Drula, R., Braicu, C. & Neagoe, I.-B. Current advances in circular RNA detection and investigation methods: are we running in circles? Wiley Interdiscip. Rev. RNA 15, e1850 (2024).

Article  CAS  PubMed  Google Scholar 

Pandey, P. R. et al. Methods for analysis of circular RNAs. Wiley Interdiscip. Rev. RNA 11, e1566 (2020).

Article  CAS  PubMed  Google Scholar 

Zhang, J., Chen, S., Yang, J. & Zhao, F. Accurate quantification of circular RNAs identifies extensive circular isoform switching events. Nat. Commun. 11, 90 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Hansen, T. B., Venø, M. T., Damgaard, C. K. & Kjems, J. Comparison of circular RNA prediction tools. Nucleic Acids Res. 44, e58 (2016).

Article  PubMed  Google Scholar 

Zeng, X., Lin, W., Guo, M. & Zou, Q. A comprehensive overview and evaluation of circular RNA detection tools. PLoS Comput. Biol. 13, e1005420 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Conn, V. M. et al. SRRM4 expands the repertoire of circular RNAs by regulating microexon inclusion. Cells 9, 2488 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Conn, V. & Conn, S. J. SplintQuant: a method for accurately quantifying circular RNA transcript abundance without reverse transcription bias. RNA 25, 1202–1210 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cooper, D. A., Cortés-López, M. & Miura, P. Genome-wide circRNA profiling from RNA-seq data. Methods Mol. Biol. 1724, 27–41 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Vo, J. N. et al. The landscape of circular RNA in cancer. Cell 176, 869–881.e13 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhong, S. et al. Identification of internal control genes for circular RNAs. Biotechnol. Lett. 41, 1111–1119 (2019).

Article  CAS  PubMed  Google Scholar 

Xu, T., Wu, J., Han, P., Zhao, Z. & Song, X. Circular RNA expression profiles and features in human tissues: a study using RNA-seq data. BMC Genomics 18, 680 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Roy, S. et al. Diagnostic efficacy of circular RNAs as noninvasive, liquid biopsy biomarkers for early detection of gastric cancer. Mol. Cancer 21, 42 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nielsen, A. F. et al. Best practice standards for circular RNA research. Nat. Methods 19, 1208–1220 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Salzman, J., Gawad, C., Wang, P. L., Lacayo, N. & Brown, P. O. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS ONE 7, e30733 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dodbele, S., Mutlu, N. & Wilusz, J. E. Best practices to ensure robust investigation of circular RNAs: pitfalls and tips. EMBO Rep 22, e52072 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li, Y. et al. Accurate identification of circRNA landscape and complexity reveals their pivotal roles in human oligodendroglia differentiation. Genome Biol. 23, 48 (2022).

Article  PubMed  PubMed Central  Google Scholar 

Conn, V. M. et al. Circular RNAs drive oncogenic chromosomal translocations within the MLL recombinome in leukemia. Cancer Cell 41, 1309–1326 (2023).

Article  CAS  PubMed  Google Scholar 

Liu, D. et al. ESRP1 controls biogenesis and function of a large abundant multiexon circRNA. Nucleic Acids Res. 52, 1387–1403 (2024).

Article  PubMed  Google Scholar 

Xiao, M.-S. & Wilusz, J. E. An improved method for circular RNA purification using RNase R that efficiently removes linear RNAs containing G-quadruplexes or structured 3′ ends. Nucleic Acids Res. 47, 8755–8769 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pandey, P. R., Rout, P. K., Das, A., Gorospe, M. & Panda, A. C. RPAD (RNase R treatment, polyadenylation, and poly(A)+ RNA depletion) method to isolate highly pure circular RNA. Methods 155, 41–48 (2019).

Article  CAS  PubMed  Google Scholar 

Guo, J. U., Agarwal, V., Guo, H. & Bartel, D. P. Expanded identification and characterization of mammalian circular RNAs. Genome Biol. 15, 409 (2014).

Article  PubMed  PubMed Central  Google Scholar 

Zhang, J. et al. Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long. Nat. Biotechnol. 39, 836–845 (2021).

Article  PubMed  Google Scholar 

Kershaw, C. J. & O’Keefe, R. T. Splint ligation of RNA with T4 DNA ligase. Methods Mol. Biol. 941, 257–269 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hofacker, I. L. & Stadler, P. F. Memory efficient folding algorithms for circular RNA secondary structures. Bioinformatics 22, 1172–1176 (2006).

Article  CAS  PubMed  Google Scholar 

Wesselhoeft, R. A., Kowalski, P. S. & Anderson, D. G. Engineering circular RNA for potent and stable translation in eukaryotic cells. Nat. Commun. 9, 2629 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Xu, T., Song, X., Wang, Y., Fu, S. & Han, P. Genome-wide analysis of the expression of circular RNA full-length transcripts and construction of the circRNA–miRNA–mRNA network in cervical cancer. Front. Cell Dev. Biol. 8, 603516 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Hardwick, S. A. et al. Spliced synthetic genes as internal controls in RNA sequencing experiments. Nat. Methods 13, 792–798 (2016).

Article  CAS  PubMed  Google Scholar 

Jiang, L. et al. Synthetic spike-in standards for RNA-seq experiments. Genome Res. 21, 1543–1551 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Conn, V., Liu, R., Gabryelska, M. & Conn, S. Use of synthetic circular RNA spike-ins (SynCRS) for normalization of circular RNA sequencing data. Zenodo https://zenodo.org/doi/10.5281/zenodo.10843759 (2024).