Genome-Wide Identification of Circular RNAs in Arabidopsis thaliana

Chen, Gang; Cui, Jiawen; Wang, Li; Zhu, Yingfang; Lu, Zhaogeng; Jin, Biao

doi:10.3389/fpls.2017.01678

Cited by 81 publications

(44 citation statements)

References 53 publications

(108 reference statements)

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“…In this study, a total of 2616 circRNAs were identified and widely existed in the whole genome of sea buckthorn. Among them, exonic circRNAs were predominant circRNAs (65.83%), which were similar to circRNAs in many species, including human, Arabidopsis and tomato [5,7,17,27]. In addition, distribution analysis showed that circRNAs have not preference between different sea buckthorn chromosome, which is consistent with the past researches [26,28,29].…”

Section: Disscusionsupporting

confidence: 84%

“…In human, ciRS-7 was reported to be a negative regulator of miR-7 [40]. Many circRNAs that contained miRNA binding sites were also found to be potential eTMs in Arabidopsis, rice and tomato [27,39]. In this study, we found that 53 DEcircRNAs contain miRNA binding sites in circRNA-miRNA-mRNA network, suggesting that these circRNAs may function as miRNA sponges in sea buckthorn fruit.…”

Section: Disscusionmentioning

confidence: 53%

“…Recently, accumulating studies demonstrated that circRNAs played important roles in various biological processes. In plant, circRNAs were predicted by RNA sequencing and bioinformatics tools in Arabidopsis, rice, wheat, barley, soybean, maize and kiwifruit [7,18,[27][28][29]. And some plant development related circRNAs were identified in many species.…”

Section: Disscusionmentioning

confidence: 99%

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Identification and characterization of circular RNAs during the sea buckthorn fruit development

Zhang

Chen

et al. 2019

RNA Biology

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As a rising star of noncoding RNA, circular RNAs (circRNAs) have a covalently closed loop structure, which formed by 3ʹ-5ʹ ligation during splicing. A few circRNAs were identified and thought to be transcriptional noise due to cognitive defect over the past 40 years. Recently, with the development of high-throughput RNA sequencing techniques and specific algorithms for circRNA detection and quantification, plenty of potential circRNAs were identified in many species which play important roles in various biological processes. However, researches on circRNAs in fruit ripening process were lacking. Here, we totally identified 2616 circRNAs in sea buckthorn fruit development process, which uniformly distributed in sea buckthorn chromosome. Among them, 1721 (65.8%) circRNAs were arising from the exons of their host genes, 252 circRNAs were identified as the differentially expressed circRNAs (DEcircRNAs) between three different development stages, and 181 (71.8%) DEcircRNAs had sequence similarity with 235 identified circRNAs from five know plant species. Functional annotation revealed that host genes of DEcircRNAs were predicted to be involved in carotenoid biosynthesis, lipid synthesis and plant hormone signal transduction. Additionally, 53 DEcircRNAs were predicted as the corresponding nine miRNAs sponges in sea buckthorn. Divergent reverse-transcription PCR and RT-qPCR were used for validate the differential expression and back-splicing sites of six DEcircRNAs. These results revealed the role of circRNAs in sea buckthorn fruit ripening process and promoted the noncoding RNA researches in plants.

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Section: Disscusionsupporting

confidence: 84%

Section: Disscusionmentioning

confidence: 53%

Section: Disscusionmentioning

confidence: 99%

See 1 more Smart Citation

Identification and characterization of circular RNAs during the sea buckthorn fruit development

Zhang

Chen

et al. 2019

RNA Biology

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“…Similar research found that circRNAs play an important role in the regulation and control of tomato fruits (Yin et al ). 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 , Chen et al , Conn et al , Tan et al , Zhao et al , Zhou et al ). However, at present, comprehensive studies of circRNA in plants are lacking, and the functions of circRNA have not yet been clarified.…”

Section: Introductionmentioning

confidence: 99%

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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“…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%

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 Identification of Circular RNAs in Arabidopsis thaliana

Cited by 81 publications

References 53 publications

Identification and characterization of circular RNAs during the sea buckthorn fruit development

Identification and characterization of circular RNAs during the sea buckthorn fruit development

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

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