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

Abstract

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.

Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants

“…Emerging evidence suggests that lncRNAs could directly affect drought responses by regulating the transcription of various stress-responsive genes or by recruiting complex mechanisms such as endogenous target mimics (eTM), chromatin modulation, and antisense transcription-mediated modulation [ 30 ]. Recently, genome-wide transcriptome analysis has revealed a variety of stress-responsive lncRNAs in various plant species, including six in Arabidopsis [ 112 ], Populus [ 42 ], rice [ 113 ], maize [ 114 ], foxtail millet [ 115 ], cassava [ 40 ], and switchgrass [ 116 ].…”

“…RNA Pol II transcribes lncRNAs with a 5′-cap and poly-adenylation at the 3′ tail from various genome regions, including enhancer or intron splicing regions [ 29 ]. RNA pol IV and V generate lncRNAs through RNA-dependent DNA methylation (RdDM), which serve as precursors for small interfering RNAs (siRNAs) [ 30 ]. lncRNAs, with their possible biogenesis, are illustrated in Figure 2 .…”

Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development

“…Based on their genomic localization regarding other genes, lncRNAs are broadly grouped into different classes: (1) lincRNAs or long non-coding intergenic RNAs; (2) NAT lncRNAs or natural anti-sense lncRNAs; (3) intronic lncRNAs, located in the introns; and (4) sense lncRNAs [ 3 ]. LncRNAs have been identified in many plant species and their expression in response to various abiotic and biotic stresses has been investigated, although our knowledge about lncRNA functions is still very limited [ 4 , 5 , 6 , 7 , 8 , 9 ]. However, the catalogue of lncRNAs for some plants with complex polyploidy and repeat-rich genomes, including wheat ( Triticum aestivum L.), remains mainly underexplored [ 10 ].…”

“…LncRNAs have been identified in many plant species and their expression in response to various abiotic and biotic stresses has been investigated, although our knowledge about lncRNA functions is still very limited [4][5][6][7][8][9]. However, the catalogue of lncRNAs for some plants with complex polyploidy and repeat-rich genomes, including wheat (Triticum aestivum L.), remains mainly underexplored [10].…”

From “Dark Matter” to “Star”: Insight Into the Regulation Mechanisms of Plant Functional Long Non-Coding RNAs

“…A large number of lncRNAs in plants were found by using transcriptome sequencing and bioinformatics analysis (Muers, 2011 ; Li et al, 2014 , 2019 ; Hou et al, 2017 ; Yu T. et al, 2019 ). Several studies have summarized the bioinformatics tools and database resources for plant lncRNA identification and prediction (Jha et al, 2020 ; Waseem et al, 2020 ). However, until present, only a small number of these lncRNAs have been validated by the low-throughput experimental analysis.…”