Investigations of Circular RNAs in Plants

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Plant Science".

Deadline for manuscript submissions: 1 December 2025 | Viewed by 475

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Dear Colleague,

Circular RNAs represent a family of single-stranded, endogenous, covalently closed circular RNAs lacking coding potential. Unlike the conventional linear RNAs, the circular structure of these RNAs makes them recalcitrant to RNA exonuclease degradation, suggesting vital functions. circRNAs are generated by the covalent circularization of a 3’ splice donor downstream and a 5’ splice acceptor upstream via backsplicing and are prevalent in eukaryotic cells. circRNAs have been classified as exonic (EcircRNAs), intergenic (circRNAs) and intronic (ciRNAs) based on the locations of their origins from chromosomes. In animals and humans, circRNAs perform critical roles in cellular processes, specifically in the regulation of gene expression, functioning as miRNA sponges, making R-loops, associating with RNA-binding proteins, enabling translation and alternate splicing. Nevertheless, the biological roles of circRNAs in plants are less comprehended, mainly due to the limited number of circRNAs identified using RNA seq technology. Initial studies detected circRNAs in rice and Arabidopsis, while more recent investigations have established their occurrence in various stages of development and in multiple species of plants. Further, plant circRNAs have been shown to respond to both biotic and abiotic environmental stimuli. circRNAs display a ubiquitous expression and abundance in plants. circRNA expression is often based on the type of cell, tissue and stage of development and is particularly inducible under stress conditions. Plant circRNAs have gathered increasing attention for their functions in gene regulation and stress responses. The widespread occurrence of circRNAs has recently been recognized in plants. Presently, 171118 circRNAs, belonging to 20 plant species, have been registered in PlantcircBase 7.0. Several research studies illustrate the major role of circRNAs in plant stress responses, plant growth and development, thus providing a basis for further research into their mechanisms. Previously, circRNAs were considered to be an inimitable class of non-coding RNAs. However, several studies in animal systems provide evidence for the coding ability of certain endogenous circRNAs. In contrast, the coding potential of plant circRNAs is much less explored.   

The current Special Issue invites original research articles and reviews on circRNA investigations in plants. In the future, understanding and elucidating the functions of circRNAs in plant development, stress responses and translation mechanisms by virtue of their non-coding/coding abilities would will be a major research topic. Further, the differences in the biogenesis of circRNAs between animals and plants would also be an intriguing research avenue. 

Dr. Srividhya Venkataraman
Guest Editor

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Keywords

  • plant circRNAs
  • miRNAs
  • stress responses
  • abiotic
  • biotic
  • translation
  • gene regulation
  • growth
  • development

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Published Papers (1 paper)

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28 pages, 3737 KiB  
Article
Profiling Plant circRNAs Provides Insights into the Expression of Plant Genes Involved in Viral Infection
by Ghyda Murad Hashim, Travis Haight, Xinyang Chen, Athanasios Zovoilis and Srividhya Venkataraman
Life 2025, 15(7), 1143; https://doi.org/10.3390/life15071143 - 20 Jul 2025
Viewed by 338
Abstract
Investigations of endogenous plant circular RNAs (circRNAs) in several plant species have revealed changes in their circular RNA profiles in response to biotic and abiotic stresses. Recently, circRNAs have emerged as critical regulators of gene expression. The destructive impacts on agriculture due to [...] Read more.
Investigations of endogenous plant circular RNAs (circRNAs) in several plant species have revealed changes in their circular RNA profiles in response to biotic and abiotic stresses. Recently, circRNAs have emerged as critical regulators of gene expression. The destructive impacts on agriculture due to plant viral infections necessitate better discernment of the involvement of plant circRNAs during viral infection. However, few such studies have been conducted hitherto. Sobemoviruses cause great economic impacts on important crops such as rice, turnip, alfalfa, and wheat. Our current study investigates the dynamics of plant circRNA profiles in the host Arabidopsis thaliana (A. thaliana) during infections with the sobemoviruses Turnip rosette virus (TRoV) and Rice yellow mottle virus (RYMV), as well as the small circular satellite RNA of the Lucerne transient streak virus (scLTSV), focusing on circRNA dysregulation in the host plants and its potential implications in triggering plant cellular defense responses. Towards this, two rounds of deep sequencing were conducted on the RNA samples obtained from infected and uninfected plants followed by the analysis of circular RNA profiles using RNA-seq and extensive bioinformatic analyses. We identified 760 circRNAs, predominantly encoded in exonic regions and enriched in the chloroplast chromosome, suggesting them as key sites for circRNA generation during viral stress. Gene ontology (GO) analysis indicated that these circRNAs are mostly associated with plant development and protein binding, potentially influencing the expression of their host genes. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed photosynthesis as the most affected pathway. Interestingly, the non-coding exogenous scLTSV specifically induced several circRNAs, some of which contain open reading frames (ORFs) capable of encoding proteins. Our biochemical assays demonstrated that transgenic expression of scLTSV in A. thaliana enhanced resistance to TRoV, suggesting a novel strategy for improving plant viral resistance. Our results highlight the complexity of circRNA dynamics in plant–virus interactions and offer novel insights into potential circRNA-based strategies for enhancing plant disease resistance by modulating the differential expression of circRNAs. Full article
(This article belongs to the Special Issue Investigations of Circular RNAs in Plants)
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