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Review
. 2025 May;57(5):1089-1102.
doi: 10.1038/s41588-025-02157-7. Epub 2025 Apr 17.

Circular RNA discovery with emerging sequencing and deep learning technologies

Affiliations
Review

Circular RNA discovery with emerging sequencing and deep learning technologies

Jinyang Zhang et al. Nat Genet. 2025 May.

Abstract

Circular RNA (circRNA) represents a type of RNA molecule characterized by a closed-loop structure that is distinct from linear RNA counterparts. Recent studies have revealed the emerging role of these circular transcripts in gene regulation and disease pathogenesis. However, their low expression levels and high sequence similarity to linear RNAs present substantial challenges for circRNA detection and characterization. Recent advances in long-read and single-cell RNA sequencing technologies, coupled with sophisticated deep learning-based algorithms, have revolutionized the investigation of circRNAs at unprecedented resolution and scale. This Review summarizes recent breakthroughs in circRNA discovery, characterization and functional analysis algorithms. We also discuss the challenges associated with integrating large-scale circRNA sequencing data and explore the potential future development of artificial intelligence (AI)-driven algorithms to unlock the full potential of circRNA research in biomedical applications.

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Conflict of interest statement

Competing interests: The authors declare no competing interests.

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References

    1. Hansen, T. B. et al. Natural RNA circles function as efficient microRNA sponges. Nature 495, 384–388 (2013). - PubMed - DOI
    1. Memczak, S. et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495, 333–338 (2013). - PubMed - DOI
    1. Abdelmohsen, K. et al. Identification of HuR target circular RNAs uncovers suppression of PABPN1 translation by CircPABPN1. RNA Biol. 14, 361–369 (2017). - PubMed - PMC - DOI
    1. Zhao, Q. et al. Targeting mitochondria-located circRNA SCAR alleviates NASH via reducing mROS output. Cell 183, 76–93 (2020). - PubMed - DOI
    1. Huang, D. et al. Tumour circular RNAs elicit anti-tumour immunity by encoding cryptic peptides. Nature 625, 593–602 (2024). - PubMed - DOI

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