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Non-Coding RNA and Their Regulatory Roles in Plant
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Non-Coding RNA and Their Regulatory Roles in Plant

A special issue of Non-Coding RNA (ISSN 2311-553X). This special issue belongs to the section "Computational Biology".

Deadline for manuscript submissions: closed (20 October 2024) | Viewed by 13271

Special Issue Editor

Prof. Dr. Sujay Paul

E-Mail Website1 Website2
Guest Editor
Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Queretaro 76130, Mexico
Interests: ncRNAs in human diseases; gene regulation; biomarker; therapy; anticancer phytochemicals; plant microRNA; nanotechnology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Regulatory non-coding RNAs (ncRNAs), which can be short or long ncRNAs (lncRNAs), control a wide range of biological processes in plants. ncRNAs have a variety of forms, including microRNAs (miRNAs), small interfering RNAs (siRNAs), lncRNAs, circular RNAs (circRNAs), and derived ncRNAs, depending on their mode of biogenesis and function. Through interactions with homologous sequences, ncRNAs function as riboregulators to control plants’ development, growth, and stress response signaling. Insights into the roles of non-coding RNAs in plant biology might be of great importance to understand the regulatory pathways used in different plant processes and the development of genetically modified improved crop varieties via ncRNA manipulation.

For this Special Issue, the goal is to solicit submission of any articles to understand the regulatory roles of plant non-coding RNAs and their applications for crop improvement. The subtopics are as follows:

  • The identification and functional characterization of microRNA, lncRNAs, and other ncRNAs in plant.
  • ncRNA-based transgenic and biotechnology.
  • CRISPR-based editing of plant ncRNAs.
  • Computational tools for the functional analysis of plant ncRNAs.
  • Plant ncRNA databases.
  • Understanding the mechanistic roles of ncRNAs in plants’ stress response signaling.
  • Novel techniques, methods, and ideas for analyzing plant ncRNAs.
  • High-throughput sequencing-based analysis of plant ncRNAs.

Prof. Dr. Sujay Paul
Guest Editor

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. Non-Coding RNA is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). 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

  • plant
  • ncRNAs
  • growth and development
  • stress response signaling
  • transgenic
  • gene regulation

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Published Papers (5 papers)

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19 pages, 3783 KiB  
Article
Analysis of lncRNAs in Lupinus mutabilis (Tarwi) and Their Potential Role in Drought Response
by Manuel Hidalgo, Cynthia Ramos and Gaston Zolla
Non-Coding RNA 2023, 9(5), 48; https://doi.org/10.3390/ncrna9050048 - 23 Aug 2023
Viewed by 3089
Abstract
Lupinus mutabilis is a legume with high agronomic potential and available transcriptomic data for which lncRNAs have not been studied. Therefore, our objective was to identify, characterize, and validate the drought-responsive lncRNAs in L. mutabilis. To achieve this, we used a multilevel [...] Read more.
Lupinus mutabilis is a legume with high agronomic potential and available transcriptomic data for which lncRNAs have not been studied. Therefore, our objective was to identify, characterize, and validate the drought-responsive lncRNAs in L. mutabilis. To achieve this, we used a multilevel approach based on lncRNA prediction, annotation, subcellular location, thermodynamic characterization, structural conservation, and validation. Thus, 590 lncRNAs were identified by at least two algorithms of lncRNA identification. Annotation with the PLncDB database showed 571 lncRNAs unique to tarwi and 19 lncRNAs with homology in 28 botanical families including Solanaceae (19), Fabaceae (17), Brassicaceae (17), Rutaceae (17), Rosaceae (16), and Malvaceae (16), among others. In total, 12 lncRNAs had homology in more than 40 species. A total of 67% of lncRNAs were located in the cytoplasm and 33% in exosomes. Thermodynamic characterization of S03 showed a stable secondary structure with −105.67 kcal/mol. This structure included three regions, with a multibranch loop containing a hairpin with a SECIS-like element. Evaluation of the structural conservation by CROSSalign revealed partial similarities between L. mutabilis (S03) and S. lycopersicum (Solyc04r022210.1). RT-PCR validation demonstrated that S03 was upregulated in a drought-tolerant accession of L. mutabilis. Finally, these results highlighted the importance of lncRNAs in tarwi improvement under drought conditions. Full article
(This article belongs to the Special Issue Non-Coding RNA and Their Regulatory Roles in Plant)
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Review

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37 pages, 2513 KiB  
Review
The Emerging Applications of Artificial MicroRNA-Mediated Gene Silencing in Plant Biotechnology
by Luis Alberto Bravo-Vázquez, Ana Marta Castro-Pacheco, Rodrigo Pérez-Vargas, Joceline Fernanda Velázquez-Jiménez and Sujay Paul
Non-Coding RNA 2025, 11(2), 19; https://doi.org/10.3390/ncrna11020019 - 2 Mar 2025
Viewed by 802
Abstract
Improving crop yield potential is crucial to meet the increasing demands of a rapidly expanding global population in an ever-changing and challenging environment. Therefore, different technological approaches have been proposed over the last decades to accelerate plant breeding. Among them, artificial microRNAs (amiRNAs) [...] Read more.
Improving crop yield potential is crucial to meet the increasing demands of a rapidly expanding global population in an ever-changing and challenging environment. Therefore, different technological approaches have been proposed over the last decades to accelerate plant breeding. Among them, artificial microRNAs (amiRNAs) represent an innovative tool with remarkable potential to assist plant improvement. MicroRNAs (miRNAs) are a group of endogenous, small (20–24 nucleotides), non-coding RNA molecules that play a crucial role in gene regulation. They are associated with most biological processes of a plant, including reproduction, development, cell differentiation, biotic and abiotic stress responses, metabolism, and plant architecture. In this context, amiRNAs are synthetic molecules engineered to mimic the structure and function of endogenous miRNAs, allowing for the targeted silencing of specific nucleic acids. The current review explores the diverse applications of amiRNAs in plant biology and agriculture, such as the management of infectious agents and pests, the engineering of plant metabolism, and the enhancement of plant resilience to abiotic stress. Moreover, we address future perspectives on plant amiRNA-based gene silencing strategies, highlighting the need for further research to fully comprehend the potential of this technology and to translate its scope toward the widespread adoption of amiRNA-based strategies for plant breeding. Full article
(This article belongs to the Special Issue Non-Coding RNA and Their Regulatory Roles in Plant)
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26 pages, 2100 KiB  
Review
RNA Metabolism and the Role of Small RNAs in Regulating Multiple Aspects of RNA Metabolism
by Pranav Dawar, Indra Adhikari, Swarupa Nanda Mandal and Bhumika Jayee
Non-Coding RNA 2025, 11(1), 1; https://doi.org/10.3390/ncrna11010001 - 24 Dec 2024
Viewed by 2009
Abstract
RNA metabolism is focused on RNA molecules and encompasses all the crucial processes an RNA molecule may or will undergo throughout its life cycle. It is an essential cellular process that allows all cells to function effectively. The transcriptomic landscape of a cell [...] Read more.
RNA metabolism is focused on RNA molecules and encompasses all the crucial processes an RNA molecule may or will undergo throughout its life cycle. It is an essential cellular process that allows all cells to function effectively. The transcriptomic landscape of a cell is shaped by the processes such as RNA biosynthesis, maturation (RNA processing, folding, and modification), intra- and inter-cellular transport, transcriptional and post-transcriptional regulation, modification, catabolic decay, and retrograde signaling, all of which are interconnected and are essential for cellular RNA homeostasis. In eukaryotes, sRNAs, typically 20–31 nucleotides in length, are a class of ncRNAs found to function as nodes in various gene regulatory networks. sRNAs are known to play significant roles in regulating RNA population at the transcriptional, post-transcriptional, and translational levels. Along with sRNAs, such as miRNAs, siRNAs, and piRNAs, new categories of ncRNAs, i.e., lncRNAs and circRNAs, also contribute to RNA metabolism regulation in eukaryotes. In plants, various genetic screens have demonstrated that sRNA biogenesis mutants, as well as RNA metabolism pathway mutants, exhibit similar growth and development defects, misregulated primary and secondary metabolism, as well as impaired stress response. In addition, sRNAs are both the “products” and the “regulators” in broad RNA metabolism networks; gene regulatory networks involving sRNAs form autoregulatory loops that affect the expression of both sRNA and the respective target. This review examines the interconnected aspects of RNA metabolism with sRNA regulatory pathways in plants. It also explores the potential conservation of these pathways across different kingdoms, particularly in plants and animals. Additionally, the review highlights how cellular RNA homeostasis directly impacts adaptive responses to environmental changes as well as different developmental aspects in plants. Full article
(This article belongs to the Special Issue Non-Coding RNA and Their Regulatory Roles in Plant)
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12 pages, 1577 KiB  
Review
SVALKA: A Long Noncoding Cis-Natural Antisense RNA That Plays a Role in the Regulation of the Cold Response of Arabidopsis thaliana
by Nicholas M. Kiger and Susan J. Schroeder
Non-Coding RNA 2024, 10(6), 59; https://doi.org/10.3390/ncrna10060059 - 28 Nov 2024
Viewed by 1256
Abstract
RNA plays important roles in the regulation of gene expression in response to environmental stimuli. SVALKA, a long noncoding cis-natural antisense RNA, is a key component of regulating the response to cold temperature in Arabidopsis thaliana. There are three mechanisms through [...] Read more.
RNA plays important roles in the regulation of gene expression in response to environmental stimuli. SVALKA, a long noncoding cis-natural antisense RNA, is a key component of regulating the response to cold temperature in Arabidopsis thaliana. There are three mechanisms through which SVALKA fine tunes the transcriptional response to cold temperatures. SVALKA regulates the expression of the CBF1 (C-Repeat Dehydration Binding Factor 1) transcription factor through a collisional transcription mechanism and a dsRNA and DICER mediated mechanism. SVALKA also interacts with Polycomb Repressor Complex 2 to regulate the histone methylation of CBF3. Both CBF1 and CBF3 are key components of the COLD REGULATED (COR) regulon that direct the plant’s response to cold temperature over time, as well as plant drought adaptation, pathogen responses, and growth regulation. The different isoforms of SVALKA and its potential to form dynamic RNA conformations are important features in regulating a complex gene network in concert with several other noncoding RNA. This review will summarize the three mechanisms through which SVALKA participates in gene regulation, describe the ways that dynamic RNA structures support the function of regulatory noncoding RNA, and explore the potential for improving agricultural genetic engineering with a better understanding of the roles of noncoding RNA. Full article
(This article belongs to the Special Issue Non-Coding RNA and Their Regulatory Roles in Plant)
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25 pages, 846 KiB  
Review
The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling
by Amit Yadav, Jyotirmaya Mathan, Arvind Kumar Dubey and Anuradha Singh
Non-Coding RNA 2024, 10(1), 13; https://doi.org/10.3390/ncrna10010013 - 7 Feb 2024
Cited by 21 | Viewed by 4712
Abstract
Plant species utilize a variety of regulatory mechanisms to ensure sustainable productivity. Within this intricate framework, numerous non-coding RNAs (ncRNAs) play a crucial regulatory role in plant biology, surpassing the essential functions of RNA molecules as messengers, ribosomal, and transfer RNAs. ncRNAs represent [...] Read more.
Plant species utilize a variety of regulatory mechanisms to ensure sustainable productivity. Within this intricate framework, numerous non-coding RNAs (ncRNAs) play a crucial regulatory role in plant biology, surpassing the essential functions of RNA molecules as messengers, ribosomal, and transfer RNAs. ncRNAs represent an emerging class of regulators, operating directly in the form of small interfering RNAs (siRNAs), microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). These ncRNAs exert control at various levels, including transcription, post-transcription, translation, and epigenetic. Furthermore, they interact with each other, contributing to a variety of biological processes and mechanisms associated with stress resilience. This review primarily concentrates on the recent advancements in plant ncRNAs, delineating their functions in growth and development across various organs such as root, leaf, seed/endosperm, and seed nutrient development. Additionally, this review broadens its scope by examining the role of ncRNAs in response to environmental stresses such as drought, salt, flood, heat, and cold in plants. This compilation offers updated information and insights to guide the characterization of the potential functions of ncRNAs in plant growth, development, and stress resilience in future research. Full article
(This article belongs to the Special Issue Non-Coding RNA and Their Regulatory Roles in Plant)
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