Regulation of miRNAs in Plants

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Cell Biology".

Deadline for manuscript submissions: closed (30 November 2020) | Viewed by 7733

Special Issue Editor


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Guest Editor
Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
Interests: gene silencing; smallRNAs

Special Issue Information

Dear Colleagues,

Micro RNAs (miRNAs) are central components of the regulatory networks controlling plant development and adaptive responses. Since their discovery nearly 20 years ago, scientists have linked these small molecules to a large variety of biological processes, including plant responses to biotic and abiotic stresses, physiological and adaptive development, the regulation of gene transcription, DNA repair, and even the communication between organisms.

As key elements in plant homeostasis, miRNAs’ production, activity, and stability are tightly regulated by numerous factors. Fine-tuning of the transcription, processing, and turnover of miRNAs allows for a balance between gene expression and RNA silencing. Moreover, each miRNA responds, mostly in a tissue-specific manner, to a particular set of signals. This specific regulation of a given miRNA may, or may not, be conserved among plant species, also giving these molecules an evolutionary implication. The study of the neo-functionalization of conserved miRNAs, as well as the study of species-specific miRNAs, emerged as fundamental research topics to understand natural variation among plants, especially in agronomically important species.

This Special Issue on the “Regulation of miRNAs in Plants” aims to gather vibrant articles exploring both the regulatory functions of miRNAs, as well as the regulation of the miRNA pathway itself. We welcome original research papers as well as reviews of the wide range of topics related to miRNA regulation in model and non-model plants. It aims to provide a space to present and discuss exciting results that are of interest to the community of RNA silencing in plants.

Prof. Dr. Pablo Manavella
Guest Editor

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Published Papers (3 papers)

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Research

13 pages, 778 KiB  
Article
Whole-Genome Doubling Affects Pre-miRNA Expression in Plants
by Salvatore Esposito, Riccardo Aversano, Pasquale Tripodi and Domenico Carputo
Plants 2021, 10(5), 1004; https://doi.org/10.3390/plants10051004 - 18 May 2021
Cited by 1 | Viewed by 2266
Abstract
Whole-genome doubling (polyploidy) is common in angiosperms. Several studies have indicated that it is often associated with molecular, physiological, and phenotypic changes. Mounting evidence has pointed out that micro-RNAs (miRNAs) may have an important role in whole-genome doubling. However, an integrative approach that [...] Read more.
Whole-genome doubling (polyploidy) is common in angiosperms. Several studies have indicated that it is often associated with molecular, physiological, and phenotypic changes. Mounting evidence has pointed out that micro-RNAs (miRNAs) may have an important role in whole-genome doubling. However, an integrative approach that compares miRNA expression in polyploids is still lacking. Here, a re-analysis of already published RNAseq datasets was performed to identify microRNAs’ precursors (pre-miRNAs) in diploids (2x) and tetraploids (4x) of five species (Arabidopsis thaliana L., Morus alba L., Brassica rapa L., Isatis indigotica Fort., and Solanum commersonii Dun). We found 3568 pre-miRNAs, three of which (pre-miR414, pre-miR5538, and pre-miR5141) were abundant in all 2x, and were absent/low in their 4x counterparts. They are predicted to target more than one mRNA transcript, many belonging to transcription factors (TFs), DNA repair mechanisms, and related to stress. Sixteen pre-miRNAs were found in common in all 2x and 4x. Among them, pre-miRNA482, pre-miRNA2916, and pre-miRNA167 changed their expression after polyploidization, being induced or repressed in 4x plants. Based on our results, a common ploidy-dependent response was triggered in all species under investigation, which involves DNA repair, ATP-synthesis, terpenoid biosynthesis, and several stress-responsive transcripts. In addition, an ad hoc pre-miRNA expression analysis carried out solely on 2x vs. 4x samples of S. commersonii indicated that ploidy-dependent pre-miRNAs seem to actively regulate the nucleotide metabolism, probably to cope with the increased requirement for DNA building blocks caused by the augmented DNA content. Overall, the results outline the critical role of microRNA-mediated responses following autopolyploidization in plants. Full article
(This article belongs to the Special Issue Regulation of miRNAs in Plants)
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14 pages, 3083 KiB  
Article
Extensive Analysis of miRNA Trimming and Tailing Indicates that AGO1 Has a Complex Role in miRNA Turnover
by Axel J. Giudicatti, Ariel H. Tomassi, Pablo A. Manavella and Agustin L. Arce
Plants 2021, 10(2), 267; https://doi.org/10.3390/plants10020267 - 30 Jan 2021
Cited by 5 | Viewed by 3033
Abstract
MicroRNAs are small regulatory RNAs involved in several processes in plants ranging from development and stress responses to defense against pathogens. In order to accomplish their molecular functions, miRNAs are methylated and loaded into one ARGONAUTE (AGO) protein, commonly known as AGO1, to [...] Read more.
MicroRNAs are small regulatory RNAs involved in several processes in plants ranging from development and stress responses to defense against pathogens. In order to accomplish their molecular functions, miRNAs are methylated and loaded into one ARGONAUTE (AGO) protein, commonly known as AGO1, to stabilize and protect the molecule and to assemble a functional RNA-induced silencing complex (RISC). A specific machinery controls miRNA turnover to ensure the silencing release of targeted-genes in given circumstances. The trimming and tailing of miRNAs are fundamental modifications related to their turnover and, hence, to their action. In order to gain a better understanding of these modifications, we analyzed Arabidopsis thaliana small RNA sequencing data from a diversity of mutants, related to miRNA biogenesis, action, and turnover, and from different cellular fractions and immunoprecipitations. Besides confirming the effects of known players in these pathways, we found increased trimming and tailing in miRNA biogenesis mutants. More importantly, our analysis allowed us to reveal the importance of ARGONAUTE 1 (AGO1) loading, slicing activity, and cellular localization in trimming and tailing of miRNAs. Full article
(This article belongs to the Special Issue Regulation of miRNAs in Plants)
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12 pages, 2051 KiB  
Article
Computational Identification and Comparative Analysis of Conserved miRNAs and Their Putative Target Genes in the Juglans regia and J. microcarpa Genomes
by Le Wang, Tingting Zhu, Karin R. Deal, Jan Dvorak and Ming-Cheng Luo
Plants 2020, 9(10), 1330; https://doi.org/10.3390/plants9101330 - 09 Oct 2020
Cited by 1 | Viewed by 1931
Abstract
MicroRNAs (miRNAs) are important factors for the post-transcriptional regulation of protein-coding genes in plants and animals. They are discovered either by sequencing small RNAs or computationally. We employed a sequence-homology-based computational approach to identify conserved miRNAs and their target genes in Persian (English) [...] Read more.
MicroRNAs (miRNAs) are important factors for the post-transcriptional regulation of protein-coding genes in plants and animals. They are discovered either by sequencing small RNAs or computationally. We employed a sequence-homology-based computational approach to identify conserved miRNAs and their target genes in Persian (English) walnut, Juglans regia, and its North American wild relative, J. microcarpa. A total of 119 miRNA precursors (pre-miRNAs) were detected in the J. regia genome and 121 in the J. microcarpa genome and miRNA target genes were predicted and their functional annotations were performed in both genomes. In the J. regia genome, 325 different genes were targets; 87.08% were regulated by transcript cleavage and 12.92% by translation repression. In the J. microcarpa genome, 316 different genes were targets; 88.92% were regulated by transcript cleavage and 11.08% were regulated by translation repression. Totals of 1.3% and 2.0% of all resistance gene analogues (RGA) and 2.7% and 2.6% of all transcription factors (TFs) were regulated by miRNAs in the J. regia and J. microcarpa genomes, respectively. Juglans genomes evolved by a whole genome duplication (WGD) and consist of eight pairs of fractionated homoeologous chromosomes. Within each pair, the chromosome that has more genes with greater average transcription also harbors more pre-miRNAs and more target genes than its homoeologue. While only minor differences were detected in pre-miRNAs between the J. regia and J. microcarpa genomes, about one-third of the pre-miRNA loci were not conserved between homoeologous chromosome within each genome. Pre-miRNA and their corresponding target genes showed a tendency to be collocated within a subgenome. Full article
(This article belongs to the Special Issue Regulation of miRNAs in Plants)
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