Deciphering the roles of circRNAs on chilling injury in tomato

Zuo, Jinhua; Wang, Qing; Zhu, Beiwei; Luo, Yunbo; Gao, Lipu

doi:10.1016/j.bbrc.2016.07.032

Cited by 148 publications

(140 citation statements)

References 26 publications

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“…We found that six of the 62 differentially expressed circRNAs had putative miRNA-binding sites (Table 2), and totally 26 miRNAs were predicted. Moreover, all the six differentially expressed circRNAs had three to eight miRNA-binding sites, which was similar to that reported in human (Memczak et al, 2013), but was significantly higher than that reported in rice (Lu et al, 2015) and tomato (Zuo et al, 2016). …”

Section: Resultssupporting

confidence: 82%

“…The GO analysis on predicted mRNAs showed that the targets of differentially expressed circRNAs under dehydration stress were associated with various functions involving in different cellular components, biological process, and molecular functions. The differential expressions of circRNAs have already been reported in rice responding to Pi-starvation stress (Ye et al, 2015), and in tomato fruits suffering from chilling stress (Zuo et al, 2016), suggesting that circRNAs might play a role in responding to environmental stress. According to the report in rice (Lu et al, 2015), the mechanism of circRNAs participating in the stress response should be attributed that it exhibit alternative splicing circularization patterns and act as a negative regulator of their parental genes.…”

Section: Resultsmentioning

confidence: 82%

“…A recently deep sequencing research in tomato identified 854 circRNAs (615 exons), in which 163 exhibiting chilling responsive expression (Zuo et al, 2016). The 88 identified circRNAs number and 6.8 percentages of exons were not as many as previous reports in other plants.…”

Section: Resultsmentioning

confidence: 99%

“…We identified the circRNAs in wheat using CIRI algorithm (Gao et al, 2015). It is an efficient and unbiased algorithm for the de novo identification of circRNAs, which has already been used in some organizations including animals, humans, and plants (Hansen et al, 2016; Zuo et al, 2016). CIRI has been proven to be more useful when conducting more unbiased circRNA analyses or in poorly annotated organisms, comparing to other algorithms (Hansen et al, 2016).…”

Section: Resultsmentioning

confidence: 99%

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Identification of Circular RNAs and Their Targets in Leaves of Triticum aestivum L. under Dehydration Stress

et al. 2017

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Circular RNAs (circRNAs) are a type of newly identified non-coding RNAs through high-throughput deep sequencing, which play important roles in miRNA function and transcriptional controlling in human, animals, and plants. To date, there is no report in wheat seedlings regarding the circRNAs identification and roles in the dehydration stress response. In present study, the total RNA was extracted from leaves of wheat seedlings under dehydration-stressed and well-watered conditions, respectively. Then, the circRNAs enriched library based deep sequencing was performed and the circRNAs were identified using bioinformatics tools. Around 88 circRNAs candidates were isolated in wheat seedlings leaves while 62 were differentially expressed in dehydration-stressed seedlings compared to well-watered control. Among the dehydration responsive circRNAs, six were found to act as 26 corresponding miRNAs sponges in wheat. Sixteen circRNAs including the 6 miRNAs sponges and other 10 randomly selected ones were further validated to be circular by real-time PCR assay, and 14 displayed consistent regulation patterns with the transcriptome sequencing results. After Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the targeted mRNAs functions, the circRNAs were predicted to be involved in dehydration responsive process, such as photosynthesis, porphyrin, and chlorophyll metabolism, oxidative phosphorylation, amino acid biosynthesis, and metabolism, as well as plant hormone signal transduction, involving auxin, brassinosteroid, and salicylic acid. Herein, we revealed a possible connection between the regulations of circRNAs with the expressions of functional genes in wheat leaves associated with dehydration resistance.

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Section: Resultssupporting

confidence: 82%

Section: Resultsmentioning

confidence: 82%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

Identification of Circular RNAs and Their Targets in Leaves of Triticum aestivum L. under Dehydration Stress

et al. 2017

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“…Discovery of thousands of circRNAs across a range of plant species have been summarized in other review paper, 47 and recently demonstrated in horticultural plants, for example, Solanum lycopersicum 48 and Actinidia chinensis . 18 However, little is known about the function of circRNAs in plants.…”

Section: Classification and Functions Of Plant Ncrnasmentioning

confidence: 99%

New technologies accelerate the exploration of non-coding RNAs in horticultural plants

Liu

Mewalal

et al. 2017

Hortic Res

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Non-coding RNAs (ncRNAs), that is, RNAs not translated into proteins, are crucial regulators of a variety of biological processes in plants. While protein-encoding genes have been relatively well-annotated in sequenced genomes, accounting for a small portion of the genome space in plants, the universe of plant ncRNAs is rapidly expanding. Recent advances in experimental and computational technologies have generated a great momentum for discovery and functional characterization of ncRNAs. Here we summarize the classification and known biological functions of plant ncRNAs, review the application of next-generation sequencing (NGS) technology and ribosome profiling technology to ncRNA discovery in horticultural plants and discuss the application of new technologies, especially the new genome-editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems, to functional characterization of plant ncRNAs.

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Chilling Injury in Tropical Crops after Harvest

Heyes

2018

Annual Plant Reviews Online

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Tropical crops suffer from chilling injury after harvest, which has historically limited their global trade. The primary cause of chilling injury relates to membrane dysfunction leading to altered Ca2+flux and upregulation of cold‐regulated genes via C‐repeat binding factors (CBFs). Secondary damage results from generation of free radicals. Chilling injury leads to a diversity of internal and external symptoms in tropical crops. The most serious are those which occur only internally or take time to display after fresh products leave the chilling environment, as these symptoms are likely to lead to product rejection after purchase. Techniques for the detection of chilling injury by non‐destructive technologies are reviewed. A wide range of techniques has been tested empirically for reducing chilling susceptibility in tropical crops (step‐down cooling, hormetic treatments, intermittent warming, atmosphere modification, chemical treatments, and pre‐harvest manipulation) and is reviewed here. Faster progress may be possible if treatments can be based on knowledge of underlying mechanisms; for example, maximal heat shock protein gene expression may be an indicator of effective heat treatments. Options for introducing greater chilling tolerance through breeding are discussed, using wild relatives or introduced CBFs. Improved technologies are already leading to increased trade in tropical products which is beneficial for tropical economies.

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Deciphering the roles of circRNAs on chilling injury in tomato

Cited by 148 publications

References 26 publications

Identification of Circular RNAs and Their Targets in Leaves of Triticum aestivum L. under Dehydration Stress

Identification of Circular RNAs and Their Targets in Leaves of Triticum aestivum L. under Dehydration Stress

New technologies accelerate the exploration of non-coding RNAs in horticultural plants

Chilling Injury in Tropical Crops after Harvest

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