Recent advancements in RNA sequencing technologies, dedicated circRNA annotation workflows, and bioinformatics have shed light on the significance of circRNA in various cellular processes and their role in diseases. At CD Genomics, we offer state-of-the-art circRNA sequencing services to help you explore this exciting field.

What is circRNA?

Circular RNAs (circRNAs) represent a captivating class of non-coding RNA molecules characterized by their unique structural attributes. Unlike linear RNA, circRNAs lack the conventional 5' terminal cap and 3' terminal poly(A) tail, instead forming a closed-loop structure held together by covalent bonds. Remarkably, circRNAs, once dismissed as incidental by-products, have undergone a paradigm shift in scientific perception over the years. They have swiftly transitioned from obscurity to prominence, emerging as a dazzling star in the realm of non-coding RNAs.

So, what sets circRNA apart?

Distinguishing circRNA from its linear counterpart unveils a profound contrast. Firstly, linear RNA undergoes splicing via the GU/AG sequence in introns, connecting the upstream and downstream exons. In contrast, circRNA generation involves reverse splicing, where the terminal end of a downstream exon fuses to the initial end of the upstream exon. This unique splicing process contributes to the exceptional stability of circRNA, both in vitro and in vivo. The crux of this stability lies in its exclusive covalent closed-loop structure, which serves as a shield against degradation by nucleic acid exonucleases.

CircRNAs manifest an intriguing versatility in their formation. While selective splicing can lead to the creation of covalently closed-loop exon circRNA when the 3' end of one exon bonds with the 5' end of another, this is merely the tip of the iceberg. CircRNAs are not confined to exon-based origins; they can also emanate from introns, spacer regions, and even non-transcribed regions within genes through a mechanism known as "back splicing."

The biogenesis of circRNAs. (Nielsen et al., 2022)

Function of circRNA in Biological Processes

In the realm of non-coding RNA molecules, circular RNA (circRNA) has emerged as a remarkable player, wielding significant influence in an array of biological processes. Its unique structure and functions introduce a novel dimension to cellular diversity and regulation, intimately intertwined with gene expression, cell signaling, and the development of diseases.

• miRNA Sponge: The Competitive Endogenous RNA (ceRNA) Mechanism

CircRNAs, enriched with multiple miRNA binding sites, take on the role of miRNA sponges. This captivating function allows them to absorb and orchestrate the activity of specific miRNAs, thereby exerting a profound impact on miRNAs' regulatory interactions with their target genes. This mechanism, known as the competitive endogenous RNA (ceRNA) mechanism, plays a crucial role in fine-tuning gene expression.

Please read the article Overview of Competing Endogenous RNA (ceRNA), for more details.

• Transcriptional Regulation

Certain circRNAs demonstrate their versatility by engaging with transcription factors and RNA-binding proteins. This interaction extends to the modulation of chromatin structure and the activity of transcription factors, ultimately regulating the transcriptional level of genes. These circRNAs act as fine-tuners of gene expression, navigating the intricate landscape of cellular processes.

The function of circRNAs. (Nielsen et al., 2022)

• Protein Interactions: The "Protein Sponges"

Some circRNAs take on a role akin to that of a protein sponge, impacting the stability and function of proteins. This interaction extends to protein-protein and protein-nucleic acid interactions, adding yet another layer to the intricate web of cellular regulation and control. CircRNAs, in this context, are pivotal orchestrators of protein-related functions.

• Translation Initiation

CircRNAs transcend their non-coding roles and step into the realm of protein translation. Their involvement in this process is independent of the traditional 5' cap structure, facilitated by the presence of internal ribosome entry sites (IRES). Additionally, the methylation modification m6A can drive the translation of circRNAs to synthesize proteins, and these remarkable molecules can harness other sequence elements, such as IRES-like elements, to initiate translation.

• Disease Association

Recent research has unearthed a compelling link between circRNAs and various diseases, spanning tumors, cardiovascular conditions, and neurological disorders. CircRNAs wield their influence over the onset and progression of these diseases by shaping cellular metabolism, influencing signaling pathways, and intricately modulating gene expression. They emerge as crucial players in the complex landscape of disease pathogenesis.

Applications of Circular RNA (circRNA)

The global impact of the recent pandemic has propelled mRNA therapy into the limelight, sparking enthusiasm within the research community for its development. Yet, it's essential to acknowledge that mRNA, despite its promise, is not without limitations, including issues of stability that may hinder its full potential. In this context, circular RNA (circRNA) has emerged as a rising star—a "dark horse," if you will. Current research has unveiled the outstanding potential of circRNAs as both clinical diagnostic markers and therapeutic tools.

• Biomarkers and Clinical Diagnostics

CircRNAs have shown strong associations with the onset and progression of various diseases, spanning cancer, cardiovascular conditions, neurological disorders, and more. Their unique attributes make them valuable candidates as biomarkers for early disease detection, diagnosis, and prognostic assessment.

Four distinct features set circRNAs apart:

High Abundance: CircRNAs are characterized by their significant expression levels or temporal accumulation, making them readily detectable in diverse biological samples and cells. In some cases, their abundance even surpasses that of homologous linear mRNAs.

High Specificity: CircRNAs exhibit a high degree of specificity, with distinct and diverse expression patterns across different cell types, tissues, and developmental stages.

High Conservation: Despite the unconventional method of circRNA formation, certain sequence regions within circRNAs exhibit conservation across species. In fact, research has identified 5-30% similarities in conserved circRNAs between directly homologous genes in mice and humans.

High Stability: Thanks to their unique structural specificity, circRNAs resist degradation by linear mRNA decay mechanisms. This resilience allows for their easy detection in bodily fluids, including saliva and blood.

• Therapeutic Targeting and Drug Development

Revealing the mechanisms of circRNA involvement in various diseases has opened doors for targeted therapy and novel drug development. By manipulating the functions of circRNAs, therapeutic strategies can be devised to tackle specific diseases effectively. Additionally, circRNAs have promising applications in drug delivery, including the design of drug-carrying nanoparticles.

• Gene Editing and Gene Therapy

The malleability of circRNAs has ignited a spark in the field of gene editing and therapy. Techniques such as CRISPR-Cas can be employed to precisely edit circRNAs, altering their sequence or structure to modulate their functions. Moreover, circRNAs can be harnessed as valuable tools for gene therapy, carrying specific sequences to enhance the expression of target genes.

Reference:

1. Nielsen, Anne F., et al. "Best practice standards for circular RNA research." Nature methods 19.10 (2022): 1208-1220.