Abstract
Circular RNAs (circRNAs) are emerging species of mRNA splicing products with largely unknown functions. Although several computational pipelines for circRNA identification have been developed, these methods strictly rely on uniquely mapped reads overlapping back-splice junctions (BSJs) and lack approaches to model the statistical significance of the identified circRNAs. Here, we reported a systematic computational approach to identify circRNAs by simultaneously utilizing BSJ overlapping reads and discordant BSJ spanning reads to identify circRNAs. Moreover, we developed a novel procedure to estimate the P-values of the identified circRNAs. A computational cross-validation and experimental validations demonstrated that our method performed favorably compared to existing circRNA detection tools. We created a standalone tool, CircRNAFisher, to implement the method, which might be valuable to computational and experimental scientists studying circRNAs.
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References
Hsu MT, Kung HJ, Davidson N. An electron microscope study of Sindbis virus RNA. Cold Spring Harb Symp Quant Biol. 1974;38:943–50.
Hewlett MJ, Pettersson RF, Baltimore D. Circular forms of Uukuniemi virion RNA: an electron microscopic study. J Virol. 1977;21:1085–93.
Hsu MT, Coca-Prados M. Electron microscopic evidence for the circular form of RNA in the cytoplasm of eukaryotic cells. Nature. 1979;280:339–40.
Cocquerelle C, Daubersies P, Majerus MA, Kerckaert JP, Bailleul B. Splicing with inverted order of exons occurs proximal to large introns. EMBO J. 1992;11:1095–8.
Saad FA, Vitiello L, Merlini L, Mostacciuolo ML, Oliviero S, Danieli GA. A 3′ consensus splice mutation in the human dystrophin gene detected by a screening for intra-exonic deletions. Hum Mol Genet. 1992;1:345–6.
Bailleul B. During in vivo maturation of eukaryotic nuclear mRNA, splicing yields excised exon circles. Nucleic Acids Res. 1996;24:1015–9.
Zaphiropoulos PG. Circular RNAs from transcripts of the rat cytochrome P450 2C24 gene: correlation with exon skipping. Proc Natl Acad Sci USA. 1996;93:6536–41.
Danan M, Schwartz S, Edelheit S, Sorek R. Transcriptome-wide discovery of circular RNAs in Archaea. Nucleic Acids Res. 2011;40:3131–42. gkr1009
Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS ONE. 2012;7:e30733.
Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013;495:333–8.
Jeck WR, Sorrentino JA, Wang K, Slevin MK, Burd CE, Liu J, et al. Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA. 2013;19:141–57.
Glazar P, Papavasileiou P, Rajewsky N. circBase: a database for circular RNAs. RNA. 2014;20:1666–70.
Burd CE, Jeck WR, Liu Y, Sanoff HK, Wang Z, Sharpless NE. Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. PLoS Genet. 2010;6:e1001233.
Gao Y, Wang J, Zhao F. CIRI: an efficient and unbiased algorithm for de novo circular RNA identification. Genome Biol. 2015;16:4.
Gao Y, Zhang J, Zhao F. Circular RNA identification based on multiple seed matching. Brief Bioinf. (2017) https://doi.org/10.1093/bib/bbx014.
Zhang XO, Wang HB, Zhang Y, Lu X, Chen LL, Yang L. Complementary sequence-mediated exon circularization. Cell. 2014;159:134–47.
Kim D, Salzberg SL. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol. 2011;12:R72.
Danan M, Schwartz S, Edelheit S, Sorek R. Transcriptome-wide discovery of circular RNAs in Archaea. Nucleic Acids Res. 2012;40:3131–42.
Jeck WR, Sharpless NE. Detecting and characterizing circular RNAs. Nat Biotechnol. 2014;32:453–61.
Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, et al. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res. 2010;38:e178.
Gao Y, Zhao F. Computational strategies for exploring circular RNAs. Trends Genet. 2018;34:389–400.
Hansen TB. Improved circRNA identification by combining prediction algorithms. Front Cell Dev Biol. 2018;6:20.
Consortium EP. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2004;306:636–40.
Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, et al. The UCSC Genome Browser Database. Nucleic Acids Res. 2003;31:51–4.
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.
John S, Sabo PJ, Thurman RE, Sung MH, Biddie SC, Johnson TA, et al. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat Genet. 2011;43:264–8.
Keller W. The RNA lariat: a new ring to the splicing of mRNA precursors. Cell. 1984;39:423–5.
Salzman J, Chen RE, Olsen MN, Wang PL, Brown PO. Cell-type specific features of circular RNA expression. PLoS Genet. 2013;9:e1003777.
Chakravarti IM, Laha RG. Handbook of Methods of Applied Statistics. New York: Wiley; 1967.
Acknowledgements
This work was supported in part by the National Natural Science Foundation of China (NSFC) grant 31671380.
Author contributions
P.W. and Y.-C.L. conceived and designed the experiments; G.-Y.J., D.-l.W., and M.-Z.X. performed the experiments, analyzed the data and wrote the paper; and Y.-W.L., Y.-C.P., Y.-Q.Y., and J.-M.X. discussed and edited the manuscript. All the authors have read and approved the final manuscript.
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Jia, Gy., Wang, Dl., Xue, Mz. et al. CircRNAFisher: a systematic computational approach for de novo circular RNA identification. Acta Pharmacol Sin 40, 55–63 (2019). https://doi.org/10.1038/s41401-018-0063-1
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DOI: https://doi.org/10.1038/s41401-018-0063-1
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