Circular RNA discovery with emerging sequencing and deep learning technologies
- PMID: 40247051
- DOI: 10.1038/s41588-025-02157-7
Circular RNA discovery with emerging sequencing and deep learning technologies
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.
© 2025. Springer Nature America, Inc.
Conflict of interest statement
Competing interests: The authors declare no competing interests.
Similar articles
-
The bioinformatics toolbox for circRNA discovery and analysis.Brief Bioinform. 2021 Mar 22;22(2):1706-1728. doi: 10.1093/bib/bbaa001. Brief Bioinform. 2021. PMID: 32103237 Free PMC article. Review.
-
Circular RNAs and Their Emerging Roles in Immune Regulation.Front Immunol. 2018 Dec 18;9:2977. doi: 10.3389/fimmu.2018.02977. eCollection 2018. Front Immunol. 2018. PMID: 30619334 Free PMC article. Review.
-
Full-length circRNA sequencing method using low-input RNAs and profiling of circRNAs in MPTP-PD mice on a nanopore platform.Analyst. 2024 Oct 7;149(20):5118-5130. doi: 10.1039/d4an00715h. Analyst. 2024. PMID: 39240088
-
CIRI-Deep Enables Single-Cell and Spatial Transcriptomic Analysis of Circular RNAs with Deep Learning.Adv Sci (Weinh). 2024 Apr;11(14):e2308115. doi: 10.1002/advs.202308115. Epub 2024 Feb 2. Adv Sci (Weinh). 2024. PMID: 38308181 Free PMC article.
-
Deep Computational Circular RNA Analytics from RNA-seq Data.Methods Mol Biol. 2018;1724:9-25. doi: 10.1007/978-1-4939-7562-4_2. Methods Mol Biol. 2018. PMID: 29322437
Cited by
-
Circular RNA profiling identifies circ_0001522, circ_0001278, and circ_0001801 as predictors of unfavorable prognosis and drivers of triple-negative breast cancer hallmarks.Cell Death Discov. 2025 Jul 9;11(1):316. doi: 10.1038/s41420-025-02576-9. Cell Death Discov. 2025. PMID: 40634303 Free PMC article.
References
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources