Search PubMedSearch

PubMed · 39699815

Quantitative Real-Time PCR for Circular RNA Detection and Analysis.

Abstract

In eukaryotes, nearly 2% of the genome represented by the coding proteins. However, emerging evidence suggest more than 75% of the human genome referred to as noncoding part also plays a crucial role in governing major regulatory pathways. Noncoding RNAs can be categorized into several groups, such as microRNAs (miRNAs), small nuclear RNA (snRNAs), small nucleolar RNA (snoRNAs), transfer RNA (tRNA), and circular RNA (circRNAs), which contribute to this regulatory landscape. Circular RNAs (circRNAs) are identified as a new class of regulatory noncoding RNAs with gene regulatory roles by acting as miRNA or RNA binding protein sponges or interacting with proteins. Researchers employ quantitative real-time PCR methods to examine circular RNA expression utilizing divergent primers for identification and quantification.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Amit Kumar Rai, Venkata Naga Srikanth Garikipati. 2025. Quantitative Real-Time PCR for Circular RNA Detection and Analysis.. https://doi.org/10.1007/978-1-0716-4342-6_11

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

Target site selection and P1 engineering enable highly efficient circular RNA production via end-to-end self-targeting and splicing.

Circular RNAs (circRNAs) are more stable than linear RNAs, enabling expanding applications in RNA vaccines and therapeutics. We previously developed an in vitro circRNA preparation method based on end-to-end self-targeting and splicing (STS) using the Tetrahymena group I intron, which generates circRNAs without extraneous sequences. However, self-circularization efficiency declines as gene of interest (GOI) length increases, limiting its application to longer GOIs. Here, we systematically optimized key determinants of STS efficiency, including target site selection and P1 construct engineering. Target site screening revealed that selection of optimal target sites within each GOI markedly improved self-circularization efficiency. Moreover, engineering of the P1 construct, including incorporation of a polyA10 sequence upstream of the internal guide sequence of the intron and an antisense sequence complementary to the target site and its upstream region at the 5' side of polyA10, further enhanced efficiency. Notably, the optimized STS strategy achieved up to two-fold higher self-circularization efficiency than the conventional permuted intron-exon (PIE) method for long GOIs (∼8 K-nt). Collectively, these results establish an improved STS workflow for efficient circRNA production without extraneous sequences across a wide range of GOI lengths, outperforming the PIE method for long GOIs, and broadening biomedical applications.

RNA, Circular

Detecting and quantifying circular RNAs in terabyte-scale RNA-seq datasets with CIRI3.

To address recent challenges in circular RNA (circRNA) analysis, we present CIRI3, a tool for circRNA detection and quantification in terabyte-scale RNA-sequencing datasets. Using dynamic multithreaded task partitioning and a blocking search strategy for junction reads, CIRI3 is an order of magnitude faster than existing tools, while providing increased accuracy. We identified differentially spliced circRNAs across 2,535 cancer-related samples, and constructed a pretraining model and a biomarker network provided as the CIRIonco database.

RNA, Circular

A Dual-Selection System for Enhanced Efficiency and Fidelity of Circular RNA Overexpression.

Circular RNAs (circRNAs) are essential regulators of cellular processes, but are challenging to study using traditional methods. Overexpression approaches, such as the use of linearized plasmids and viral vectors, often result in high rates of false-positive clones, where cells retain selection markers without expressing the target circRNA. This study addresses this limitation by developing a dual-selection circRNA system designed to enhance the accuracy and reliability of circRNA overexpression. Our system integrates a fluorescent reporter gene upstream of the circRNA expression cassette, under a shared promoter, and a downstream antibiotic resistance marker, allowing for both antibiotic selection and flow cytometric cell-sorting to identify and enrich cells with genuine circRNA expression. We successfully incorporated this system into an inducible lentiviral vector for controlled overexpression in various cell types. The dual-selection circRNA system offers a significant advance for circRNA research and studies of other RNA species where accurate and reliable overexpression is essential.

RNA, Circular