nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs | BMC Bioinformatics

  • Sanger HL, Klotz G, Riesner D, Gross HJ, Kleinschmidt AK. Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc Natl Acad Sci. 1976;73(11):3852–6. doi.org/10.1073/pnas.73.11.3852.

    Article 
    CAS 

    Google Scholar
     

  • Arnberg AC, Van Ommen G-JB, Grivell LA, Van Bruggen EFJ, Borst P. Some yeast mitochondrial RNAs are circular. Cell. 1980;19(2):313–9. doi.org/10.1016/0092-8674(80)90505-X.

    Article 
    CAS 

    Google Scholar
     

  • Kos A, Dijkema R, Arnberg AC, van der Meide PH, Schellekens H. The hepatitis delta (δ) virus possesses a circular RNA. Nature. 1986;323:558–60. doi.org/10.1038/323558a0.

    Article 
    CAS 

    Google Scholar
     

  • Cocquerelle C, Mascrez B, Hétuin D, Bailleul B. Mis-splicing yields circular RNA molecules. FASEB J. 1993;7(1):155–60. doi.org/10.1096/fasebj.7.1.7678559.

    Article 
    CAS 

    Google Scholar
     

  • Qian L, Vu MN, Carter M, Wilkinson MF. A spliced intron accumulates as a lariat in the nucleus of T cells. Nucleic Acids Res. 1992;20(20):5345–50. doi.org/10.1093/nar/20.20.5345.

    Article 
    CAS 

    Google Scholar
     

  • 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(2):1–12. doi.org/10.1371/journal.pone.0030733.

    Article 
    CAS 

    Google Scholar
     

  • Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M, Loewer A, Ziebold U, Landthaler M, Kocks C, le Noble F, Rajewsky N. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013;495:333–8. doi.org/10.1038/nature11928.

    Article 
    CAS 

    Google Scholar
     

  • Memczak S, Papavasileiou P, Peters O, Rajewsky N. Identification and characterization of circular RNAs as a new class of putative biomarkers in human blood. PLoS ONE. 2015;10(10):1–13. doi.org/10.1371/journal.pone.0141214.

    Article 
    CAS 

    Google Scholar
     

  • Bahn JH, Zhang Q, Li F, Chan T-M, Lin X, Kim Y, Wong DTW, Xiao X. The landscape of microRNA, piwi-interacting RNA, and circular RNA in human saliva. Clin Chem. 2015;61(1):221–30. doi.org/10.1373/clinchem.2014.230433.

    Article 
    CAS 

    Google Scholar
     

  • Li P, Chen S, Chen H, Mo X, Li T, Shao Y, Xiao B, Guo J. Using circular RNA as a novel type of biomarker in the screening of gastric cancer. Clin Chim Acta. 2015;444:132–6. doi.org/10.1016/j.cca.2015.02.018. arXiv:2568.9795.

    Article 
    CAS 

    Google Scholar
     

  • Bachmayr-Heyda A, Reiner AT, Auer K, Sukhbaatar N, Aust S, Bachleitner-Hofmann T, Mesteri I, Grunt TW, Zeillinger R, Pils D. Correlation of circular RNA abundance with proliferation: exemplified with colorectal and ovarian cancer, idiopathic lung fibrosis and normal human tissues. Sci Rep. 2015;5(8057):1–10. doi.org/10.1038/srep08057.

    Article 
    CAS 

    Google Scholar
     

  • Zhong Z, Lv M, Chen J. Screening differential circular RNA expression profiles reveals the regulatory role of circTCF25-miR-103a-3p/miR-107-CDK6 pathway in bladder carcinoma. Sci Rep. 2016. doi.org/10.1038/srep30919.

    Article 

    Google Scholar
     

  • Tan WLW, Lim BTS, Anene-Nzelu CGO, Ackers-Johnson M, Dashi A, See K, Tiang Z, Lee DP, Chua WW, Luu TDA, Li PYQ, Richards AM, Foo RSY. A landscape of circular RNA expression in the human heart. Cardiovasc Res. 2016;113(3):298–309. doi.org/10.1093/cvr/cvw250.

    Article 
    CAS 

    Google Scholar
     

  • Panda AC, Abdelmohsen K, Gorospe M. RT-qPCR detection of senescence-associated circular RNAs. Methods Mol Biol. 2017;1534:79–87. doi.org/10.1007/978-1-4939-6670-7_7. arXiv:2781.2869.

    Article 
    CAS 

    Google Scholar
     

  • Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B, Damgaard CK, Kjems J. Natural RNA circles function as efficient microRNA sponges. Nature. 2013;495:384–8. doi.org/10.1038/nature11993.

    Article 
    CAS 

    Google Scholar
     

  • Thomas LF, Sætrom P. Circular RNAs are depleted of polymorphisms at microRNA binding sites. Bioinformatics. 2014;30(16):2243–6. doi.org/10.1093/bioinformatics/btu257.

  • Denzler R, Agarwal V, Stefano J, Bartel D, Stoffel M. Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance. Mol Cell. 2014;54(5):766–76. doi.org/10.1016/j.molcel.2014.03.045.

  • Hsiao K-Y, Lin Y-C, Gupta SK, Chang N, Yen L, Sun HS, Tsai S-J. Noncoding effects of circular RNA CCDC66 promote colon cancer growth and metastasis. Cancer Res. 2017;77(9):2339–50. doi.org/10.1158/0008-5472.CAN-16-1883.

    Article 
    CAS 

    Google Scholar
     

  • Gaffo E, Bonizzato A, Te Kronnie G, Bortoluzzi S. CirComPara: a multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data. Noncoding RNA. 2017;3:1. doi.org/10.3390/ncrna3010008.

    Article 
    CAS 

    Google Scholar
     

  • Gaffo E, Buratin A, Dal Molin A, Bortoluzzi S. Sensitive, reliable and robust circRNA detection from RNA-seq with CirComPara2. Brief Bioinf. 2022;23(1):418. doi.org/10.1093/bib/bbab418.

    Article 
    CAS 

    Google Scholar
     

  • Liu Z, Ding H, She J, Chen C, Zhang W, Yang E. DEBKS: a tool to detect differentially expressed circular RNA. Genom Proteom Bioinform. 2021. doi.org/10.1016/j.gpb.2021.01.003.

    Article 

    Google Scholar
     

  • Hossain MdT, Peng Y, Feng S, Wei Y. FcircSEC: an R package for full length circRNA sequence extraction and classification. Int J Genom. 2020;2020:9084901. doi.org/10.1155/2020/9084901.

    Article 
    CAS 

    Google Scholar
     

  • Aufiero S, Reckman YJ, Tijsen AJ, Pinto YM, Creemers EE. circRNAprofiler: an R-based computational framework for the downstream analysis of circular RNAs. BMC Bioinform. 2020;21(1):1–9. doi.org/10.1186/s12859-020-3500-3.

    Article 
    CAS 

    Google Scholar
     

  • Jakobi T, Uvarovskii A, Dieterich C. Circtools: a one-stop software solution for circular RNA research. Bioinformatics. 2019;35(13):2326–8. doi.org/10.1093/bioinformatics/bty948. arXiv:3046.2173.

    Article 
    CAS 

    Google Scholar
     

  • Chen L, Wang F, Bruggeman EC, Li C, Yao B. circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs. Bioinformatics. 2020;36(2):539–45. doi.org/10.1093/bioinformatics/btz606.

    Article 
    CAS 

    Google Scholar
     

  • Li L, Bu D, Zhao Y. CircRNAwrap: a flexible pipeline for circRNA identification, transcript prediction, and abundance estimation. FEBS Lett. 2019;593(11):1179–89. doi.org/10.1002/1873-3468.13423.

    Article 
    CAS 

    Google Scholar
     

  • Humphreys DT, Fossat N, Demuth M, Tam PPL, Ho JWK. Ularcirc: visualization and enhanced analysis of circular RNAs via back and canonical forward splicing. Nucleic Acids Res. 2019;47(20):123. doi.org/10.1093/nar/gkz718.

    Article 
    CAS 

    Google Scholar
     

  • Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017;35:316–9. doi.org/10.1038/nbt.3820.

    Article 
    CAS 

    Google Scholar
     

  • Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020;38:276–8. doi.org/10.1038/s41587-020-0439-x.

    Article 
    CAS 

    Google Scholar
     

  • Docker. www.docker.com/

  • Apptainer. apptainer.org/

  • Andrews S. FastQC: a quality control tool for high throughput sequence data.

  • Bushnell B. BBMap. SourceForge. sourceforge.net/projects/bbmap

  • Zhang X-O, Dong R, Zhang Y, Zhang J-L, Luo Z, Zhang J, Chen L-L, Yang L. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res. 2016;26(9):1277–87. doi.org/10.1101/gr.202895.115.

    Article 
    CAS 

    Google Scholar
     

  • Westholm J, Miura P, Olson S, Shenker S, Joseph B, Sanfilippo P, Celniker S, Graveley B, Lai E. Genome-wide analysis of drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation. Cell Rep. 2014;9(5):1966–80. doi.org/10.1016/j.celrep.2014.10.062.

    Article 
    CAS 

    Google Scholar
     

  • Cheng J, Metge F, Dieterich C. Specific identification and quantification of circular RNAs from sequencing data. Bioinformatics. 2016;32(7):1094–6. doi.org/10.1093/bioinformatics/btv656.

    Article 
    CAS 

    Google Scholar
     

  • Zhang J, Chen S, Yang J, Zhao F. Accurate quantification of circular RNAs identifies extensive circular isoform switching events. Nat Commun. 2020;11(90):1–14. doi.org/10.1038/s41467-019-13840-9.

    Article 
    CAS 

    Google Scholar
     

  • Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res. 2010;38(18):178. doi.org/10.1093/nar/gkq622.

    Article 
    CAS 

    Google Scholar
     

  • Otto C, Stadler PF, Hoffmann S. Lacking alignments? The next-generation sequencing mapper segemehl revisited. Bioinformatics. 2014;30(13):1837–43. doi.org/10.1093/bioinformatics/btu146. arXiv:2462.6854.

    Article 
    CAS 

    Google Scholar
     

  • Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21. doi.org/10.1093/bioinformatics/bts635.

    Article 
    CAS 

    Google Scholar
     

  • Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. 2013; arXiv:1303.3997.

  • Gao Y, Wang J, Zhao F. CIRI: an efficient and unbiased algorithm for de novo circular RNA identification. Genome Biol. 2015;16(1):4. doi.org/10.1186/s13059-014-0571-3. arXiv:2558.3365.

    Article 
    CAS 

    Google Scholar
     

  • Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in Drosophila. Genome Biol. 2003;5(1):1–14. doi.org/10.1186/gb-2003-5-1-r1.

    Article 

    Google Scholar
     

  • Agarwal V, Bell GW, Nam J-W, Bartel DP. Predicting effective microRNA target sites in mammalian mRNAs. eLife. 2015. doi.org/10.7554/eLife.05005.

    Article 

    Google Scholar
     

  • Clark PM, Chitnis N, Shieh M, Kamoun M, Johnson FB, Monos D. Novel and haplotype specific MicroRNAs encoded by the major histocompatibility complex. Sci Rep. 2018;8(3832):1–10. doi.org/10.1038/s41598-018-19427-6.

    Article 
    CAS 

    Google Scholar
     

  • Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12:357–60. doi.org/10.1038/nmeth.3317.

    Article 
    CAS 

    Google Scholar
     

  • Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 2016;11:1650–67. doi.org/10.1038/nprot.2016.095.

    Article 
    CAS 

    Google Scholar
     

  • Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):1–21. doi.org/10.1186/s13059-014-0550-8.

    Article 
    CAS 

    Google Scholar
     

  • Cao D. An autoregulation loop in fust-1 for circular RNA regulation in Caenorhabditis elegans. Genetics. 2021;219(3):145. doi.org/10.1093/genetics/iyab145. arXiv:3474.0247.

    Article 

    Google Scholar
     

  • nf-core/fetchngs. github.com/nf-core/fetchngs

  • Zeng X, Lin W, Guo M, Zou Q. A comprehensive overview and evaluation of circular RNA detection tools. PLoS Comput Biol. 2017;13(6):1005420. doi.org/10.1371/journal.pcbi.1005420.

    Article 
    CAS 

    Google Scholar
     

  • Glažar P, Papavasileiou P, Rajewsky N. circBase: a database for circular RNAs. RNA. 2014;20(11):1666–70. doi.org/10.1261/rna.043687.113.

    Article 
    CAS 

    Google Scholar
     

  • Chen X, Han P, Zhou T, Guo X, Song X, Li Y. circRNADb: a comprehensive database for human circular RNAs with protein-coding annotations. Sci Rep. 2016;6(34985):1–6. doi.org/10.1038/srep34985.

    Article 
    CAS 

    Google Scholar
     

  • Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, The RGASP Consortium, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P. Systematic evaluation of spliced alignment programs for RNA-seq data. Nat Methods. 2013;10(12):1185. doi.org/10.1038/nmeth.2722

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