Circular RNAs: Diversity, formation, functions, and identification mechanism with a focus on endogenous circular RNAs

Abstract

Circular RNAs (circRNAs) constitute a distinct class of noncoding RNAs (ncRNAs) defined by their covalently closed loop configuration, which confers exceptional stability against exonucleolytic degradation. Initially dismissed as splicing byproducts, circRNAs now have been established as critical regulators of gene expression across eukaryotic organisms. This review consolidates the current understanding of circRNAs biogenesis, diversity, and functional roles of endogenous circRNAs. Generated through back-splicing of pre-mRNA, circRNAs are classified into exonic, exon-intron, and intronic subtypes. Each of these exhibits unique subcellular localization and regulatory capabilities. In animal systems, circRNAs such as Drosophila melanogaster mbl-derived circRNAs and murine Sry circRNAs are implicated in growth regulation and testicular development, respectively. In humans, circRNAs like ciRS-7 serve as microRNA (miRNA) sponges, modulating neuronal development and contributing to pathologies such as Alzheimer's disease and atherosclerosis. Furthermore, circRNAs associated with NF-90/NF-110 play pivotal roles in immunological responses, influencing viral infection outcomes. In plants, circRNAs not only regulate developmental processes and stress adaptation, including auxin signaling, floral development, and fruit maturation. However, they also enhance resilience to biotic and abiotic stresses through their roles in rice disease resistance and tomato chilling tolerance. This review critically evaluates detection methodologies, including RNA-sequencing, RNase-R assays, and computational algorithms, highlighting their precision and inherent limitations. Despite significant advances, challenges persist in distinguishing functional circRNAs from artifacts and elucidating their molecular mechanisms. This review also highlights the evolutionary conservation and functional versatility of circRNAs, emphasizing their potential as biomarkers and therapeutic targets. Future investigations should prioritize the establishment of standardized databases and innovative approaches to deepen understanding of circRNA dynamics in eukaryotic systems, offering insights into their roles in health, disease, and agricultural productivity.