| LncRNAs were initially considered "noise" in genomic transcription, byproducts of RNA polymerase II transcription with no biological function. In 1984, the first eukaryotic lncRNA, H19, was discovered in mice. The 2.3 kb gene is highly expressed during embryonic development. Since then, a growing body of research has demonstrated the crucial role of lncRNAs in numerous biological processes, and lncRNAs have begun to attract widespread attention. Compared to mammalian lncRNAs, plant lncRNA research lags behind, though plant lncRNA research has been catching up. Plant lncRNA research can reveal new, previously unknown mechanisms controlling plant growth and differentiation. lncRNAs act as regulators in a variety of biological processes, including flowering, male sterility, nutrient metabolism, and biotic and abiotic stresses. With the advancement of high-throughput sequencing technology, an increasing number of lncRNAs have been identified, but their specific roles and functions remain unclear. Therefore, the field of lncRNA research remains a vast mystery, holding immense research value. |
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| Figure 1: Classification of LncRNAs based on their relationship with protein-coding genes Classification of LncRNAs |
| Definition of LncRNA |
| Long noncoding RNA is a type of noncoding RNA (ncRNA) with a length greater than 200 nt. It does not have the function of encoding proteins and acts directly in the form of RNA. It regulates the expression of protein-coding genes at the transcriptional and post-transcriptional levels in the form of bait molecules, signal molecules, guide molecules and scaffold molecules, and participates in life processes such as cell differentiation and individual development. |
| Classification of LncRNAs |
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| LncRNA generation |
| Plants have evolved the most diverse transcriptional machinery of any eukaryotic group to date. This enzymatic machinery includes two novel nuclear DNA-dependent RNA polymerases specialized for lncRNA synthesis. These specialized enzymes contribute to the complexity of lncRNA production in plants. |
| Table 1. lncRNAs in plants |
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| AG, asexual; AtTR, telomerase RNA subunit; circRNA, circular RNA; FLC, floral locus C; IPS1, phosphate-starvation-induced substance 1; lncRNA, long noncoding RNA; LSU, large ribosomal subunit; P5SM, 5S rRNA structure mimic; RdDM, RNA-directed DNA methylation; SEP3, SEPALLATA3; snRNA, small nuclear RNA; snoRNA, small nucleolar RNA; SSU, small ribosomal subunit; TE, transposable element; TLC1, telomerase component 1. |
| LncRNAs function in a variety of ways, with the following four main functions: |
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1. Signaling molecules As a signaling molecule, lncRNA can be transcribed at specific times and locations, respond to different stimuli, sense the cellular environment, and regulate the expression of related genes. 2. Decoy molecules LncRNA acts as a bait molecule and has many miRNA recognition sites. LncRNA can competitively inhibit miRNA from binding to its target sites, thereby regulating gene transcription and expression. 3. Guide molecules LncRNA acts as a guide molecule that can bind to proteins or specific regions of DNA, and then guide the ribonucleoprotein complex to locate a specific target. 4. Skeleton molecules LncRNA can act as a skeleton molecule to combine epigenetic modification enzymes or chromatin modification factors, thereby regulating gene expression. |
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Case Study |
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Case Study 1: Research on Arabidopsis |
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To investigate the regulatory functions of lncRNAs on gene expression in plants, the authors performed strand-specific RNA-seq after rRNA depletion of total RNA samples. Combined with bioinformatics analysis, they systematically identified and analyzed lncRNAs in the model plant Arabidopsis thaliana. A total of 6,510 lncRNAs were identified, including 4,050 NAT-lncRNAs and 2,460 lincRNAs (Figure 2). |
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Figure 2: LncRNA Annotation in Arabidopsis |
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This study found that, in different tissues or under stress conditions, the expression of natural antisense transcripts (NATs), which are transcribed in the opposite direction to protein-coding genes, is often positively correlated with and required for the expression of their cognate genes. The authors further identified MAS, a NAT-lncRNA generated from the MADS of the MAF4 locus. MAS is induced by low temperature and is essential for the activation of MAF4 transcription and the suppression of precocious flowering. MAS activates MAF4 by interacting with WDR5a (a core component of the COMPASS-like complex), recruiting WDR5a to MAF4 to enhance histone 3 lysine 4 trimethylation (H3K4me3). This study significantly expands the lncRNA repertoire in Arabidopsis thaliana and reveals the role of NAT-lncRNAs in regulating gene expression during vernalization and other biological processes. This study provides a rich resource and a solid foundation for understanding the functions and mechanisms of lncRNAs in plants. The mechanistic understanding of MAS's positive regulation of MAF4 transcription has important implications for understanding the functional mechanisms of numerous NAT-lncRNAs in plants. |
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Figure 3. MAS-mediated recruitment of WDR5a to MAF4 |
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Case Study 2: Research on rice |
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The authors removed rRNA from the total RNA of the samples and then used a strand-specific library construction method to sequence and analyze rice samples from four different reproductive developmental stages. They identified 2224 rice lncRNAs, including 1624 lincRNAs and 600 antisense lncRNAs (lncRNTs) (Figure 4). Compared with Arabidopsis and animals, rice lincRNAs have obvious tissue specificity and developmental stage (reproductive development process) specificity. |
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This study utilized an existing rice mutant database to analyze the role of lncRNAs in reproductive development. The results revealed a series of lincRNAs that play a regulatory role in rice reproductive development. CeRNA analysis also revealed that miR160 or miR64 play a role in reproductive development through ceRNA interactions. Finally, the article analyzed the differences between the T-DNA insertion mutant XLOC_057324 and the wild type, revealing that the mutant exhibited early heading but low reproductive capacity. This analysis identified a lncRNA, XLOC_057324, associated with rice panicle development and sexual reproduction. |
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Figure 5. Functional Analysis of lncRNA XLOC_057324 |
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Qihengxing Plant rRNA removal kit facilitates plant lncRNA research |
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Above Wheat total RNA was used as the sample, with a total RNA input of 1.1 μg; total RNA: untreated total RNA sample; rRNA depletion treatment: total RNA was subjected to rRNA depletion. Half of the treated total RNA was reverse transcribed, while 0.55 μg of the untreated total RNA was reverse transcribed. GADPH, 18S, and 28S rRNA genes were then quantified by qPCR. |
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Ordering Information |
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