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The World of Plant Non-coding RNAs
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The World of Plant Non-coding RNAs

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (31 January 2023) | Viewed by 30172

Special Issue Editors

Prof. Dr. Ivan Minkov

E-Mail Website
Guest Editor
Department of Plant Physiology and Plant Molecular Biology, University of Plovdiv, 24 Tsar Assen str., Plovdiv 4000, Bulgaria
Interests: plant molecular biology; systems biology; bioinformatics; plant biotechnology; plant virology; plant farming; plant stress
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Vesselin Baev

E-Mail Website
Guest Editor
Department of Molecular Biology, University of Plovdiv, 4000 Plovdiv, Bulgaria
Interests: bioinformatics; NGS; tool development; genomics; metagenomics; transcriptomics
Special Issues, Collections and Topics in MDPI journals
Dr. Andreas Gisel

E-Mail Website
Guest Editor
1. Institute of Biomedical Technologies (ITB), CNR, Bari, Italy
2. International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
Interests: plant and human bioinformatics; NGS data analysis; tool development; epigenetics; smallRNA; bulk and single-cell transcriptomics; DNA-methylation; development of biological databases; education and training

Special Issue Information

Dear Colleagues,

Non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs), short interfering RNAs (siRNAs), and long non-coding RNAs (lncRNAs), have emerged as critical regulators in plants on the level of the direct interaction with transcripts, but also indirect as a vehicle for DNA methylation and the consequent regulation of gene expression. Furthermore, these hidden players of gene regulation have been found to form a complex network and have key roles in diverse regulatory pathways involved in plant development, plant health, and environmental and disease responses. The technical breakthrough of genome sequencing, especially next-generation sequencing and advanced bioinformatics tools, has dramatically improved the process of the discovery of novel ncRNAs, including their essential roles in plants. Nevertheless, there is a need for further in-depth studies of ncRNAs highlighting the essential hotspots of regulatory pathways in these plant processes.

After the success of the first edition of the Special Issue, “Plant Non-Coding RNAs”, here, we present the second edition, “The World of Plant Non-Coding RNAs”, where we encourage authors to submit manuscripts related to both wet-lab and/or dry-lab studies that can provide a comprehensive understanding of these fascinating molecules and the complex mechanisms that they are involved in.

Prof. Dr. Ivan Minkov
Prof. Dr. Vesselin Baev
Dr. Andreas Gisel
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • non-coding RNAs
  • microRNAs
  • lncRNAs and circRNAs
  • abiotic and biotic stress
  • plant health

Published Papers (15 papers)

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Editorial

Jump to: Research, Review

3 pages, 185 KiB  
Editorial
The Fascinating World of Plant Non-Coding RNAs
by Vesselin Baev, Andreas Gisel and Ivan Minkov
Int. J. Mol. Sci. 2023, 24(12), 10341; https://doi.org/10.3390/ijms241210341 - 19 Jun 2023
Viewed by 805
Abstract
Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), short interfering RNAs (siRNAs), and long non-coding RNAs (lncRNAs), have emerged as pivotal regulators within the plant kingdom [...] Full article
(This article belongs to the Special Issue The World of Plant Non-coding RNAs)

Research

Jump to: Editorial, Review

20 pages, 13000 KiB  
Article
Combined lncRNA and mRNA Expression Profiles Identified the lncRNA–miRNA–mRNA Modules Regulating the Cold Stress Response in Ammopiptanthus nanus
by Ming Zhu, Qianshi Dong, Jie Bing, Songbuerbatu, Lamei Zheng, Tashi Dorjee, Qi Liu, Yijun Zhou and Fei Gao
Int. J. Mol. Sci. 2023, 24(7), 6502; https://doi.org/10.3390/ijms24076502 - 30 Mar 2023
Cited by 4 | Viewed by 1514
Abstract
Long non-coding RNAs (lncRNAs) have been shown to play critical regulatory roles in plants. Ammopiptanthus nanus can survive under severe low-temperature stress, and lncRNAs may play crucial roles in the gene regulation network underlying the cold stress response in A. nanus. To [...] Read more.
Long non-coding RNAs (lncRNAs) have been shown to play critical regulatory roles in plants. Ammopiptanthus nanus can survive under severe low-temperature stress, and lncRNAs may play crucial roles in the gene regulation network underlying the cold stress response in A. nanus. To investigate the roles of lncRNAs in the cold stress response of A. nanus, a combined lncRNA and mRNA expression profiling under cold stress was conducted. Up to 4890 novel lncRNAs were identified in A. nanus and 1322 of them were differentially expressed under cold stress, including 543 up-regulated and 779 down-regulated lncRNAs. A total of 421 lncRNAs were found to participate in the cold stress response by forming lncRNA–mRNA modules and regulating the genes encoding the stress-related transcription factors and enzymes in a cis-acting manner. We found that 31 lncRNAs acting as miRNA precursors and 8 lncRNAs acting as endogenous competitive targets of miRNAs participated in the cold stress response by forming lncRNA–miRNA–mRNA regulatory modules. In particular, a cold stress-responsive lncRNA, TCONS00065739, which was experimentally proven to be an endogenous competitive target of miR530, contributed to the cold stress adaptation by regulating TZP in A. nanus. These results provide new data for understanding the biological roles of lncRNAs in response to cold stress in plants. Full article
(This article belongs to the Special Issue The World of Plant Non-coding RNAs)
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15 pages, 13829 KiB  
Article
Long Non-Coding RNA lncWOX11a Suppresses Adventitious Root Formation of Poplar by Regulating the Expression of PeWOX11a
by Na Ran, Sian Liu, Haoran Qi, Jiali Wang, Tengfei Shen, Wenlin Xu and Meng Xu
Int. J. Mol. Sci. 2023, 24(6), 5766; https://doi.org/10.3390/ijms24065766 - 17 Mar 2023
Cited by 7 | Viewed by 2469
Abstract
Long non-coding RNAs (lncRNAs), a class of poorly conserved transcripts without protein-encoding ability, are widely involved in plant organogenesis and stress responses by mediating the transmission and expression of genetic information at the transcriptional, posttranscriptional, and epigenetic levels. Here, we cloned and characterized [...] Read more.
Long non-coding RNAs (lncRNAs), a class of poorly conserved transcripts without protein-encoding ability, are widely involved in plant organogenesis and stress responses by mediating the transmission and expression of genetic information at the transcriptional, posttranscriptional, and epigenetic levels. Here, we cloned and characterized a novel lncRNA molecule through sequence alignment, Sanger sequencing, transient expression in protoplasts, and genetic transformation in poplar. lncWOX11a is a 215 bp transcript located on poplar chromosome 13, ~50 kbp upstream of PeWOX11a on the reverse strand, and the lncRNA may fold into a series of complex stem–loop structures. Despite the small open reading frame (sORF) of 51 bp within lncWOX11a, bioinformatics analysis and protoplast transfection revealed that lncWOX11a has no protein-coding ability. The overexpression of lncWOX11a led to a decrease in the quantity of adventitious roots on the cuttings of transgenic poplars. Further, cis-regulatory module prediction and CRISPR/Cas9 knockout experiments with poplar protoplasts demonstrated that lncWOX11a acts as a negative regulator of adventitious rooting by downregulating the WUSCHEL-related homeobox gene WOX11, which is supposed to activate adventitious root development in plants. Collectively, our findings imply that lncWOX11a is essential for modulating the formation and development of adventitious roots. Full article
(This article belongs to the Special Issue The World of Plant Non-coding RNAs)
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23 pages, 5905 KiB  
Article
Identification and Functional Prediction of CircRNAs in Leaves of F1 Hybrid Poplars with Different Growth Potential and Their Parents
by Weixi Zhang, Zhengsai Yuan, Jing Zhang, Xiaohua Su, Qinjun Huang, Qi Liu and Changjun Ding
Int. J. Mol. Sci. 2023, 24(3), 2284; https://doi.org/10.3390/ijms24032284 - 23 Jan 2023
Cited by 3 | Viewed by 1506
Abstract
Circular RNAs (CircRNAs) regulate plant growth and development; however, their role in poplar heterosis is unclear. We identified 3722 circRNAs in poplar leaves, most of which were intergenic (57.2%) and exonic (40.2%). The expression of circRNAs in F1 hybrids with high growth potential [...] Read more.
Circular RNAs (CircRNAs) regulate plant growth and development; however, their role in poplar heterosis is unclear. We identified 3722 circRNAs in poplar leaves, most of which were intergenic (57.2%) and exonic (40.2%). The expression of circRNAs in F1 hybrids with high growth potential was higher than that in those with low growth potential. Non-additive expression of circRNAs and single-parent expression of circRNAs (SPE-circRNAs) might regulate poplar heterosis through microRNA sponging and protein translation, respectively. DECs among F1 hybrids with different growth potentials might regulate the growth potential of poplar via microRNA sponging. Correlation analysis between circRNA expression and its parent gene expression showed that SPE-M circRNA (circRNAs expressed by male parent only) might regulate poplar heterosis by inhibiting parent gene expression, while other circRNAs might regulate poplar heterosis by enhancing parent gene expression. Weighted correlation network analysis of gene/circRNA expression showed that circRNAs mainly regulate poplar heterosis via carbohydrate metabolism, amino acid metabolism, energy metabolism, and material transport. In addition, we identified seven circRNAs that positively or negatively regulate poplar heterosis. Thus, non-additively expressed circRNAs and SPE circRNAs are involved in regulating poplar heterosis, and DECs among F1 hybrids with different growth potentials were involved in regulating poplar growth potential. Full article
(This article belongs to the Special Issue The World of Plant Non-coding RNAs)
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17 pages, 790 KiB  
Article
Wheat Long Noncoding RNAs from Organelle and Nuclear Genomes Carry Conserved microRNA Precursors Which May Together Comprise Intricate Networks in Insect Responses
by Bala Ani Akpinar, Tugdem Muslu, Gadi V. P. Reddy, Munevver Dogramaci and Hikmet Budak
Int. J. Mol. Sci. 2023, 24(3), 2226; https://doi.org/10.3390/ijms24032226 - 23 Jan 2023
Cited by 5 | Viewed by 1974
Abstract
Long noncoding RNAs (lncRNAs) are a diverse class of noncoding RNAs that are typically longer than 200 nucleotides but lack coding potentials. Advances in deep sequencing technologies enabled a better exploration of this type of noncoding transcripts. The poor sequence conservation, however, complicates [...] Read more.
Long noncoding RNAs (lncRNAs) are a diverse class of noncoding RNAs that are typically longer than 200 nucleotides but lack coding potentials. Advances in deep sequencing technologies enabled a better exploration of this type of noncoding transcripts. The poor sequence conservation, however, complicates the identification and annotation of lncRNAs at a large scale. Wheat is among the leading food staples worldwide whose production is threatened by both biotic and abiotic stressors. Here, we identified putative lncRNAs from durum wheat varieties that differ in stem solidness, a major source of defense against wheat stem sawfly, a devastating insect pest. We also analyzed and annotated lncRNAs from two bread wheat varieties, resistant and susceptible to another destructive pest, orange wheat blossom midge, with and without infestation. Several putative lncRNAs contained potential precursor sequences and/or target regions for microRNAs, another type of regulatory noncoding RNAs, which may indicate functional networks. Interestingly, in contrast to lncRNAs themselves, microRNAs with potential precursors within the lncRNA sequences appeared to be highly conserved at the sequence and family levels. We also observed a few putative lncRNAs that have perfect to near-perfect matches to organellar genomes, supporting the recent observations that organellar genomes may contribute to the noncoding transcript pool of the cell. Full article
(This article belongs to the Special Issue The World of Plant Non-coding RNAs)
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20 pages, 3465 KiB  
Article
Transcriptional Regulation of zma-MIR528a by Action of Nitrate and Auxin in Maize
by Eduardo Luján-Soto, Paola I. Aguirre de la Cruz, Vasti T. Juárez-González, José L. Reyes, María de la Paz Sanchez and Tzvetanka D. Dinkova
Int. J. Mol. Sci. 2022, 23(24), 15718; https://doi.org/10.3390/ijms232415718 - 11 Dec 2022
Cited by 3 | Viewed by 1843
Abstract
In recent years, miR528, a monocot-specific miRNA, has been assigned multifaceted roles during development and stress response in several plant species. However, the transcription regulation and the molecular mechanisms controlling MIR528 expression in maize are still poorly explored. Here we analyzed the zma- [...] Read more.
In recent years, miR528, a monocot-specific miRNA, has been assigned multifaceted roles during development and stress response in several plant species. However, the transcription regulation and the molecular mechanisms controlling MIR528 expression in maize are still poorly explored. Here we analyzed the zma-MIR528a promoter region and found conserved transcription factor binding sites related to diverse signaling pathways, including the nitrate (TGA1/4) and auxin (AuxRE) response networks. Accumulation of both pre-miR528a and mature miR528 was up-regulated by exogenous nitrate and auxin treatments during imbibition, germination, and maize seedling establishment. Functional promoter analyses demonstrated that TGA1/4 and AuxRE sites are required for transcriptional induction by both stimuli. Overall, our findings of the nitrogen- and auxin-induced zma-MIR528a expression through cis-regulatory elements in its promoter contribute to the knowledge of miR528 regulome. Full article
(This article belongs to the Special Issue The World of Plant Non-coding RNAs)
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12 pages, 2811 KiB  
Article
Identification of Species-Specific MicroRNAs Provides Insights into Dynamic Evolution of MicroRNAs in Plants
by Zhonglong Guo, Zheng Kuang, Yang Deng, Lei Li and Xiaozeng Yang
Int. J. Mol. Sci. 2022, 23(22), 14273; https://doi.org/10.3390/ijms232214273 - 17 Nov 2022
Cited by 3 | Viewed by 1661
Abstract
MicroRNAs (miRNAs) are an important class of regulatory small RNAs that program gene expression, mainly at the post-transcriptional level. Although sporadic examples of species-specific miRNAs (termed SS-miRNAs) have been reported, a genome-scale study across a variety of distant species has not been assessed. [...] Read more.
MicroRNAs (miRNAs) are an important class of regulatory small RNAs that program gene expression, mainly at the post-transcriptional level. Although sporadic examples of species-specific miRNAs (termed SS-miRNAs) have been reported, a genome-scale study across a variety of distant species has not been assessed. Here, by comprehensively analyzing miRNAs in 81 plant species phylogenetically ranging from chlorophytes to angiosperms, we identified 8048 species-specific miRNAs from 5499 families, representing over 61.2% of the miRNA families in the examined species. An analysis of the conservation from different taxonomic levels supported the high turnover rate of SS-miRNAs, even over short evolutionary distances. A comparison of the intrinsic features between SS-miRNAs and NSS-miRNAs (non-species-specific miRNAs) indicated that the AU content of mature miRNAs was the most striking difference. Our data further illustrated a significant bias of the genomic coordinates towards SS-miRNAs lying close to or within genes. By analyzing the 125,267 putative target genes for the 7966 miRNAs, we found the preferentially regulated functions of SS-miRNAs related to diverse metabolic processes. Collectively, these findings underscore the dynamic evolution of miRNAs in the species-specific lineages. Full article
(This article belongs to the Special Issue The World of Plant Non-coding RNAs)
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17 pages, 1848 KiB  
Article
In-Plant Persistence and Systemic Transport of Nicotiana benthamiana Retrozyme RNA
by Alexander A. Lezzhov, Eugene A. Tolstyko, Anastasia K. Atabekova, Denis A. Chergintsev, Sergey Y. Morozov and Andrey G. Solovyev
Int. J. Mol. Sci. 2022, 23(22), 13890; https://doi.org/10.3390/ijms232213890 - 11 Nov 2022
Cited by 2 | Viewed by 1338
Abstract
Retrozymes are nonautonomous retrotransposons with hammerhead ribozymes in their long terminal repeats (LTRs). Retrozyme transcripts can be self-cleaved by the LTR ribozyme, circularized, and can undergo RNA-to-RNA replication. Here, we demonstrate that the Nicotiana benthamiana genome contains hundreds of retrozyme loci, of which [...] Read more.
Retrozymes are nonautonomous retrotransposons with hammerhead ribozymes in their long terminal repeats (LTRs). Retrozyme transcripts can be self-cleaved by the LTR ribozyme, circularized, and can undergo RNA-to-RNA replication. Here, we demonstrate that the Nicotiana benthamiana genome contains hundreds of retrozyme loci, of which nine represent full-length retrozymes. The LTR contains a promoter directing retrozyme transcription. Although retrozyme RNA is easily detected in plants, the LTR region is heavily methylated, pointing to its transcriptional silencing, which can be mediated by 24 nucleotide-long retrozyme-specific RNAs identified in N. benthamiana. A transcriptome analysis revealed that half of the retrozyme-specific RNAs in plant leaves have no exact matches to genomic retrozyme loci, containing up to 13% mismatches with the closest genomic sequences, and could arise as a result of many rounds of RNA-to-RNA replication leading to error accumulation. Using a cloned retrozyme copy, we show that retrozyme RNA is capable of replication and systemic transport in plants. The presented data suggest that retrozyme loci in the N. benthamiana genome are transcriptionally inactive, and that circular retrozyme RNA can persist in cells due to its RNA-to-RNA replication and be transported systemically, emphasizing functional and, possibly, evolutionary links of retrozymes to viroids—noncoding circular RNAs that infect plants. Full article
(This article belongs to the Special Issue The World of Plant Non-coding RNAs)
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18 pages, 6080 KiB  
Article
Integrated Analysis of Transcriptome and Small RNAome Reveals the Regulatory Network for Rapid Growth in Mikania micrantha
by Xiaowei Mo, Haolang Chen, Xiaolan Yang, Beixin Mo, Lei Gao and Yu Yu
Int. J. Mol. Sci. 2022, 23(18), 10596; https://doi.org/10.3390/ijms231810596 - 13 Sep 2022
Cited by 2 | Viewed by 1402
Abstract
M. micrantha has caused huge ecological damage and economic losses worldwide due to its rapid growth and serious invasion. However, the underlying molecular mechanisms of its rapid growth and environmental adaption remain unclear. Here, we performed transcriptome and small RNA sequencing with five [...] Read more.
M. micrantha has caused huge ecological damage and economic losses worldwide due to its rapid growth and serious invasion. However, the underlying molecular mechanisms of its rapid growth and environmental adaption remain unclear. Here, we performed transcriptome and small RNA sequencing with five tissues of M. micrantha to dissect miRNA-mediated regulation in M. micrantha. WGCNA and GO enrichment analysis of transcriptome identified the gene association patterns and potential key regulatory genes for plant growth in each tissue. The genes highly correlated with leaf and stem tissues were mainly involved in the chlorophyll synthesis, response to auxin, the CAM pathway and other photosynthesis-related processes, which promoted the fast growth of M. micrantha. Importantly, we identified 350 conserved and 192 novel miRNAs, many of which displayed differential expression patterns among tissues. PsRNA target prediction analysis uncovered target genes of both conserved and novel miRNAs, including GRFs and TCPs, which were essential for plant growth and development. Further analysis revealed that miRNAs contributed to the regulation of tissue-specific gene expression in M. micrantha, such as mmi-miR396 and mmi-miR319. Taken together, our study uncovered the miRNA-mRNA regulatory networks and the potential vital roles of miRNAs in modulating the rapid growth of M. micrantha. Full article
(This article belongs to the Special Issue The World of Plant Non-coding RNAs)
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18 pages, 15170 KiB  
Article
Integrated Degradome and Srna Sequencing Revealed miRNA-mRNA Regulatory Networks between the Phloem and Developing Xylem of Poplar
by Changjun Ding, Tengfei Shen, Na Ran, Heng Zhang, Huixin Pan, Xiaohua Su and Meng Xu
Int. J. Mol. Sci. 2022, 23(9), 4537; https://doi.org/10.3390/ijms23094537 - 20 Apr 2022
Cited by 8 | Viewed by 2090
Abstract
Lignin and cellulose are the most abundant natural organic polymers in nature. MiRNAs are a class of regulatory RNAs discovered in mammals, plants, viruses, and bacteria. Studies have shown that miRNAs play a role in lignin and cellulose biosynthesis by targeting key enzymes. [...] Read more.
Lignin and cellulose are the most abundant natural organic polymers in nature. MiRNAs are a class of regulatory RNAs discovered in mammals, plants, viruses, and bacteria. Studies have shown that miRNAs play a role in lignin and cellulose biosynthesis by targeting key enzymes. However, the specific miRNAs functioning in the phloem and developing xylem of Populus deltoides are still unknown. In this study, a total of 134 miRNAs were identified via high-throughput small RNA sequencing, including 132 known and two novel miRNAs, six of which were only expressed in the phloem. A total of 58 differentially expressed miRNAs (DEmiRNAs) were identified between the developing xylem and the phloem. Among these miRNAs, 21 were significantly upregulated in the developing xylem in contrast to the phloem and 37 were significantly downregulated. A total of 2431 target genes of 134 miRNAs were obtained via high-throughput degradome sequencing. Most target genes of these miRNAs were transcription factors, including AP2, ARF, bHLH, bZIP, GRAS, GRF, MYB, NAC, TCP, and WRKY genes. Furthermore, 13 and nine miRNAs were involved in lignin and cellulose biosynthesis, respectively, and we validated the miRNAs via qRT-PCR. Our study explores these miRNAs and their regulatory networks in the phloem and developing xylem of P.deltoides and provides new insight into wood formation. Full article
(This article belongs to the Special Issue The World of Plant Non-coding RNAs)
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23 pages, 5208 KiB  
Article
miRNA Profiling and Its Role in Multi-Omics Regulatory Networks Connected with Somaclonal Variation in Cucumber (Cucumis sativus L.)
by Magdalena Ewa Pawełkowicz, Agnieszka Skarzyńska, Marek Daniel Koter, Szymon Turek and Wojciech Pląder
Int. J. Mol. Sci. 2022, 23(8), 4317; https://doi.org/10.3390/ijms23084317 - 13 Apr 2022
Cited by 4 | Viewed by 2571
Abstract
The role of miRNAs in connection with the phenomenon of somaclonal variation, which occurs during plant in vitro culture, remains uncertain. This study aims to investigate the possible role of miRNAs in multi-omics regulatory pathways in cucumber somaclonal lines. For this purpose, we [...] Read more.
The role of miRNAs in connection with the phenomenon of somaclonal variation, which occurs during plant in vitro culture, remains uncertain. This study aims to investigate the possible role of miRNAs in multi-omics regulatory pathways in cucumber somaclonal lines. For this purpose, we performed sRNA sequencing (sRNA-seq) from cucumber fruit samples identified 8, 10 and 44 miRNAs that are differentially expressed between somaclones (S1, S2, S3 lines) and the reference B10 line of Cucumis sativus. For miRNA identification, we use ShortStack software designed to filter miRNAs from sRNAs according to specific program criteria. The identification of predicted in-silico targets revealed 2,886 mRNAs encoded by 644 genes. The functional annotation of miRNA’s target genes and gene ontology classification revealed their association with metabolic processes, response to stress, multicellular organism development, biosynthetic process and catalytic activity. We checked with bioinformatic analyses for possible interactions at the level of target proteins, differentially expressed genes (DEGs) and genes affected by genomic polymorphisms. We assume that miRNAs can indirectly influence molecular networks and play a role in many different regulatory pathways, leading to somaclonal variation. This regulation is supposed to occur through the process of the target gene cleavage or translation inhibition, which in turn affects the proteome, as we have shown in the example of molecular networks. This is a new approach combining levels from DNA-seq through mRNA-seq, sRNA-seq and in silico PPI in the area of plants’ somaclonal variation. Full article
(This article belongs to the Special Issue The World of Plant Non-coding RNAs)
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Review

Jump to: Editorial, Research

15 pages, 1109 KiB  
Review
Beyond Loading: Functions of Plant ARGONAUTE Proteins
by Chao Liang, Xiaoliu Wang, Hualong He, Chi Xu and Jie Cui
Int. J. Mol. Sci. 2023, 24(22), 16054; https://doi.org/10.3390/ijms242216054 - 7 Nov 2023
Viewed by 1325
Abstract
ARGONAUTE (AGO) proteins are key components of the RNA-induced silencing complex (RISC) that mediates gene silencing in eukaryotes. Small-RNA (sRNA) cargoes are selectively loaded into different members of the AGO protein family and then target complementary sequences to in-duce transcriptional repression, mRNA cleavage, [...] Read more.
ARGONAUTE (AGO) proteins are key components of the RNA-induced silencing complex (RISC) that mediates gene silencing in eukaryotes. Small-RNA (sRNA) cargoes are selectively loaded into different members of the AGO protein family and then target complementary sequences to in-duce transcriptional repression, mRNA cleavage, or translation inhibition. Previous reviews have mainly focused on the traditional roles of AGOs in specific biological processes or on the molecular mechanisms of sRNA sorting. In this review, we summarize the biological significance of canonical sRNA loading, including the balance among distinct sRNA pathways, cross-regulation of different RISC activities during plant development and defense, and, especially, the emerging roles of AGOs in sRNA movement. We also discuss recent advances in novel non-canonical functions of plant AGOs. Perspectives for future functional studies of this evolutionarily conserved eukaryotic protein family will facilitate a more comprehensive understanding of the multi-faceted AGO proteins. Full article
(This article belongs to the Special Issue The World of Plant Non-coding RNAs)
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15 pages, 1058 KiB  
Review
MicroRNA398: A Master Regulator of Plant Development and Stress Responses
by Jing Li, Qiaoqiao Song, Zhi-Fang Zuo and Lin Liu
Int. J. Mol. Sci. 2022, 23(18), 10803; https://doi.org/10.3390/ijms231810803 - 16 Sep 2022
Cited by 12 | Viewed by 2278
Abstract
MicroRNAs (miRNAs) play crucial roles in plant development and stress responses, and a growing number of studies suggest that miRNAs are promising targets for crop improvement because they participate in the regulation of diverse, important agronomic traits. MicroRNA398 (miR398) is a conserved miRNA [...] Read more.
MicroRNAs (miRNAs) play crucial roles in plant development and stress responses, and a growing number of studies suggest that miRNAs are promising targets for crop improvement because they participate in the regulation of diverse, important agronomic traits. MicroRNA398 (miR398) is a conserved miRNA in plants and has been shown to control multiple stress responses and plant growth in a variety of species. There are many studies on the stress response and developmental regulation of miR398. To systematically understand its function, it is necessary to summarize the evolution and functional roles of miR398 and its target genes. In this review, we analyze the evolution of miR398 in plants and outline its involvement in abiotic and biotic stress responses, in growth and development and in model and non-model plants. We summarize recent functional analyses, highlighting the role of miR398 as a master regulator that coordinates growth and diverse responses to environmental factors. We also discuss the potential for fine-tuning miR398 to achieve the goal of simultaneously improving plant growth and stress tolerance. Full article
(This article belongs to the Special Issue The World of Plant Non-coding RNAs)
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19 pages, 1397 KiB  
Review
MicroRNAs in Medicinal Plants
by Mingyang Sun, Shiqiang Xu, Yu Mei, Jingyu Li, Yan Gu, Wenting Zhang and Jihua Wang
Int. J. Mol. Sci. 2022, 23(18), 10477; https://doi.org/10.3390/ijms231810477 - 9 Sep 2022
Cited by 12 | Viewed by 2448
Abstract
Medicinal plant microRNAs (miRNAs) are an endogenous class of small RNA central to the posttranscriptional regulation of gene expression. Biosynthetic research has shown that the mature miRNAs in medicinal plants can be produced from either the standard messenger RNA splicing mechanism or the [...] Read more.
Medicinal plant microRNAs (miRNAs) are an endogenous class of small RNA central to the posttranscriptional regulation of gene expression. Biosynthetic research has shown that the mature miRNAs in medicinal plants can be produced from either the standard messenger RNA splicing mechanism or the pre-ribosomal RNA splicing process. The medicinal plant miRNA function is separated into two levels: (1) the cross-kingdom level, which is the regulation of disease-related genes in animal cells by oral intake, and (2) the intra-kingdom level, which is the participation of metabolism, development, and stress adaptation in homologous or heterologous plants. Increasing research continues to enrich the biosynthesis and function of medicinal plant miRNAs. In this review, peer-reviewed papers on medicinal plant miRNAs published on the Web of Science were discussed, covering a total of 78 species. The feasibility of the emerging role of medicinal plant miRNAs in regulating animal gene function was critically evaluated. Staged progress in intra-kingdom miRNA research has only been found in a few medicinal plants, which may be mainly inhibited by their long growth cycle, high demand for growth environment, immature genetic transformation, and difficult RNA extraction. The present review clarifies the research significance, opportunities, and challenges of medicinal plant miRNAs in drug development and agricultural production. The discussion of the latest results furthers the understanding of medicinal plant miRNAs and helps the rational design of the corresponding miRNA/target genes functional modules. Full article
(This article belongs to the Special Issue The World of Plant Non-coding RNAs)
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19 pages, 845 KiB  
Review
The Multiverse of Plant Small RNAs: How Can We Explore It?
by Zdravka Ivanova, Georgi Minkov, Andreas Gisel, Galina Yahubyan, Ivan Minkov, Valentina Toneva and Vesselin Baev
Int. J. Mol. Sci. 2022, 23(7), 3979; https://doi.org/10.3390/ijms23073979 - 2 Apr 2022
Cited by 3 | Viewed by 3571
Abstract
Plant small RNAs (sRNAs) are a heterogeneous group of noncoding RNAs with a length of 20–24 nucleotides that are widely studied due to their importance as major regulators in various biological processes. sRNAs are divided into two main classes—microRNAs (miRNAs) and small interfering [...] Read more.
Plant small RNAs (sRNAs) are a heterogeneous group of noncoding RNAs with a length of 20–24 nucleotides that are widely studied due to their importance as major regulators in various biological processes. sRNAs are divided into two main classes—microRNAs (miRNAs) and small interfering RNAs (siRNAs)—which differ in their biogenesis and functional pathways. Their identification and enrichment with new structural variants would not be possible without the use of various high-throughput sequencing (NGS) techniques, allowing for the detection of the total population of sRNAs in plants. Classifying sRNAs and predicting their functional role based on such high-performance datasets is a nontrivial bioinformatics task, as plants can generate millions of sRNAs from a variety of biosynthetic pathways. Over the years, many computing tools have been developed to meet this challenge. Here, we review more than 35 tools developed specifically for plant sRNAs over the past few years and explore some of their basic algorithms for performing tasks related to predicting, identifying, categorizing, and quantifying individual sRNAs in plant samples, as well as visualizing the results of these analyzes. We believe that this review will be practical for biologists who want to analyze their plant sRNA datasets but are overwhelmed by the number of tools available, thus answering the basic question of how to choose the right one for a particular study. Full article
(This article belongs to the Special Issue The World of Plant Non-coding RNAs)
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