Long Non-Coding RNAs as Endogenous Target Mimics and Exploration of Their Role in Low Nutrient Stress Tolerance in Plants

Borah, Priyanka; Das, Antara; Milner, Matthew J.; Ali, Arif; Bentley, Alison R.; Pandey, Renu

doi:10.3390/genes9090459

Cited by 38 publications

(29 citation statements)

References 123 publications

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“…This complex includes the curly leaf (CLF) subunit, possessing histone methyltransferase activity and catalyzing H3K27me3 deposition at FLC [ 21 ]. A drought-responsive lncRNA, drought induced lncRNA ( DRIR ), acts to regulate the activity of the FUT4 gene encoding fucosyltransferase, resulting in enhanced tolerance to drought ( Figure 3 A) [ 81 ].…”

Section: Classification Of Lncrnasmentioning

confidence: 99%

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

Waseem

Liu

Xia

2020

IJMS

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Long non-coding RNAs (lncRNAs) are pervasive transcripts of longer than 200 nucleotides and indiscernible coding potential. lncRNAs are implicated as key regulatory molecules in various fundamental biological processes at transcriptional, post-transcriptional, and epigenetic levels. Advances in computational and experimental approaches have identified numerous lncRNAs in plants. lncRNAs have been found to act as prime mediators in plant growth, development, and tolerance to stresses. This review summarizes the current research status of lncRNAs in planta, their classification based on genomic context, their mechanism of action, and specific bioinformatics tools and resources for their identification and characterization. Our overarching goal is to summarize recent progress on understanding the regulatory role of lncRNAs in plant developmental processes such as flowering time, reproductive growth, and abiotic stresses. We also review the role of lncRNA in nutrient stress and the ability to improve biotic stress tolerance in plants. Given the pivotal role of lncRNAs in various biological processes, their functional characterization in agriculturally essential crop plants is crucial for bridging the gap between phenotype and genotype.

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Section: Classification Of Lncrnasmentioning

confidence: 99%

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

Waseem

Liu

Xia

2020

IJMS

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“…A vast number of studies have shown that lncRNAs are methodical mediators of multiple biological processes, including transcriptional gene silencing and the regulation of mRNA expression and chromatin structure (Nejat & Mantri, 2018). Reports have confirmed that many lncRNAs are major participants in flowering regulation, male sterility, nutrition metabolism, and disease resistance (Borah et al, 2018;Chen et al, 2018;Jain et al, 2017;Xin et al, 2011;Zhang et al, 2014b). Moreover, lncR-NAs are sensitive to biotic and abiotic stresses and may play a key role in stress-signaling pathways to enhance plant defense capabilities (Wang, Liu, Zhao, Chen, & Zhang, 2015a;Zhang, Mujahid, Hou, Nallamilli, & Peng, 2013).…”

Section: Introductionmentioning

confidence: 99%

Genome‐wide lncRNAs identification and association analysis for cold‐responsive genes at the booting stage in rice (Oryza sativa L.)

et al. 2020

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Long non-coding RNAs (lncRNAs) are essential regulators of a broad range of biological processes in plants. The spectacular progress made in next-generation sequencing technologies has enabled a genome-wide identification of lncRNAs in multiple plant species. In this study, a genome-wide lncRNA sequencing technology was used to identify cold-responsive lncRNAs at the booting stage in rice by comparing a tolerant variety, Kongyu131 (KY131) and a sensitive variety, Dongnong422 (DN422). A total of 1485 lncRNAs were identified, and 566 of these lncRNAs were defined as differential lncRNAs by comparing four samples. GO and KEGG enrichment analyses were performed, focusing on the cis-and trans-target genes of the differential lncRNAs. To identify cold-responsive genes, a meta-analysis was used to integrate 35 cold-tolerant QTLs at the booting stage. In summary, 12 candidate genes and their target lncRNAs were identified by qRT-PCR. LncTar was used to identify the interaction between lncRNAs and the candidate genes. In addition, 130 rice cultivars with rich genetic diversity were collected to verify the association of candidate genes with cold-resistance. The results revealed that five SNPs in LOC_Os07g42940, three SNP and one InDel in LOC_Os02g03410 were associated with cold-resistance at a significant level using association analysis. This study provides new gene resources and insights into cold-resistance research for rice.

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“…LncRNAs have been shown to regulate phosphate homeostasis in plants by a novel mechanism called target mimicry [ 27 , 45 ]. Two endogenous lncRNA target mimics (eTMs) were identified in rice, namely eTM159 and eTM408, which target two Fe-related miR159 and miR408 ( Figure 5 E) [ 41 ].…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic Profiling of Fe-Responsive lncRNAs and Their Regulatory Mechanism in Rice

Wang

Sun

Liao

et al. 2021

Genes

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Iron (Fe) deficiency directly affects crop growth and development, ultimately resulting in reduced crop yield and quality. Recently, long non-coding RNAs (lncRNAs) have been demonstrated to play critical regulatory roles in a multitude of pathways across numerous species. However, systematic screening of lncRNAs responding to Fe deficiency and their regulatory mechanism in plants has not been reported. In this work, 171 differently expressed lncRNAs (DE-lncRNAs) were identified based on analysis of strand-specific RNA-seq data from rice shoots and roots under Fe-deficient conditions. We also found several lncRNAs, which could generate miRNAs or act as endogenous target mimics to regulate expression of Fe-related genes. Analysis of interaction networks and gene ontology enrichment revealed that a number of DE-lncRNAs were associated with iron transport and photosynthesis, indicating a possible role of lncRNAs in regulation of Fe homeostasis. Moreover, we identified 76 potential lncRNA targets of OsbHLH156, a key regulator for transcriptional response to Fe deficiency. This study provides insight into the potential functions and regulatory mechanism of Fe-responsive lncRNAs and would be an initial and reference for any further studies regarding lncRNAs involved in Fe deficiency in plants.

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Long Non-Coding RNAs as Endogenous Target Mimics and Exploration of Their Role in Low Nutrient Stress Tolerance in Plants

Cited by 38 publications

References 123 publications

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

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

Genome‐wide lncRNAs identification and association analysis for cold‐responsive genes at the booting stage in rice (Oryza sativa L.)

Transcriptomic Profiling of Fe-Responsive lncRNAs and Their Regulatory Mechanism in Rice

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