Emerging roles of long non-coding RNAs in plant response to biotic and abiotic stresses

Nejat, Naghmeh; Mantri, Nitin

doi:10.1080/07388551.2017.1312270

Cited by 114 publications

(71 citation statements)

References 114 publications

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“…LncRNAs function as key regulators of diverse mechanisms in biological processes, e.g., acting as scaffolds, decoys or signals through genomic targeting by cis or trans, and resulting in the downregulation or overexpression of target genes [6,7]. Studies on lncRNAs in plants have shown that they play important roles in a wide range of biological processes, especially in reproductive development and responses to environmental stresses [3,8].…”

Section: Introductionmentioning

confidence: 99%

Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing

et al. 2020

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Background: Long non-coding RNAs (lncRNAs) play important roles in the regulation of plant responses to environmental stress by acting as essential regulators of gene expression. However, whether and how lncRNAs are involved in cold acclimation-dependent freezing tolerance in plants remains largely unknown. Medicago truncatula is a prominent model for studies of legume genomics, and distinguished by its cold-acclimation characteristics. To determine the roles of lncRNAs in plant cold stress response, we conducted genome-wide high-throughput sequencing in the legume model plant M. truncatula. Results: RNA-seq data were generated from twelve samples for the four treatments, i.e., non-cold treated leaves and roots, cold-treated leaves and roots of M. truncatula Jemalong A17 seedlings. A total of 1204 million raw reads were generated. Of them, 1150 million filtered reads after quality control (QC) were subjected to downstream analysis. A large number of 24,368 unique lncRNAs were identified from the twelve samples. Among these lncRNAs, 983 and 1288 were responsive to cold treatment in the leaves and roots, respectively. We further found that the intronic-lncRNAs were most sensitive to the cold treatment. The cold-responsive lncRNAs were unevenly distributed across the eight chromosomes in M. truncatula seedlings with obvious preferences for locations. Further analyses revealed that the cold-responsive lncRNAs differed between leaves and roots. The putative target genes of the lncRNAs were predicted to mainly involve the processes of protein translation, transport, metabolism and nucleic acid transcription. Furthermore, the networks of a tandem array of CBF/DREB1 genes that were reported to be located in a major freezing tolerance QTL region on chromosome 6 and their related lncRNAs were dissected based on their gene expression and chromosome location. Conclusions:We identified a comprehensive set of lncRNAs that were responsive to cold treatment in M. truncatula seedlings, and discovered tissue-specific cold-responsive lncRNAs in leaves and roots. We further dissected potential regulatory networks of CBF Intergenic RNA (MtCIR1) and MtCBFs that play critical roles in response and adaptation of M. truncatula to cold stress.

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Section: Introductionmentioning

confidence: 99%

Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing

et al. 2020

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“…Although RNA-Seq facilitates the identification of numerous lncRNAs in many plant species, only a few lncRNAs were annotated and characterized (Liu et al 2015). For instance, several studies showed that some lncRNAs are involved in biotic and abiotic stresses (Nejat & Mantri 2017). An Arabidopsis lncRNA known as ELENA1 interacts with MED19a to regulate PR1 expression functions in increased resistance against Pseudomonas syringae pv tomato DC3000 (Seo et al 2017).…”

Section: Discussionmentioning

confidence: 99%

“…Due to the rapid advance of next-generation sequencing (NGS) techniques and bioinformatics tools, a large number of lncRNAs have been identified from various organisms such as animals and plants (Sun et al 2017b). However, lncRNAs have been identified in a limited number of plant species such as Arabidopsis thaliana, medicago, potato, rice, strawberry, tomato (Solanum lycopersicum), and maize (Guo & Liu 2017;Kang et al 2017;Nejat & Mantri 2017;Scarano et al 2017;Zheng et al 2017;Zhu et al 2017). Furthermore, studies revealing functional roles of identified lncRNAs in plants are rare.…”

Section: Introductionmentioning

confidence: 99%

Peer Review #2 of "Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with Tomato yellow leaf curl virus (v0.1)"

2019

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Long non-coding RNAs (lncRNAs) play an important role in regulating many biological processes. In this study, tomato seeds were first irradiated by neutrons. Eight tomato mutants were then selected and infected by Tomato yellow leaf curl virus (TYLCV). RNA sequencing followed by bioinformatics analyses identified 1,563 tomato lncRNAs. About half of the lncRNAs were derived from intergenic regions, whereas antisense lncRNAs accounted for 35%. There were fewer lncRNAs identified in our study than in other studies identifying tomato lncRNAs. Functional classification of 794 lncRNAs associated with tomato genes showed that many lncRNAs were associated with binding functions required for interactions with other molecules and localized in the cytosol and membrane. In addition, we identified 19 up-regulated and 11 down-regulated tomato lncRNAs by comparing TYLCV infected plants to non-infected plants using previously published data. Based on these results, the lncRNAs identified in this study provide important resources for characterization of tomato lncRNAs in response to TYLCV infection.

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“…The literature investigating the role of lncRNAs in various biological processes of plants has increased over the last 10 years [19,21,22]. These efforts have identified a myriad of molecular functions for lncRNAs (Table 1).…”

Section: Capturing Lncrnas In Plantmentioning

confidence: 99%

The Emerging Role of Long Non-Coding RNAs in Plant Defense Against Fungal Stress

Zhang

Guo

et al. 2020

IJMS

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Growing interest and recent evidence have identified long non-coding RNA (lncRNA) as the potential regulatory elements for eukaryotes. LncRNAs can activate various transcriptional and post-transcriptional events that impact cellular functions though multiple regulatory functions. Recently, a large number of lncRNAs have also been identified in higher plants, and an understanding of their functional role in plant resistance to infection is just emerging. Here, we focus on their identification in crop plant, and discuss their potential regulatory functions and lncRNA-miRNA-mRNA network in plant pathogen stress responses, referring to possible examples in a model plant. The knowledge gained from a deeper understanding of this colossal special group of plant lncRNAs will help in the biotechnological improvement of crops.

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Emerging roles of long non-coding RNAs in plant response to biotic and abiotic stresses

Cited by 114 publications

References 114 publications

Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing

Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing

Peer Review #2 of "Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with Tomato yellow leaf curl virus (v0.1)"

The Emerging Role of Long Non-Coding RNAs in Plant Defense Against Fungal Stress

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