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Othman, S.M.I.S.; Mustaffa, A.F.; Che-Othman, M.H.; Samad, A.F.A.; Goh, H.; Zainal, Z.; Ismail, I. miRNA Biogenesis and Its Regulation in Plant Transcripts. Encyclopedia. Available online: https://encyclopedia.pub/entry/41801 (accessed on 03 May 2024).
Othman SMIS, Mustaffa AF, Che-Othman MH, Samad AFA, Goh H, Zainal Z, et al. miRNA Biogenesis and Its Regulation in Plant Transcripts. Encyclopedia. Available at: https://encyclopedia.pub/entry/41801. Accessed May 03, 2024.
Othman, Syed Muhammad Iqbal Syed, Arif Faisal Mustaffa, M. Hafiz Che-Othman, Abdul Fatah A. Samad, Hoe-Han Goh, Zamri Zainal, Ismanizan Ismail. "miRNA Biogenesis and Its Regulation in Plant Transcripts" Encyclopedia, https://encyclopedia.pub/entry/41801 (accessed May 03, 2024).
Othman, S.M.I.S., Mustaffa, A.F., Che-Othman, M.H., Samad, A.F.A., Goh, H., Zainal, Z., & Ismail, I. (2023, March 02). miRNA Biogenesis and Its Regulation in Plant Transcripts. In Encyclopedia. https://encyclopedia.pub/entry/41801
Othman, Syed Muhammad Iqbal Syed, et al. "miRNA Biogenesis and Its Regulation in Plant Transcripts." Encyclopedia. Web. 02 March, 2023.
miRNA Biogenesis and Its Regulation in Plant Transcripts
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This entry is adapted from the peer-reviewed paper 10.3390/plants12030669

The regulatory gene-expression network in plants involves several layers of regulatory components that control the biogenesis of genes, including signal transduction, chromatin remodeling, transcription factors, transcription, post-transcription, and translation. MicroRNA (miRNA) is one of the critical components in regulating gene expression at the post-transcriptional level, playing essential roles in various molecular and developmental processes

microRNA miRNA decoy non-coding RNA

1. Introduction

The global crop output is perpetually at risk due to ongoing climate change [1][2][3], with the impact of climate change expected to increase in the future [4]. Abiotic stresses resulting from climate change affect various physiological processes in plants, such as increasing transpiration rate, reducing carbon uptake, and decreasing respiration efficiency, which is caused by an interruption of the stomatal mechanism. These changes ultimately decrease crop productivity [5]. Despite these challenges, there is a need to increase agricultural yields by 70% in the next 30 years to support the global population, which is predicted to double by 2050 [6]. Thus, there is a dire need to explore and utilize various approaches to understand gene regulation and manipulation to ensure better plant performance and productivity [7].
The regulatory gene-expression network in plants involves several layers of regulatory components that control the biogenesis of genes, including signal transduction, chromatin remodeling, transcription factors, transcription, post-transcription, and translation [8][9][10][11][12][13]. MicroRNA (miRNA) is one of the critical components in regulating gene expression at the post-transcriptional level, playing essential roles in various molecular and developmental processes [14]. miRNAs are short, non-coding RNAs, approximately 19–24 nucleotides long. They confer gene-silencing abilities by cleaving messenger RNA (mRNA) and restricting the translation of transcripts [15][16]. miRNA has been found to play essential roles in various biological processes, including plant growth and development as well as biotic and abiotic stress responses [17][18][19][20]. Many miRNAs have been found to influence plant performance and yield-related agronomic traits, making them attractive targets for crop improvement [21][22].
Several approaches have been developed to help us understand the functions of miRNA in regulating gene expression, including the overexpression of MIRNA (MIR) genes, artificial miRNA (amiRNA), anti-microRNA oligonucleotides (AMOs), RNA interference (RNAi), transcription-activator-like effector nucleases (TALEN), clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease 9 (CRISPR/Cas9), and target mimics [23][24][25][26][27][28]. Traditionally, the overexpression and knockdown/knockout techniques are used in the functional investigations of miRNAs, which result in a gain-of-function (GoF) or loss-of-function (LoF), respectively. However, miRNA genetic mutants are less effective as their miRNAs are small in size and have numerous members with overlapping functions that spread over the intergenic regions [29]. Furthermore, miRNA overexpression does not completely demonstrate its role, as miRNA can regulate gene expression when it is upregulated or downregulated [30]. Since the discovery of the INDUCED BY PHOSPHATE STARVATION 1 (IPS1) gene that downregulates miR399 activity in plants, a new way to inhibit miRNA using a mimicking target transcript strategy has been invented [31]. These contents focus on the short tandem target mimic (STTM) as a reliable tool for studying the function of miRNA, including its potential to regulate specific plant traits in a tissue-specific and inducible manner.
The study of miRNA function in plants has been aided by the development of various mimicking tools which can potentially improve plant traits. It is important to carefully consider the effectiveness and stability of these tools when choosing a strategy for decoying miRNA in post-transcription stages. STTM is a promising tool for suppressing miRNA expression in various plant species, tissues, and developmental stages. 

2. miRNA Biogenesis and Its Regulation in Plant Transcripts

Initially, MIR genes are transcribed from gene promoters by RNA polymerase II, producing single-stranded RNAs that form a coiled-hairpin secondary structure due to near-perfect complementary repeat sequences. This process produces RNA duplexes known as primary transcripts (pri-miRNAs) [32]. The length and structure of these pri-miRNAs vary between miRNAs and typically range between 100 and 400 nucleotides [33][34]. These synthesized pri-miRNAs are then stabilized by the RNA-binding protein Dawdle (DDL). The conversion of pri-miRNA to the precursor miRNA (pre-miRNA) is carried out in plants by the nuclease-cleaving protein Dicer-Like 1 (DCL1) [35]. This conversion is conducted with the joint action of double-stranded RNA-binding protein Hyponastic Leaves 1 (HYL1) and the zinc-finger protein Serrate (SE) [36][37]. The DCL1, HYL1, and SE proteins can form dicing complexes and process pri-miRNAs into pre-miRNAs in dicing bodies (D-bodies) [38][39][40].
After the conversion of pri-miRNA into pre-miRNA, a miRNA/miRNA* duplex consisting of the guide strand (miRNA) and the passenger strand (miRNA*) will be produced through the action of DCL1. DCL1 cleaves the pre-miRNA, which is then methylated at the 3′ ends by sRNA methyltransferase Hua Enhancer 1 (HEN1) to protect it from exonuclease-mediated degradation [32][41]. The methylated miRNA/miRNA* duplex is then transported into the cytoplasm by the plant homolog of cytoplasmic exportin-5 protein, Hasty (HST) [42]. The miRNA duplex will be loaded into Argonaute 1 (AGO1) to form the RNA-induced silencing complex (RISC). The AGO protein is considered the most crucial structural protein in the RISC complex. It has four domains: namely, the N-terminal domain (N), the PIWI/Argonaute/Zwille (PAZ) domain, the MID domain, and the P-element-induced wimpy testis (PIWI) domain. The PAZ domain binds RNA, while the PIWI domain possesses RNase H activity [14]. The formation then turns the guide miRNA into a single strand while the passenger miRNA* is degraded. After that, miRNA-RISC carries out the mRNA-silencing interaction through translation inhibition or mRNA cleavage [38]. Subsequently, the RISC complex with guide miRNA (3′–5′) will recognize and bind to the target mRNA by complementary base pairing [43].
In plants, miRNAs usually show sequences that are almost perfectly complementary to target transcripts. Many miRNAs facilitate RISCs to target mRNA by the direct cleavage of mRNA that strongly represses gene expression. In addition, this process of repression can also be achieved by interfering with mRNA after its assembly with ribosomes in the cytosol or endoplasmic reticulum, a process called translational inhibition [44][45]. The miRNA-RISC cleaving targets usually depend on the complementarity of the 10–11th nucleotides from the 5′ end of the miRNA. Complementary-sequence base pairing in this region will cleave the mRNA, while non-complementary bases pairing sequences will inhibit mRNA at translation stages [14]. However, the findings on how miRNAs affect plant phenotypes are still not fully understood, as individual miRNAs can regulate the expression of many genes under different conditions [46].

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Subjects: Plant Sciences
Contributors MDPI registered users' name will be linked to their SciProfiles pages. To register with us, please refer to https://encyclopedia.pub/register :
Syed Muhammad Iqbal Syed Othman
,
Arif Faisal Mustaffa
,
M. Hafiz Che-Othman
,
Abdul Fatah A. Samad
,
Hoe-Han Goh
,
Zamri Zainal
,
Ismanizan Ismail
View Times: 319
Revisions: 3 times (View History)
Update Date: 06 Mar 2023
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