miRNA alteration is an important mechanism in sugarcane response to low-temperature environment

Yang, Yuting; Zhang, Xu; Su, Yachun; Zou, Jiake; Wang, Zhoutao; Xu, Liping; Que, Youxiong

doi:10.1186/s12864-017-4231-3

Cited by 68 publications

(37 citation statements)

References 73 publications

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“…Mutum et al () identified miR6196 from the drought‐tolerant rice variety Nagina 22. Yang et al () found that miR6196 showed significant differential expression under cold stress and was specifically differentially expressed in sugarcane cultivars ROC22 (relatively cold‐sensitive). We constructed the ceRNA network of TCONS_00031790, TCONS_00014332, TCONS_00014717 and TCONS_00005674, novel_circ_001543, novel_circ_000876, Csa1M690240.1, Csa6M091930.1, Csa7M405830.1 and miR9748.…”

Section: Discussionmentioning

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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Section: Discussionmentioning

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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“…Yongbin Ou et al found that stu-miR4414 was down-regulated in the frozen potato tubers [ 47 ], which is similar to our results in S. aculeatissimum . Interestingly, miR5813 was also found to be involved in cold stress in Sugarcane [ 48 ]. In tomato, miR5813 was also verified to be involved in environmental stress [ 49 ].…”

Section: Discussionmentioning

confidence: 99%

Cold-responsive miRNAs and their target genes in the wild eggplant species Solanum aculeatissimum

Liu

Zhang

et al. 2017

BMC Genomics

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BackgroundLow temperature is an important abiotic stress in plant growth and development, especially for thermophilic plants. Eggplants are thermophilic vegetables, although the molecular mechanism of their response to cold stress remains to be elucidated. MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that play an essential role during plant development and stress responses. Although the role of many plant miRNAs in facilitating chilling tolerance has been verified, little is known about the mechanisms of eggplant chilling tolerance.ResultsHere, we used high-throughput sequencing to extract the miRNA and target genes expression profiles of Solanum aculeatissimum (S. aculeatissimum) under low temperature stress at different time periods(0 h, 2 h, 6 h, 12 h, 24 h). Differentially regulated miRNAs and their target genes were analyzed by comparing the small RNA (sRNA) and miRBase 20.0 databases using BLAST or BOWTIE, respectively. Fifty-six down-regulated miRNAs and 28 up-regulated miRNAs corresponding to 220 up-regulated mRNAs and 94 down-regulated mRNAs, respectively, were identified in S. aculeatissimum. Nine significant differentially expressed miRNAs and twelve mRNAs were identified by quantitative Real-time PCR and association analysis, and analyzed for their GO function enrichment and KEGG pathway association.ConclusionsIn summary, numerous conserved and novel miRNAs involved in the chilling response were identified using high-throughput sequencing, which provides a theoretical basis for the further study of low temperature stress-related miRNAs and the regulation of cold-tolerance mechanisms of eggplant at the miRNA level.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4341-y) contains supplementary material, which is available to authorized users.

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“…Under cold stress, polar and lateral auxin transports are altered, resulting in slower growth [1,9,89]. As for microRNAs, a large number of miRNA has been implicated in regulating the low-temperature response in different plant species [30,[90][91][92][93]. Although these studies represent a link 1) between auxin and cold stress, and 2) between miRNA and cold stress, the mechanistic link between microRNA and auxin in regulating plant cold stress response remains elusive.…”

Section: Discussionmentioning

confidence: 99%

Deciphering miRNAs involved in crosstalk between auxin and cold stress in Arabidopsis roots

Aslam

Sakai

Yuan

et al. 2020

Preprint

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Background: The phytohormone auxin and microRNA-mediated regulation of gene expressions are key regulators for plant growth and development at both optimal and under low-temperature stress conditions. However, the mechanistic link between microRNA and auxin in regulating plant cold stress response remains elusive. Results: To better understand the role of microRNA in the crosstalk between auxin and cold stress responses, we took advantage of the mutants of Arabidopsis thaliana with altered response to auxin transport and signal. Screening of the mutants for root growth recovery after cold stress at 4°C revealed that the auxin signaling mutant, solitary root 1 ( slr1; mutation in Aux/IAA14), shows a hypersensitive response to cold stress. Genome-wide expression analysis of miRNA in wild-type and slr1 mutant roots using next-generation sequencing revealed 180 known and 71 novel cold-responsive microRNAs. Cold stress also increased the abundance of 26 nt-31 nt small RNA population in slr1 compared with wild-type. Comparative analysis of microRNA expression shows significant differential expression of 13 known and 7 novel miRNAs in slr1 at 4°C compared with wild-type. Target gene expression analysis of the members from one potential candidate miRNAs, miR169 revealed the possible involvement of miR169- NF-YA module in the auxin-mediated cold stress response. Conclusions: Taken together, these results indicate that SLR/IAA14, a transcriptional repressor of auxin signaling, plays a crucial role in integrating miRNA in auxin and cold responses.

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miRNA alteration is an important mechanism in sugarcane response to low-temperature environment

Cited by 68 publications

References 73 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.)

Cold-responsive miRNAs and their target genes in the wild eggplant species Solanum aculeatissimum

Deciphering miRNAs involved in crosstalk between auxin and cold stress in Arabidopsis roots

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