An updated database of virus circular RNAs provides new insights into the biogenesis mechanism of the molecule

References

• Lai X, Bazin J, Webb S, et al. Advances in experimental medicine and biology. Adv Exp Med Biol. 2018;1087:329–343. doi:10.1007/978-981-13-1426-1_26.
   PubMed Web of Science ®Google Scholar
• Cai Z, Fan Y, Zhang Z, et al. VirusCircBase: a database of virus circular RNAs. Brief Bioinform. 2021;22:2182–2190. doi:10.1093/bib/bbaa052.
   PubMed Web of Science ®Google Scholar
• Sanger HL, Klotz G, Riesner D, et al. Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc Natl Acad Sci USA. 1976;73:3852–3856. doi:10.1073/pnas.73.11.3852.
   PubMed Web of Science ®Google Scholar
• Ashwal-Fluss R, Meyer M, Pamudurti NR, et al. circRNA biogenesis competes with pre-mRNA splicing. Mol Cell. 2014;56:55–66. doi:10.1016/j.molcel.2014.08.019.
   PubMed Web of Science ®Google Scholar
• Quan G, Li J. Circular RNAs: biogenesis, expression and their potential roles in reproduction. J Ovarian Res. 2018;11:1–12. doi:10.1186/s13048-018-0381-4.
   PubMed Web of Science ®Google Scholar
• Lasda E, Parker R. Circular RNAs: diversity of form and function. RNA. 2014;20:1829–1842. doi:10.1261/rna.047126.114.
   PubMed Web of Science ®Google Scholar
• Liu X, Zhang Y, Zhou S, et al. Circular RNA: an emerging frontier in RNA therapeutic targets, RNA therapeutics, and mRNA vaccines. J Controlled Release. 2022;348:84–94. doi:10.1016/j.jconrel.2022.05.043.
   PubMed Web of Science ®Google Scholar
• Lasda E, Parker R. Circular RNAs: diversity of form and function. RNA. 2014;20:1829–1842. doi:10.1261/rna.047126.114.
   PubMed Web of Science ®Google Scholar
• Wang PL, Bao Y, Yee M-C, et al. Circular RNA is expressed across the eukaryotic tree of life. PLoS One. 2014;9:e90859. doi:10.1371/journal.pone.0090859.
   PubMed Web of Science ®Google Scholar
• Burd CE, Jeck WR, Liu Y, et al. Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. PLoS Genet. 2010;6:e1001233. doi:10.1371/journal.pgen.1001233.
   PubMed Web of Science ®Google Scholar
• Najafi S. The emerging roles and potential applications of circular RNAs in ovarian cancer: a comprehensive review. J Cancer Res Clin Oncol. 2023;149:2211–2234. doi:10.1007/s00432-022-04328-z.
   PubMed Web of Science ®Google Scholar
• Zhang Z-h, Wang Y, Zhang Y, et al. The function and mechanisms of action of circular RNAs in Urologic Cancer. Mol Cancer. 2023;22:61. doi:10.1186/s12943-023-01766-2.
   PubMed Web of Science ®Google Scholar
• Vo JN, Cieslik M, Zhang Y, et al. The landscape of circular RNA in cancer. Cell. 2019;176:869–881.e13. doi:10.1016/j.cell.2018.12.021.
   PubMed Web of Science ®Google Scholar
• Gao Y, Zhang J, Zhao F. Circular RNA identification based on multiple seed matching. Brief Bioinform. 2018;19:803–810. doi:10.1093/bib/bbx014.
   PubMed Web of Science ®Google Scholar
• Westholm JO, Miura P, Olson S, et al. Genome-wide analysis of Drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation. Cell Rep. 2014;9:1966–1980. doi:10.1016/j.celrep.2014.10.062.
   PubMed Web of Science ®Google Scholar
• Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013;495:333–338. doi:10.1038/nature11928.
   PubMed Web of Science ®Google Scholar
• Zhang X-O, Wang H-B, Zhang Y, et al. Complementary sequence-mediated exon circularization. Cell. 2014;159:134–147. doi:10.1016/j.cell.2014.09.001.
   PubMed Web of Science ®Google Scholar
• Wang K, Singh D, Zeng Z, et al. MapSplice: accurate mapping of RNA-Seq reads for splice junction discovery. Nucleic Acids Res. 2010;38:e178–e178. doi:10.1093/nar/gkq622.
   PubMed Web of Science ®Google Scholar
• Glažar P, Papavasileiou P, Rajewsky N. circBase: a database for circular RNAs. RNA. 2014;20:1666–1670. doi:10.1261/rna.043687.113.
   PubMed Web of Science ®Google Scholar
• Wu W, Ji P, Zhao F. scRNA-Seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation. Genome Biol. 2020;21:1–14. doi:10.1186/s13059-019-1906-x.
   Web of Science ®Google Scholar
• Zhang W, Liu Y, Min Z, et al. circMine: a comprehensive database to integrate, analyze and visualize human disease–related circRNA transcriptome. Nucleic Acids Res. 2022;50:D83–D92. doi:10.1093/nar/gkab809.
   PubMed Web of Science ®Google Scholar
• Xu X, Du T, Mao W, et al. PlantcircBase 7.0: full-length transcripts and conservation of plant circRNAs. Plant Commun. 2022;3:100343. doi:10.1016/j.xplc.2022.100343.
   PubMedGoogle Scholar
• Xin R, Gao Y, Gao Y, et al. isoCirc catalogs full-length circular RNA isoforms in human transcriptomes. Nat Commun. 2021;12:266. doi:10.1038/s41467-020-20459-8.
   PubMed Web of Science ®Google Scholar
• Zheng Y, Ji P, Chen S, et al. Reconstruction of full-length circular RNAs enables isoform-level quantification. Genome Med. 2019;11:1–20. doi:10.1186/s13073-019-0614-1.
   PubMed Web of Science ®Google Scholar
• Amarasinghe SL, Su S, Dong X, et al. Opportunities and challenges in long-read sequencing data analysis. Genome Biol. 2020;21:1–16. doi:10.1186/s13059-020-1935-5.
   Web of Science ®Google Scholar
• Hou L, Zhang J, Zhao F. Full-length circular RNA profiling by nanopore sequencing with CIRI-long. Nat Protoc. 2023;18:1795–1813. doi:10.1038/s41596-023-00815-w.
   PubMed Web of Science ®Google Scholar
• Stefanov SR, Meyer IM. CYCLeR—a novel tool for the full isoform assembly and quantification of circRNAs. Nucleic Acids Res. 2023;51:e10–e10. doi:10.1093/nar/gkac1100.
   PubMed Web of Science ®Google Scholar
• Chaitanya K. Structure and organization of virus genomes. Genome Genomics: From Archaea Eukaryotes. Springer Nature Singapore Pte Ltd; 2019.
   Google Scholar
• Tan KE, Lim YY. Viruses join the circular RNA world. FEBS J. 2021;288:4488–4502. doi:10.1111/febs.15639.
   PubMed Web of Science ®Google Scholar
• Huang J-t, Chen J-n, Gong L-p, et al. Identification of virus-encoded circular RNA. Virology. 2019;529:144–151. doi:10.1016/j.virol.2019.01.014.
   PubMed Web of Science ®Google Scholar
• Liu Q, Shuai M, Xia Y. Knockdown of EBV-encoded circRNA circRPMS1 suppresses nasopharyngeal carcinoma cell proliferation and metastasis through sponging multiple miRNAs. Cancer Manag Res. 2019;11:8023–8031. doi:10.2147/CMAR.S218967.
   PubMed Web of Science ®Google Scholar
• Ng YC, Chung W-C, Kang H-R, et al. A DNA-sensing–independent role of a nuclear RNA helicase, DHX9, in stimulation of NF-κB–mediated innate immunity against DNA virus infection. Nucleic Acids Res. 2018;46:9011–9026. doi:10.1093/nar/gky742.
   PubMed Web of Science ®Google Scholar
• Sekiba K, Otsuka M, Ohno M, et al. DHX9 regulates production of hepatitis B virus-derived circular RNA and viral protein levels. Oncotarget. 2018;9:20953–20964. doi:10.18632/oncotarget.25104.
   PubMedGoogle Scholar
• Zhu M, Liang Z, Pan J, et al. Hepatocellular carcinoma progression mediated by hepatitis B virus-encoded circRNA HBV_circ_1 through interaction with CDK1. Mol Ther-Nucleic Acids. 2021;25:668–682. doi:10.1016/j.omtn.2021.08.011.
   PubMedGoogle Scholar
• Niu M, Ju Y, Lin C, et al. Characterizing viral circRNAs and their application in identifying circRNAs in viruses. Brief Bioinform. 2022;23:bbab404. doi:10.1093/bib/bbab404.
   PubMed Web of Science ®Google Scholar
• Barbagallo D, Palermo CI, Barbagallo C, et al. Competing endogenous RNA network mediated by circ_3205 in SARS-CoV-2 infected cells. Cell Mol Life Sci. 2022;79:75. doi:10.1007/s00018-021-04119-8.
   PubMed Web of Science ®Google Scholar
• Chen S, Zheng J, Zhang B, et al. Identification and characterization of virus-encoded circular RNAs in host cells. Microb Genom. 2022;8. doi:10.1099/mgen.0.000848.
   Web of Science ®Google Scholar
• Li I, Chen YG. Emerging roles of circular RNAs in innate immunity. Curr Opin Immunol. 2021;68:107–115. doi:10.1016/j.coi.2020.10.010.
   PubMed Web of Science ®Google Scholar
• Fu P, Wu Y, Zhang Z, et al. VIGA: an one-stop tool for eukaryotic Virus Identification and Genome Assembly from next-generation-sequencing data. bioRxiv, 2023.2006.2014.545025. doi:10.1101/2023.06.14.545025.
   Google Scholar
• Andrews S. FastQC: a quality control tool for high throughput sequence data. Babraham bioinformatics. Cambridge: Babraham Institute; 2010.
   Google Scholar
• Chen S, Zhou Y, Chen Y, et al. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–i890. doi:10.1093/bioinformatics/bty560.
   PubMed Web of Science ®Google Scholar
• Zhou C, Liu S, Song W, et al. Characterization of viral RNA splicing using whole-transcriptome datasets from host species. Sci Rep. 2018;8:1–14.
   PubMed Web of Science ®Google Scholar
• Yao W, Pan J, Liu Z, et al. The cellular and viral circRNAome induced by respiratory syncytial virus infection. mBio. 2021;12:e0307521. doi:10.1128/mBio.03075-21.
   PubMed Web of Science ®Google Scholar
• Gao Y, Wang J, Zheng Y, et al. Comprehensive identification of internal structure and alternative splicing events in circular RNAs. Nat Commun. 2016;7:12060. doi:10.1038/ncomms12060.
   PubMed Web of Science ®Google Scholar
• Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-Seq aligner. Bioinformatics. 2013;29:15–21. doi:10.1093/bioinformatics/bts635.
   PubMed Web of Science ®Google Scholar
• Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923–930. doi:10.1093/bioinformatics/btt656.
   PubMed Web of Science ®Google Scholar
• Wu T, Hu E, Xu S, et al. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation (Cambridge (Mass.)). 2021;2:100141. doi:10.1016/j.xinn.2021.100141.
   PubMedGoogle Scholar
• Zhu W, Brendel V. Identification, characterization and molecular phylogeny of U12-dependent introns in the Arabidopsis thaliana genome. Nucleic Acids Res. 2003;31:4561–4572. doi:10.1093/nar/gkg492.
   PubMed Web of Science ®Google Scholar
• Levine A, Durbin R. A computational scan for U12-dependent introns in the human genome sequence. Nucleic Acids Res. 2001;29:4006–4013. doi:10.1093/nar/29.19.4006.
   PubMed Web of Science ®Google Scholar
• Gao Y, Wang J, Zheng Y, et al. Comprehensive identification of internal structure and alternative splicing events in circular RNAs. Nat Commun. 2016;7:12060. doi:10.1038/ncomms12060.
   PubMed Web of Science ®Google Scholar
• Ye C-Y, Zhang X, Chu Q, et al. Full-length sequence assembly reveals circular RNAs with diverse non-GT/AG splicing signals in rice. RNA Biol. 2017;14:1055–1063. doi:10.1080/15476286.2016.1245268.
   PubMed Web of Science ®Google Scholar
• Chu Q, Bai P, Zhu X, et al. Characteristics of plant circular RNAs. Brief Bioinform. 2018;21:135–143. doi:10.1093/bib/bby111.
   Web of Science ®Google Scholar
• Ji P, Wu W, Chen S, et al. Expanded expression landscape and prioritization of circular RNAs in mammals. Cell Rep. 2019;26:3444–3460.e5. doi:10.1016/j.celrep.2019.02.078.
   PubMed Web of Science ®Google Scholar
• Tagawa T, Oh D, Santos J, et al. Characterizing expression and regulation of gamma-herpesviral circular RNAs. Front Microbiol. 2021;12:670542. doi:10.3389/fmicb.2021.670542.
   PubMed Web of Science ®Google Scholar
• Zhao J, Lee EE, Kim J, et al. Transforming activity of an oncoprotein-encoding circular RNA from human papillomavirus. Nat Commun. 2019;10:2300. doi:10.1038/s41467-019-10246-5.
   PubMed Web of Science ®Google Scholar
• Chasseur AS, Trozzi G, Istasse C, et al. Marek’s disease virus virulence genes encode circular RNAs. J Virol. 2022;96:e00321–e00322. doi:10.1128/jvi.00321-22.
   PubMed Web of Science ®Google Scholar
• Eger N, Schoppe L, Schuster S, et al. Circular RNA splicing. Adv Exp Med Biol. 2018;(1087):41–52. doi:10.1007/978-981-13-1426-1_4.
   PubMed Web of Science ®Google Scholar
• Cao X, Xu X, Dong J, et al. Genome-wide identification and functional analysis of circRNAs in Trichophyton rubrum conidial and mycelial stages. BMC Genom. 2022;23:1–18.
   PubMed Web of Science ®Google Scholar
• Aktaş T, Avşar Ilık İ, Maticzka D, et al. DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome. Nature. 2017;544:115–119. doi:10.1038/nature21715.
   PubMed Web of Science ®Google Scholar
• Li X, Liu C-X, Xue W, et al. Coordinated circRNA biogenesis and function with NF90/NF110 in viral infection. Mol Cell. 2017;67:214–227.e217. doi:10.1016/j.molcel.2017.05.023.
   PubMed Web of Science ®Google Scholar