Identification and characterization of circRNAs involved in the regulation of low nitrogen-promoted root growth in hexaploid wheat

Ren, Yongzhe; Yue, Huifang; Li, Le; Yan, Xu; Wang, Zhiqiang; Xin, Zhouping; Lin, Tongbao

doi:10.1186/s40659-018-0194-3

Cited by 35 publications

(30 citation statements)

References 38 publications

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“…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.…”

Section: Discussionsupporting

confidence: 90%

“…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%

“…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%

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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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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Zhang

Liu

Zhu

et al. 2020

IJMS

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“…For example, circRNAs can function as transcriptional and posttranscriptional regulators, miRNA sponges, small nucleolar RNAs (snoRNAs), RNA processing intermediates, and transcriptional cis-regulators [19][20][21]. Moreover, increasing amounts of evidence have indicated that circRNAs play a key role in plant responses to abiotic stress [20,[22][23][24][25][26]. For example, cir-cRNAs are involved in plant dehydration and immune responses [26], chilling stress [27], heat stress [20], dehydration [28], infection by pathogenic bacteria [19,21], and LP stress [29].…”

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confidence: 99%

Transcriptome-wide identification of novel circular RNAs in soybean in response to low-phosphorus stress

Lü

et al. 2020

PLoS ONE

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Low-phosphorus (LP) stress is a major factor limiting the growth and yield of soybean. Circular RNAs (circRNAs) are novel noncoding RNAs that play a crucial role in plant responses to abiotic stress. However, how LP stress mediates the biogenesis of circRNAs in soybean remains unclear. Here, to explore the response mechanisms of circRNAs to LP stress, the roots of two representative soybean genotypes with different P-use efficiency, Bogao (a LPsensitive genotype) and Nannong 94156 (a LP-tolerant genotype), were used for the construction of RNA sequencing (RNA-seq) libraries and circRNA identification. In total, 371 novel circRNA candidates, including 120 significantly differentially expressed (DE) cir-cRNAs, were identified across different P levels and genotypes. More DE circRNAs were significantly regulated by LP stress in Bogao than in NN94156, suggesting that the tolerant genotype was less affected by LP stress than the sensitive genotype was; in other words, NN94156 may have a better ability to maintain P homeostasis under LP stress. Moreover, a positive correlation was observed between the expression patterns of P stress-induced cir-cRNAs and their circRNA-host genes. Gene Ontology (GO) enrichment analysis of these circRNA-host genes and microRNA (miRNA)-targeted genes indicated that these DE cir-cRNAs were involved mainly in defense responses, ADP binding, nucleoside binding, organic substance catabolic processes, oxidoreductase activity, and signal transduction. Together, our results revealed that LP stress can significantly alter the genome-wide profiles of circRNAs and indicated that the regulation of circRNAs was both genotype and environment specific in response to LP stress. LP-induced circRNAs might provide a rich resource for LP-responsive circRNA candidates for future studies.

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“…Meanwhile, some TaSPL genes were targeted by other miRNAs, such as TaSPL16 and TaSPL13 targeted by miR9780, TaSPL2-B and TaSPL14-D by miR9677b and TaSPL3 by miR319. As reported, miR9780 may be involved in low-nitrogen-promoted root growth [71], miR9677b in pollen development [72] and miR319 in the development of embryo patterning and leaf morphogenesis [73]. These results revealed that complex regulatory network between TaSPL genes and miRNAs affected the potential function of TaSPL genes, which should be con rmed by genetic modi cation in the expression levels of speci c miRNAs or target TaSPL genes of wheat in future.…”

Section: Taspl Genes May Be Targets By Mir156mentioning

confidence: 51%

Genome-wide analysis of structures and characteristics of the SPL gene family in wheat (Triticum aestivum L.)

Li¹,

Shi²,

Guan³

et al. 2020

Preprint

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Background: The SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) genes encode a family of plant-specific transcription factors that contain a conservative SBP domain. SPL proteins play important roles in plant growth and development, such as plant architecture, flowering regulation, and grain yield. However, the systematic analysis of TaSPL gene family in wheat is lacking.Results: In this study, 56 TaSPL genes were identified from wheat genome and divided into eight groups (G1-G8), according to the phylogenetic analysis of TaSPL proteins among numbers of plant species. Bioinformatics method were applied to analyse the gene structure, motif, chromosome localization, segmental duplication and synteny of total TaSPL genes and the results showed that their characteristics were different among group in the exon-intron constitution, conserved and specific motif. The expansion and evolution of the TaSPL genes occurred within the wheat genome. Total 28 of 56 TaSPL genes were predicted to be putative targets for miR156, which revealed the importance of miR156-mediated regulation in wheat. Moreover, transcript level analysis of TaSPL genes in wheat tissues by qRT-PCR discovered the diversified spatiotemporal expression patterns, based on the comparison with reference RNA-seq data. Some TaSPL genes were subject to various stress treatments including drought and hormones, etc. suggesting that these part genes probably involved in responding to hormone signals during different wheat development stages. Conclusions: Our findings show that TaSPL genes may regulate the development of spike and grain, resistance to abiotic stresses, and involve in responding to hormone signals. These results could provide a fundamentally information to further study of the functions of TaSPL genes in wheat growth and development.

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Identification and characterization of circRNAs involved in the regulation of low nitrogen-promoted root growth in hexaploid wheat

Cited by 35 publications

References 38 publications

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

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

Transcriptome-wide identification of novel circular RNAs in soybean in response to low-phosphorus stress

Genome-wide analysis of structures and characteristics of the SPL gene family in wheat (Triticum aestivum L.)

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