways in response to high‐temperature stress. Moreover, indole‐3‐acetic acid (IAA) and 1‐aminocyclopropane‐l‐carboxylic acid (ACC) levels decreased in the high‐temperature treatment group, indicating that IAA and ethylene signaling might be involved in response to high‐temperature stress. In this study, we conducted a full transcriptomic analysis in response to high‐temperature stress in cucumber and, for the first time, integrated the potential ceRNA functions of lncRNAs/circRNAs. The results provide a basis for studying the potential functions of lncRNAs/circRNAs in response to high‐temperature stress.

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Section: Introductionmentioning

confidence: 91%

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

Guo

Wang

et al. 2019

Physiologia Plantarum

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“…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.…”

Section: Discussionmentioning

confidence: 99%

“…qRT-PCR was carried out with SYBR Green Master Mix (Vazyme, Nanjing, China) on a CFX 96 Real-Time PCR system (Bio-Rad, Hercules, CA, USA). The qRT-PCR procedure was as follows: 95 • C for 3 min, followed by 45 cycles of 95 • C for 30 s and 60 • C for 30 s. The 22 −∆∆Ct method was used to calculate the relative expression of circRNAs [24,69], with GAPDH as the reference gene. The primers are listed in Table S5.…”

Section: Validation Of Circrnasmentioning

confidence: 99%

“…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].…”

Section: Introductionmentioning

confidence: 99%

“…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]. Recent studies have suggested that plant circRNAs play functional roles in developmental processes and stress responses, including the responses to drought, chilling injury, nutrient deficiency, and pathogen invasion [19,20,22,24,25,30]. Based on the functions of animal circRNAs, circRNA-miRNA-mRNA networks have been generated for plants; these networks suggest that plant circRNAs may act as miRNA sponges to regulate functional gene expression [23,25,31].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

Zhang

Liu

Zhu

et al. 2020

IJMS

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Circular RNAs (circRNAs) are endogenous noncoding RNAs with covalently closed continuous loop structures that are formed by 3 -5 ligation during splicing. These molecules are involved in diverse physiological and developmental processes in eukaryotic cells. Jasmonic acid (JA) is a critical hormonal regulator of plant growth and defense. However, the roles of circRNAs in the JA regulatory network are unclear. In this study, we performed high-throughput sequencing of Arabidopsis thaliana at 24 h, 48 h, and 96 h after methyl JA (MeJA) treatment. A total of 8588 circRNAs, which were distributed on almost all chromosomes, were identified, and the majority of circRNAs had lengths between 200 and 800 bp. We identified 385 differentially expressed circRNAs (DEcircRNAs) by comparing data between MeJA-treated and untreated samples. Gene Ontology (GO) enrichment analysis of the host genes that produced the DEcircRNAs showed that the DEcircRNAs are mainly involved in response to stimulation and metabolism. Additionally, some DEcircRNAs were predicted to act as miRNA decoys. Eight DEcircRNAs were validated by qRT-PCR with divergent primers, and the junction sites of five DEcircRNAs were validated by PCR analysis and Sanger sequencing. Our results provide insight into the potential roles of circRNAs in the MeJA regulation network.

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Genome‐wide analysis of ethylene‐insensitive3 (EIN3/EIL) in Triticum aestivum

Wen-di

Yang

et al. 2020

Crop Science

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Ethylene-insensitive proteins (EIN3/EIL) are a class of nuclear localization proteins with DNA-binding activity. EIL is an important gene family in plants, and plays key roles in the ethylene signaling pathway which regulates a broad spectrum of plant growth and development, as well as defenses to various biological and abiotic stresses. Although genome-wide analyses of EIL gene family has been carried out for several plant species, no comprehensive analysis of this family in Triticum aestivum L. has been reported so far. Furthermore, there are few scattered studies on the functions of EIL genes in wheat. It is necessary to comprehensively identify and analyze the EIL gene family in wheat. In this study, BLASTp were used to identify EIL genes in the lately released reference genome of T. aestivum. The 21 TaEIL genes were sought, which can be divided into three groups (a, b, and c) according to phylogenetic relationship. The nonsynonymous/synonymous substitution rates (Ka/Ks) value showed that three homologous pairs (TaEILb.4/TaEILb.6, TaEILa.8/TaEILa.7, and TaEILa.8/TaEILa.9) experienced strongly purifying selection. The remaining 16 homologous pairs underwent positive selection with an evolutionary acceleration. Analysis of gene structure and motif, protein features, and three-dimensional structure showed that TaEILs were similar with EILs in other species such as Arabidopsis, rice, and maize. Homology analyses of EIL in T. aestivum and its progenitors showed that EIL gene discarded some redundant genes during the domestication evolution of T. aestivum and retained some useful genes. Gene expression patterns analyses and

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Identification of circular RNAs and their targets during tomato fruit ripening

Cited by 71 publications

References 55 publications

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

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

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

Genome‐wide analysis of ethylene‐insensitive3 (EIN3/EIL) in Triticum aestivum

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