| LncRNA was initially considered to be the "noise" of genome transcription, a byproduct of RNA polymerase II transcription, and had no biological function. In 1984, the first eukaryotic lncRNA, H19, was discovered in mice. It was 2.3 kb in length and highly expressed during embryonic development. Since then, more and more studies have shown that lncRNA plays an important role in many life activities, and lncRNA has begun to attract widespread attention. Compared with mammalian lncRNA, plant lncRNA research is relatively backward, and plant lncRNA research has been catching up. Plant lncRNA research can reveal unknown new mechanisms that control plant growth and differentiation. lncRNA plays the role of regulatory factors in various biological processes such as plant flowering, male sterility, nutritional metabolism, biotic and abiotic stresses. With the development of high-throughput sequencing technology, more and more lncRNAs have been identified, but their specific roles and functions are still not very clear. Therefore, the research field of lncRNA is still a very vast mysterious area with great 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 LncRNA |
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| LncRNA generation |
| Plants have evolved the most diverse transcriptional machinery among eukaryotic taxa to date. This enzymatic machinery includes two new nuclear DNA-dependent RNA polymerases that are specialized for lncRNA synthesis. These special enzymes determine the complexity of the lncRNA production mechanism 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 structural 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 have a variety of functions, and their main functions are as follows: |
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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 As a bait molecule, lncRNA has many miRNA recognition sites. lncRNA can competitively inhibit miRNA from binding to its target site, 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 to 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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In order to study the regulatory function of lncRNA on gene expression in plants, the authors removed rRNA from the total RNA of the sample and performed strand-specific RNA-seq, combined with bioinformatics analysis methods, to systematically identify and analyze lncRNA in the model plant Arabidopsis. A total of 6,510 lncRNAs were identified in this study, including 4,050 NAT-lncRNAs and 2,460 LincRNAs (Figure 2). |
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Figure 2: Annotation of LncRNA in Arabidopsis |
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The study found that the expression of natural antisense transcripts (NATs) in the opposite direction of protein-coding gene transcription is often positively correlated with the expression of their homologous genes under different tissues or stress treatment conditions and is required for their expression. The authors further identified MAS, a NAT-lncRNA generated from MADS that affects flowering 4 (MAF4) locus. MAS is low temperature-induced and indispensable for the activation of MAF4 transcription and the inhibition of precocious flowering. MAS activates MAF4 by interacting with WDR5a, a core component of the COMPASS-like complex, and introduces WDR5a into MAF4 to enhance histone 3 lysine 4 trimethylation (H3K4me3). This study greatly expanded the lncRNA library of Arabidopsis thaliana and revealed the role of NAT-lncRNA in regulating gene expression in vernalization response and other biological processes. This study provides rich resources and a good foundation for interpreting the functions and mechanisms of lncRNAs in plants; the mechanism analysis of MAS positively regulating MAF4 transcription is of great reference significance for studying the functional mechanisms of a large number of NAT-lncRNAs in plants. |
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Figure 3. MAS mediates the recruitment of WDR5a to MAF4 |
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Case Study 2: Research on rice |
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After removing rRNA from the total RNA of the samples, the authors used a strand-specific library construction method to sequence and analyze rice samples from four different reproductive development periods, identifying 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 used the existing rice mutant database to analyze lncRNA in the reproductive development process. The results showed that a series of lincRNAs have certain regulatory effects in the reproductive development of rice. After ceRNA analysis, it was found that miR160 or miR64 plays a role in the reproductive development process through ceRNA relationships. Finally, by analyzing the differences between the T-DNA inserted XLOC_057324 mutant and the wild type, the article found that the mutant had early heading but low fertility. The analysis obtained a lncRNA related to rice panicle development and sexual reproduction-XLOC_057324. |
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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, total RNA input amount: 1.1 μg; total RNA: total RNA sample without any treatment; rRNA removal treatment: total RNA was subjected to rRNA removal treatment. Half of the treated total RNA was taken for reverse transcription, and 0.55 μg of the untreated total RNA was taken for reverse transcription; then GADPH, 18S and 28S rRNA genes were quantified by qPCR. |
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Ordering Information |
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