A Nucleus-Localized Long Non-Coding RNA Enhances Drought and Salt Stress Tolerance

Qin, Tao; Zhao, Huayan; Cui, Peng; Albesher, Nour; Xiong, Liming

doi:10.1104/pp.17.00574

Cited by 285 publications

(225 citation statements)

References 80 publications

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“…A rapidly increasing number of lncRNAs have been identified in plants and associated with various biological processes, including fruit ripening (Tang et al ., ; Li et al ., ), reproduction (Zhang et al ., ,b; Huang et al ., ), disease resistance (Zhang et al ., ), stress responses (Qin et al ., ), photomorphogenesis (Wang et al ., ) and phosphate homeostasis (Franco‐Zorrilla et al ., ).…”

Section: Discussionmentioning

confidence: 99%

Systematic identification of long noncoding RNAs expressed during light‐induced anthocyanin accumulation in apple fruit

et al. 2019

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Summary Anthocyanin pigments contribute to the red color of apple (Malus × domestica) fruit and have a major influence on their ornamental, dietary and market value. In this study, we investigated the potential role of long noncoding RNAs (lncRNAs) in anthocyanin biosynthesis. RNA‐seq analysis of apple peels from the ‘Red Fuji’ cultivar during light‐induced rapid anthocyanin accumulation revealed 5297 putative lncRNAs. Differential expression analysis further showed that lncRNAs were induced during light treatment and were involved in photosynthesis. Using the miRNA−lncRNA−mRNA network and endogenous target mimic (eTM) analysis, we predicted that two differentially expressed lncRNAs, MLNC3.2 and MLNC4.6, were potential eTMs for miRNA156a and promoted the expression of the SPL2‐like and SPL33 transcription factors. Transient expression in apple fruit and stable transformation of apple callus showed that overexpression of the eTMs and SPLs promoted anthocyanin accumulation, with the opposite results in eTM and SPL‐silenced fruit. Silencing or overexpressing of miR156a also affected the expression of the identified eTMs and SPLs. These results indicated that MLNC3.2 and MLNC4.6 function as eTMs for miR156a and prevent cleavage of SPL2‐like and SPL33 by miR156a during light‐induced anthocyanin biosynthesis. Our study provides fundamental insights into lncRNA involvement in the anthocyanin biosynthetic pathway in apple fruit.

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Section: Discussionmentioning

confidence: 99%

Systematic identification of long noncoding RNAs expressed during light‐induced anthocyanin accumulation in apple fruit

et al. 2019

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“…The lncRNAs of COLDAIR and COOLAIR negatively modulate FLC by different models [14][15][16]. A large number of lncRNAs involved in the regulation of plant responses to abiotic stresses has been characterized in recent years [17][18][19].…”

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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“…Recent studies have elucidated regulatory roles of the multitude lncRNAs present in the plant genome in diverse biological processes, such as flowering, reproduction, photo‐morphogenesis, vernalization, organ development, cell cycle, biotic and abiotic stress responses, etc. . These studies suggest the versatile functionality of lncRNAs via sundry molecular interactions with different transcriptional and translational components.…”

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confidence: 78%

Long noncoding RNAs and miRNAs regulating terpene and tartaric acid biosynthesis in rose‐scented geranium

2019

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This study aimed to explore the noncoding RNAs, which have emerged as key regulatory molecules in biological processes, in rose‐scented geranium. We analyzed RNA‐seq data revealing 26 784 long noncoding RNAs (lncRNAs) and 871 miRNAs in rose‐scented geranium. A total of 466 lncRNAs were annotated using different plant lncRNA public databases. Furthermore, 372 lncRNAs and 99 miRNAs were detected that target terpene and tartarate biosynthetic pathways. An interactome, comprising of lncRNAs, miRNAs, and mRNAs, was constructed that represents a noncoding RNA regulatory network of the target mRNAs. Real‐time quantitative PCR expression validation was done for selected lncRNAs involved in the regulation of terpene and tartaric acid pathways. This study provides the first insights into the regulatory functioning of noncoding RNAs in rose‐scented geranium.

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A Nucleus-Localized Long Non-Coding RNA Enhances Drought and Salt Stress Tolerance

Cited by 285 publications

References 80 publications

Systematic identification of long noncoding RNAs expressed during light‐induced anthocyanin accumulation in apple fruit

Systematic identification of long noncoding RNAs expressed during light‐induced anthocyanin accumulation in apple fruit

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

Long noncoding RNAs and miRNAs regulating terpene and tartaric acid biosynthesis in rose‐scented geranium

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