
==== Front
Plant Physiol
Plant Physiol
plphys
Plant Physiology
0032-0889
1532-2548
Oxford University Press US

38718056
10.1093/plphys/kiae265
kiae265
News and Views
AcademicSubjects/SCI01270
AcademicSubjects/SCI01280
AcademicSubjects/SCI02286
AcademicSubjects/SCI02287
AcademicSubjects/SCI02288
Which ring is the ring? Insights from a study on maize circRNAs under drought stress
https://orcid.org/0000-0001-9898-6442
Teng Chong Assistant Features Editor, Plant Physiology, American Society of Plant Biologists
Department of Plant Sciences and Genome Center, University of California, Davis, CA 95616, USA

Author for correspondence: tcteng@ucdavis.edu
Conflict of interest statement. None declared.

9 2024
08 5 2024
08 5 2024
196 1 1617
11 4 2024
24 4 2024
17 5 2024
© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists.
2024
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pmcCircular RNA (circRNA) is a form of single-stranded RNA that adopts a covalently closed loop structure, resembling a ring. Unlike linear RNAs, circRNAs possess increased stability and longevity due to their resistance to common RNA-degrading enzymes, even though circRNAs exist at low abundances in most cases (Pisignano et al. 2023). CircRNAs have been considered the result of splicing errors since they were first discovered in the 1970s (Xu and Zhang 2021). As more and more circRNAs were found in animals and plants, it became clear that they arose due to nonsequential back-splicing of exons and occasionally introns (Zhao et al. 2019). In the past decade, a handful of examples in mammals showed circRNAs can bind microRNAs, encode peptides, and bind to proteins as scaffolds, along with other functions (Kristensen et al. 2019). Despite their prevalence, understanding their functionality has proven challenging.

A recent study conducted by Jie Xu and colleagues (Xu et al. 2024) explored the function of circRNAs in plants. Maize, an economically important crop, could greatly benefit from enhanced drought resistance. Xu et al. (2024) utilized maize recombinant inbred lines derived from drought-tolerant and -sensitive parental lines to investigate common circRNAs and screen for functional ones. To enrich circRNAs, Xu et al. (2024) employed ribosomal depletion and RNase R treatment before sequencing. Ribosomal depletion removes highly abundant ribosomal RNA molecules, allowing interrogation of less abundant RNA species such as circRNAs. Similarly, RNase R treatment removes linear RNA molecules, including polyadenylated mRNAs, thereby enriching circRNAs in the samples (Szabo and Salzman 2016). Through these methods, Xu et al. (2024) identified a total of 8,790 circRNAs.

A comprehensive bioinformatic analysis revealed several notable features of the identified circRNAs, consistent with previous observations. The majority of circRNAs were found to be exonic, often flanked by longer introns, and frequently associated with short interspersed nuclear element (SINE) repetitive sequences that facilitate back-splicing. Interestingly, approximately 7.23% exhibited higher abundance than their linear counterparts, which is not the case for most circRNAs. Furthermore, genomic DNA sites that encode circRNAs were more methylated but exhibited reduced levels of H3K9me3, a suppressive histone marker, suggesting a unique regulatory landscape governing circRNA biogenesis. These findings indicate that circRNA biogenesis is surprisingly distinct from canonical splicing sites.

Most circRNAs are exonic, and analysis of their coding potential revealed potential roles in signal transduction and drought resistance. Furthermore, a high percentage of circRNA were significantly more abundant under drought treatment compared with well-watered controls. Meanwhile, transcripts from SINE elements near circRNAs were abundant but at about the same level under drought and well-watered conditions. This difference in abundance of circRNAs compared with proximal SINE element transcripts could be attributed to increased longevity of mature circRNAs compared with splicing intermediates due to some kind of stabilization mechanisms such as translation.

Another noteworthy finding in Xu et al. (2024) is the observation that transgenic Arabidopsis lines expressing a randomly chosen maize circRNA showed improved survival rates under drought conditions compared with lines expressing linear counterparts or non-transgenic controls (Fig.), suggesting circRNAs can function differently from their linear transcript counterparts to resist drought. Interestingly, this randomly selected circRNA contains a single exon and exhibits higher abundances than its linear counterpart regardless of water availability. This finding demonstrated circRNA can play functional roles in plants, particularly in improving drought tolerance.

Figure. CircZmMED16 increased survival rate in Arabidopsis. A) A schematic diagram showing ZmMED16 and circZmMED16 are transcribed from the same locus by either canonical splicing or back-splicing, respectively. For the functional assay shown in panel B), the circZmMED16 alone was expressed from an artificial construct including just the relevant exon and its flanking introns containing the SINE insertions. B), Arabidopsis transgenic lines with constitutive expression of circZmMED16 were grown in soil either under drought (upper panel) or well-watered (lower panel) conditions compared with nontransgenic Arabidopsis and constitutive expression of ZmMED16. (Figure from Xu et al. 2024).

Overall, this study set a framework in plants to profile and discover functionally important circRNAs related to an interesting trait. Furthermore, the epigenetic markers identified in this study demonstrated that circRNA biogenesis is likely a distinct but well-regulated process rather than just the result of splicing errors. This study advances our understanding of circRNA biology in plants and opens new avenues for crop improvement.

Data availability

No new data were generated or analysed in support of this research.
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