Genome-wide identification of Arabidopsis long noncoding RNAs in response to the blue light

Sun, Zhenfei; Huang, Kai; Han, Zujing; Wang, Pan; Fang, Yuda

doi:10.1038/s41598-020-63187-1

Cited by 35 publications

(32 citation statements)

References 59 publications

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“…LncRNAs are a diverse class of RNAs, and the largest class acting as 'biological regulators' that control transcriptional regulation and genome imprinting [9,10]. Numerous noteworthy instances of lncRNAs regulating plant development, disease resistance, nutrient acquisition, and other biological processes through chromatin remodeling, histone modification, pri-mRNA alternative splicing, or acting as 'target mimicry' have been recorded [11][12][13][14][15]. However, few studies have undertaken genome-wide exploration of lncRNAs, their complex regulatory molecular mechanisms, or functional annotation [16].…”

Section: Introductionmentioning

confidence: 99%

Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation

et al. 2020

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Background The immobile nature of plants means that they can be frequently confronted by various biotic and abiotic stresses during their lifecycle. Among the various abiotic stresses, water stress, temperature extremities, salinity, and heavy metal toxicity are the major abiotic stresses challenging overall plant growth. Plants have evolved complex molecular mechanisms to adapt under the given abiotic stresses. Long non-coding RNAs (lncRNAs)—a diverse class of RNAs that contain > 200 nucleotides(nt)—play an essential role in plant adaptation to various abiotic stresses. Results LncRNAs play a significant role as ‘biological regulators’ for various developmental processes and biotic and abiotic stress responses in animals and plants at the transcription, post-transcription, and epigenetic level, targeting various stress-responsive mRNAs, regulatory gene(s) encoding transcription factors, and numerous microRNAs (miRNAs) that regulate the expression of different genes. However, the mechanistic role of lncRNAs at the molecular level, and possible target gene(s) contributing to plant abiotic stress response and adaptation, remain largely unknown. Here, we review various types of lncRNAs found in different plant species, with a focus on understanding the complex molecular mechanisms that contribute to abiotic stress tolerance in plants. We start by discussing the biogenesis, type and function, phylogenetic relationships, and sequence conservation of lncRNAs. Next, we review the role of lncRNAs controlling various abiotic stresses, including drought, heat, cold, heavy metal toxicity, and nutrient deficiency, with relevant examples from various plant species. Lastly, we briefly discuss the various lncRNA databases and the role of bioinformatics for predicting the structural and functional annotation of novel lncRNAs. Conclusions Understanding the intricate molecular mechanisms of stress-responsive lncRNAs is in its infancy. The availability of a comprehensive atlas of lncRNAs across whole genomes in crop plants, coupled with a comprehensive understanding of the complex molecular mechanisms that regulate various abiotic stress responses, will enable us to use lncRNAs as potential biomarkers for tailoring abiotic stress-tolerant plants in the future.

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Section: Introductionmentioning

confidence: 99%

Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation

et al. 2020

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“…Specific examples include the brassinosteroid response and the response to blue light in Arabidopsis, and pollen development and the heat stress response in Solanum lycopersicum. Other types of non-coding RNA include sesame, as well as in the cold response in grapevine, the drought response in mulberry, and the drought-responsive multi-tiered regulatory network in drought-tolerant rice [23,30,[51][52][53][54][55][56]. However, a role for miRNAs in regulating the MAPK cascade that operates downstream of the core ABA signaling pathway has not been confirmed in Arabidopsis.…”

Section: Discussionmentioning

confidence: 99%

Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid in Arabidopsis

Mehdi

Krishnamoorthy

Szcześniak

et al. 2021

IJMS

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miRNAs are involved in various biological processes, including adaptive responses to abiotic stress. To understand the role of miRNAs in the response to ABA, ABA-responsive miRNAs were identified by small RNA sequencing in wild-type Arabidopsis, as well as in abi1td, mkkk17, and mkkk18 mutants. We identified 10 novel miRNAs in WT after ABA treatment, while in abi1td, mkkk17, and mkkk18 mutants, three, seven, and nine known miRNAs, respectively, were differentially expressed after ABA treatment. One novel miRNA (miRn-8) was differentially expressed in the mkkk17 mutant. Potential target genes of the miRNA panel were identified using psRNATarget. Sequencing results were validated by quantitative RT-PCR of several known and novel miRNAs in all genotypes. Of the predicted targets of novel miRNAs, seven target genes of six novel miRNAs were further validated by 5′ RLM-RACE. Gene ontology analyses showed the potential target genes of ABA-responsive known and novel miRNAs to be involved in diverse cellular processes in plants, including development and stomatal movement. These outcomes suggest that a number of the identified miRNAs have crucial roles in plant responses to environmental stress, as well as in plant development, and might have common regulatory roles in the core ABA signaling pathway.

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“…These lncRNAs are enriched in certain QTLs (Quantitative Trait Loci) containing genes regulating stress‐receptive pathways (Yuan et al, 2018). lncRNAs have important roles in the modulation of nutrient uptake, growth and development of plants, adaptation of resistance capability against disease and various environmental stresses, regulating some biological activities via modification of histone and chromatin disposition in plants (Corona‐Gomez et al, 2020; Nejat & Mantri 2018; Sun et al, 2020). Chen, Shi, et al (2018) demonstrated that lncRNAs regulate the expression of genes related to various amino acids metabolic pathways (phenylalanine, methionine, and cysteine), photosynthetic metabolism, and phenylpropanoids metabolic pathways to reduce the cadmium toxicity in rice.…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Heavy metal stress in rice: Uptake, transport, signaling, and tolerance mechanisms

Kaur

Das

Bansal

et al. 2021

Physiologia Plantarum

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Heavy metal contamination of agricultural fields has become a global concern as it causes a direct impact on human health. Rice is the major food crop for almost half of the world population and is grown under diverse environmental conditions, including heavy metal‐contaminated soil. In recent years, the impact of heavy metal contamination on rice yield and grain quality has been shown through multiple approaches. In this review article, different aspects of heavy metal stress, that is uptake, transport, signaling and tolerance mechanisms, are comprehensively discussed with special emphasis on rice. For uptake, some of the transporters have specificity to one or two metal ions, whereas many other transporters are able to transport many different ions. After uptake, the intercellular signaling is mediated through different signaling pathways involving the regulation of various hormones, alteration of calcium levels, and the activation of mitogen‐activated protein kinases. Heavy metal stress signals from various intermediate molecules activate various transcription factors, which triggers the expression of various antioxidant enzymes. Activated antioxidant enzymes then scavenge various reactive oxygen species, which eventually leads to stress tolerance in plants. Non‐enzymatic antioxidants, such as ascorbate, metalloids, and even metal‐binding peptides (metallothionein and phytochelatin) can also help to reduce metal toxicity in plants. Genetic engineering has been successfully used in rice and many other crops to increase metal tolerance and reduce heavy metals accumulation. A comprehensive understanding of uptake, transport, signaling, and tolerance mechanisms will help to grow rice plants in agricultural fields with less heavy metal accumulation in grains.

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Genome-wide identification of Arabidopsis long noncoding RNAs in response to the blue light

Cited by 35 publications

References 59 publications

Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation

Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation

Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid in Arabidopsis

Heavy metal stress in rice: Uptake, transport, signaling, and tolerance mechanisms

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