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Advances in Plant RNA Biology: Non Coding RNAs in Plant Development, Defense, and Adaptation

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 December 2025) | Viewed by 2336

Special Issue Editor

Dr. Andrew Eamens

E-Mail Website
Guest Editor
Seaweed Research Group, School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
Interests: seaweed research; molecular genetics; RNA biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The various species of non-coding RNA which accumulate in plant cells, namely the microRNA (miRNA), trans-acting small-interfering RNA (tasiRNA), repeat-associated small-interfering RNA (rasiRNA), phased secondary small-interfering RNA (phasiRNA), and natural-antisense small-interfering RNA (natsiRNA) classes of small regulatory RNA are well established as master controllers of gene expression in plant development, defense responses against invading plant pathogens, and adaptive responses to environmental stress. Contempory research has identified similar gene expression regulation roles for the more recently identified species of non-coding RNAs in plant cells, including the long non-coding RNA (lncRNA), circular RNA (circRNA), transfer RNA (tRNA)-derived RNA fragments (tRFs), and tiny RNA (tiRNA) classes of regulatory non-coding RNA.

This Special Issue of IJMS aims to bring together cutting edge molecular research papers or review articles on all classes of regulatory non-coding RNA, and their protein interactors, which accumulate in plant cells and play a key role in controlling gene expression in plant development, environmental stress adaptation, pathogen defense, or plant-mediated cross kingdom communication. This Special Issue of IJMS also welcomes the inclusion of research articles which describe the development of novel biotechnology tools based on regulatory non-coding RNAs for use in the plant system to manipulate gene expression.

Dr. Andrew Eamens
Guest Editor

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Keywords

  • plant RNA biology
  • regulatory RNA
  • non-coding RNA
  • small RNA (including miRNAs and siRNAs)
  • RNA interacting proteins
  • plant development
  • plant pathogen defense
  • plant environmental stress adaptation

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Published Papers (2 papers)

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Research

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27 pages, 3642 KB  
Article
Integrative Analysis of lncRNA–RBP (RNA-Binding Protein) Regulatory Networks Reveals Molecular Targets for Enhancing Zea mays Resistance to Aspergillus flavus and Aflatoxin Contamination
by Ramya Parakkunnel, Bhojaraja Naik Keshava, Manjanagouda Siddanagouda Sannagoudar, Samudrala Prashant Jeevan Kumar, Kuldip Jayaswall, Aravindan Sundaram and Anandan Annamalai
Int. J. Mol. Sci. 2026, 27(5), 2493; https://doi.org/10.3390/ijms27052493 - 8 Mar 2026
Viewed by 846
Abstract
Aspergillus flavus infection and accumulation of carcinogenic aflatoxins are detrimental to maize (Zea mays) production and consumption. We investigated lncRNA–RBP interactions during maize–A. flavus crosstalk using transcriptomic profiling, structural analysis, molecular docking simulations, and machine learning approaches. Analysis of 18 [...] Read more.
Aspergillus flavus infection and accumulation of carcinogenic aflatoxins are detrimental to maize (Zea mays) production and consumption. We investigated lncRNA–RBP interactions during maize–A. flavus crosstalk using transcriptomic profiling, structural analysis, molecular docking simulations, and machine learning approaches. Analysis of 18 RNA-seq datasets identified 2104 lncRNAs in maize, of which 461 were differentially expressed under A. flavus infection. Distinct lncRNAs were preferentially induced under infection (e.g., Zm00001eb303170) or normal germination (e.g., Zm00001eb144150, Zm00001eb406410). RNA secondary structure predictions indicated high structural heterogeneity and thermodynamic stability, consistent with dynamic regulatory potential. Docking simulations with six key RNA binding proteins (RBPs)—including branch point bridging protein (BPB), KH domain protein, and pentatricopeptide repeat (PPR) proteins—demonstrated strong lncRNA–protein binding, with the lncRNA1–BPB complex exhibiting the highest binding affinity. ML algorithms identified the crucial role of tryptophan in determining interactions, while lncRNA17-KH and lncRNA1-BP complexes were found to have the best interaction under normal germination and A. flavus infection, respectively. The lncRNA–miRNA–mRNA regulatory network highlighted lncRNAs functioning as decoys or precursors of stress-responsive miRNAs (e.g., zma-miR156, zma-miR164, zma-miR399). These interactions targeted transcriptional regulators, splicing factors, and metabolic enzymes implicated in stress tolerance, seed germination, and systemic acquired resistance. The maize lncRNAs are active regulatory molecules embedded in complex RBP and miRNA interaction networks that fine-tune gene expression during A. flavus infection. The study provides novel insights into lncRNA-mediated resistance mechanisms and offers potential molecular targets for breeding or gene editing to mitigate aflatoxin contamination. Full article
(This article belongs to the Special Issue Advances in Plant RNA Biology: Non Coding RNAs in Plant Development, Defense, and Adaptation)
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Review

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19 pages, 1601 KB  
Review
Long Non-Coding RNAs in the Cold-Stress Response of Horticultural Plants: Molecular Mechanisms and Potential Applications
by Magdalena Wielogórska, Anna Rucińska, Yuliya Kloc and Maja Boczkowska
Int. J. Mol. Sci. 2025, 26(21), 10464; https://doi.org/10.3390/ijms262110464 - 28 Oct 2025
Cited by 1 | Viewed by 1113
Abstract
Cold stress reduces horticultural crop yield and postharvest quality by disrupting membrane fluidity, redox equilibrium, and the cell wall structure. This results in chilling injury, tissue softening, and loss of color. Long noncoding RNAs (lncRNAs) have emerged as key integrators of plant cold [...] Read more.
Cold stress reduces horticultural crop yield and postharvest quality by disrupting membrane fluidity, redox equilibrium, and the cell wall structure. This results in chilling injury, tissue softening, and loss of color. Long noncoding RNAs (lncRNAs) have emerged as key integrators of plant cold signaling pathways. LncRNAs mediate the interaction between calcium signaling systems and transcriptional cascades while coordinating hormone signaling networks, including those involving abscisic acid, jasmonic acid, ethylene, salicylic acid, and brassinosteroids. LncRNAs influence gene regulation through chromatin-based guidance, sequestration of repressive complexes, natural antisense transcriptional interference, microRNA-centered competing endogenous RNA networks, and control of RNA splicing, stability, localization, and translation. Studies in horticultural species revealed that cold-responsive lncRNAs regulate processes essential for fruit firmness, antioxidant levels, and shelf-life, including lipid modification, reactive oxygen species balance, and cell wall or cuticle remodeling. This review aims to summarize tissue- and developmental stage-specific expression patterns and highlight experimental approaches to validate RNA function, including gene editing, transcript recovery, advanced sequencing, and analysis of protein-RNA interactions. Integrating these results will facilitate the development of precise molecular markers and nodes of regulatory networks that increase cold tolerance, and improve the quality of horticultural crops. Full article
(This article belongs to the Special Issue Advances in Plant RNA Biology: Non Coding RNAs in Plant Development, Defense, and Adaptation)
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