Cotton Genomics and Genetics 2025, Vol.16, No.5, 232-240 http://cropscipublisher.com/index.php/cgg 233 Therefore, what this study aims to do is to systematically review the current research on circRNA in cotton. We will cover how they are produced, how they are expressed at different developmental stages of cotton, and how they "interact" with miRNA. In addition, it is also hoped that we can explore whether these discoveries have any new inspirations or application Spaces for cotton breeding or future biotechnology. 2 Biogenesis and Characteristics of Circular RNAs in Plants 2.1 Mechanisms of circRNA formation How is circular RNA formed? In plants, the currently known pathways for this process mainly include two types: reverse splicing and lasso cyclization. Among them, the reverse splicing path sounds like "going back"-the downstream 5 'donor site bypasses the middle region and directly connects to the upstream 3' receptor site, resulting in the formation of a closed RNA loop (Figure 1). This process is closely related to the familiar splicing mechanism, and RNA-binding proteins and long intron sequences are also often involved. However, plants are different from animals-in animals, there are often repetitive sequences or complementary sequences acting as "Bridges" at the splicing ends. But in plants, these regions are much cleaner and lack those reverse repetitions. This might mean that plants use another set of rules, or we haven't yet understood how they work (Zhao et al., 2019). As for the second mechanism-lason-driven cyclization, which is also called the "exon skipping" mode, it sounds a bit like an splicing error: skipping the middle section and processing the formed lason-like structure to obtain circular RNA (Zhang et al., 2020). Although it may not sound like the "right way", it does leave diverse traces in the plant transcriptome. 2.2 Classification of circRNAs Not all circular RNAs look the same and are classified into several types based on their different sources. The most common type is exon circular RNA (ecircRNA), which is composed only of exon sequences and usually floats in the cytoplasm. Then there is the circular intron RNA (ciRNA), which is mainly composed of intron fragments and prefers to stay in the cell nucleus. There is also a "hybrid type" called exon-intron circular RNA (EIciRNA), which has both exon and intron components and is mainly active in the nucleus (Chen et al., 2017). These different types actually reflect the complexity of their generation processes and the functional roles they may undertake respectively. 2.3 Stability, conservation, and tissue-specific expression patterns in plants One important reason why circular RNA has aroused the interest of researchers is that it is particularly resistant to "damage". Because the structure is closed, exonucases are difficult to swallow, which makes it much more stable than linear RNA (Chen et al., 2019). Among many plant species, we can also see the "presence" of the same circular RNA, which indicates that they have been preserved during evolution and may play certain key roles. But they are not "everywhere" either. The expression of circular RNAs is often selective, such as only appearing in certain tissues, specific cell types or developmental stages. Furthermore, some biological or abiotic stresses (such as drought and temperature changes) can also induce their expression (Tong et al., 2018). This specific binding stability makes one can't help but speculate that they might play a "key node" role in the plant regulatory system or could be very promising biomarkers in the future. 3 Mechanism of circRNA-Mediated miRNA Sponging in Cotton 3.1 Concept of miRNA sponges: base-pairing and sequestration of miRNAs Can circular RNA regulate miRNA? The answer is affirmative. The key lies in the fact that its sequence usually contains multiple so-called "miRNA response elements (MRes)". These regions match up with miRNA and can "stick" miRNA through base pairing-just like a molecular-level "sponge" that isolates the originally freely moving miRNA. This isolation action may seem simple, but in fact, it disrupts the original plan of miRNA to bind to mRNA targets, thereby weakening its inhibitory effect on target genes. The final result is that mRNA is more easily translated, and gene expression is subsequently upregulated. However, whether it can truly "take effect" depends on several conditions: the circRNA itself must have a certain abundance, the number of Mres cannot be too small, and it also depends on whether its affinity for miRNA is sufficient. In addition, the specific state and environment of the cells also affect the performance of this "spongy effect" (Ren et al., 2020; Made et al., 2023).
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