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

Waseem, Muhammad; Liu, Yuanlong; Xia, Rui

doi:10.3390/ijms22010086

Cited by 40 publications

(33 citation statements)

References 167 publications

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“…LncRNAs can regulate expression of genes located nearby [ 57 ]. In our study, 2209 genes were predicted as being potentially targeted by 3036 lncRNAs.…”

Section: Discussionmentioning

confidence: 99%

Waterlogging-Stress-Responsive LncRNAs, Their Regulatory Relationships with miRNAs and Target Genes in Cucumber (Cucumis sativus L.)

Kęska

Szcześniak

Adamus

et al. 2021

IJMS

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Low oxygen level is a phenomenon often occurring during the cucumber cultivation period. Genes involved in adaptations to stress can be regulated by non-coding RNA. The aim was the identification of long non-coding RNAs (lncRNAs) involved in the response to long-term waterlogging stress in two cucumber haploid lines, i.e., DH2 (waterlogging tolerant—WL-T) and DH4 (waterlogging sensitive—WL-S). Plants, at the juvenile stage, were waterlogged for 7 days (non-primed, 1xH), and after a 14-day recovery period, plants were stressed again for another 7 days (primed, 2xH). Roots were collected for high-throughput RNA sequencing. Implementation of the bioinformatic pipeline made it possible to determine specific lncRNAs for non-primed and primed plants of both accessions, highlighting differential responses to hypoxia stress. In total, 3738 lncRNA molecules were identified. The highest number (1476) of unique lncRNAs was determined for non-primed WL-S plants. Seventy-one lncRNAs were depicted as potentially being involved in acquiring tolerance to hypoxia in cucumber. Understanding the mechanism of gene regulation under long-term waterlogging by lncRNAs and their interactions with miRNAs provides sufficient information in terms of adaptation to the oxygen deprivation in cucumber. To the best of our knowledge, this is the first report concerning the role of lncRNAs in the regulation of long-term waterlogging tolerance by priming application in cucumber.

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“…LncRNAs can regulate expression of genes located nearby [ 57 ]. In our study, 2209 genes were predicted as being potentially targeted by 3036 lncRNAs.…”

Section: Discussionmentioning

confidence: 99%

Waterlogging-Stress-Responsive LncRNAs, Their Regulatory Relationships with miRNAs and Target Genes in Cucumber (Cucumis sativus L.)

Kęska

Szcześniak

Adamus

et al. 2021

IJMS

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“…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.…”

Section: Overviewmentioning

confidence: 99%

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

Chen

Liu

et al. 2021

Front. Plant Sci.

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Long non-coding RNAs (lncRNAs) play a vital role in a variety of biological functions in plant growth and development. In this study, we provided an overview of the molecular mechanisms of lncRNAs in interacting with other biomolecules with an emphasis on those lncRNAs validated only by low-throughput experiments. LncRNAs function through playing multiple roles, including sponger for sequestering RNA or DNA, guider or decoy for recruiting or hijacking transcription factors or peptides, and scaffold for binding with chromatin modification complexes, as well as precursor of microRNAs or small interfering RNAs. These regulatory roles have been validated in several plant species with a comprehensive list of 73 lncRNA–molecule interaction pairs in 16 plant species found so far, suggesting their commonality in the plant kingdom. Such initial findings of a small number of functional plant lncRNAs represent the beginning of what is to come as lncRNAs with unknown functions were found in orders of magnitude more than proteins.

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“…Long non-coding RNAs (lncRNAs) are a class of epigenetic regulatory molecules with a total length of more than 200 nucleotides; these molecules can play an important role in the regulation of gene expression (Waseem et al, 2020). LncRNA was first identified in mice in 1989 (Brannan et al, 1990) but were initially perceived to represent transcriptional noise without a biological function (Mercer and Mattick, 2013).…”

Section: Introductionmentioning

confidence: 99%

Identification and Analysis of Long Non-coding RNAs in Leuciscus waleckii Adapted to Highly Alkaline Conditions

Zhao

Liew

et al. 2021

Front. Physiol.

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Leuciscus waleckii is a freshwater fish that is known to inhabit the Dali Nor Lake, Inner Mongolia, China. The water in this lake has an HCO3–/CO32– concentration of 54 mM (pH 9.6) and a salinity of 0.6‰. The physiological mechanisms that allow this fish to tolerate these saline/alkaline conditions have yet to be elucidated. Transcriptional component analysis has shown that the expression levels of a large number of genes involved in the pathways responsible for osmo-ionoregulation and arachidonic acid metabolism pathway expression change significantly (p < 0.05) during the regulation of acid–base balance under high alkaline stress. In this study, we investigated the role of long non-coding RNAs (lncRNAs) during adaptation to high alkaline conditions. Fish were challenged to an NaHCO3-adjusted alkalinity of 0 mM, 30 mM (pH 9.44 ± 0.08), and 50 mM (pH 9.55 ± 0.06) for 20 days in the laboratory. Gill and kidney tissues were then collected for high-throughput sequencing assays. A total of 159 million clean reads were obtained by high-throughput sequencing, and 41,248 lncRNA transcripts were identified. Of these, the mean number of exons and the mean length of the lncRNA transcripts were 4.8 and 2,079 bp, respectively. Based on the analysis of differential lncRNA transcript expression, a total of 5,244 and 6,571 lncRNA transcripts were found to be differentially expressed in the gills and kidneys, respectively. Results derived from Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the coding genes were correlated with the lncRNA expression profiles. GO analysis showed that many lncRNAs were enriched in the following processes: “transporter activity,” “response to stimulus,” and “binding.” KEGG analysis further revealed that metabolic pathways were significantly enriched. A random selection of 16 lncRNA transcripts was tested by RT-qPCR; these results were consistent with our sequencing results. We found that a large number of genes, with the same expression profiles as those with differentially expressed lncRNAs, were associated with the regulation of acid–base balance, ion transport, and the excretion of ammonia and nitrogen. Collectively, our data indicate that lncRNA-regulated gene expression plays an important role in the process of adaptation to high alkaline conditions in L. waleckii.

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

Cited by 40 publications

References 167 publications

Waterlogging-Stress-Responsive LncRNAs, Their Regulatory Relationships with miRNAs and Target Genes in Cucumber (Cucumis sativus L.)

Waterlogging-Stress-Responsive LncRNAs, Their Regulatory Relationships with miRNAs and Target Genes in Cucumber (Cucumis sativus L.)

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

Identification and Analysis of Long Non-coding RNAs in Leuciscus waleckii Adapted to Highly Alkaline Conditions

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