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Cereal Circular RNAs (circRNAs): An Overview of the Computational Resources for Identification and Analysis

  • Luis M. Vaschetto
  • Celso Gaspar LitholdoJr
  • Lorena Noelia Sendín
  • Claudia Mabel Terenti Romero
  • María Paula Filippone
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2072)

Abstract

Circular RNAs (circRNAs) are a widespread class of endogenous noncoding RNAs and they have been studied in the past few years, implying important biological functions in all kingdoms of life. Recently, circRNAs have been identified in many plant species, including cereal crops, showing differential expression during stress response and developmental programs, which suggests their role in these process. In the following years, it is expected that insights into the functional roles of circRNAs can be used by cereal scientists and molecular breeders with the aim to develop new strategies for crop improvement. Here, we briefly outline the current knowledge about circRNAs in plants and we also outline available computational resources for their validation and analysis in cereal species.

Key words

Noncoding RNAs Plant circRNAs Cereal circRNAs Computational resources Molecular breeding Crop improvement 

References

  1. 1.
    Hsu MT, Coca-Prados M (1979) Electron microscopic evidence for the circular form of RNA in the cytoplasm of eukaryotic cells. Nature 280:339–340CrossRefGoogle Scholar
  2. 2.
    Cocquerelle C, Daubersies P, Majérus MA et al (1992) Splicing with inverted order of exons occurs proximal to large introns. EMBO J 11:1095–1098CrossRefGoogle Scholar
  3. 3.
    Salzman J, Gawad C, Wang PL et al (2012) Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One 7:e30733CrossRefGoogle Scholar
  4. 4.
    Memczak S, Jens M, Elefsinioti A et al (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495:333–338CrossRefGoogle Scholar
  5. 5.
    Ye CY, Chen L, Liu C et al (2015) Widespread noncoding circular RNAs in plants. New Phytol 208:88–95CrossRefGoogle Scholar
  6. 6.
    Ye CY, Xu H, Shen EH et al (2014) Genome-wide identification of non-coding RNAs interacted with microRNAs in soybean. Front Plant Sci 5:743CrossRefGoogle Scholar
  7. 7.
    Hansen TB, Jensen TI, Clausen BH et al (2013) Natural RNA circles function as efficient microRNA sponges. Nature 495:384–388CrossRefGoogle Scholar
  8. 8.
    Ashwal-Fluss R, Meyer M, Pamudurti NR et al (2014) circRNA biogenesis competes with pre-mRNA splicing. Mol Cell 56:55–66CrossRefGoogle Scholar
  9. 9.
    Lukiw WJ (2013) Circular RNA (circRNA) in Alzheimer’s disease (AD). Front Genet 4:307PubMedPubMedCentralGoogle Scholar
  10. 10.
    Wang Y, Mo Y, Gong Z et al (2017) Circular RNAs in human cancer. Mol Cancer 16:25CrossRefGoogle Scholar
  11. 11.
    Lu T, Cui L, Zhou Y et al (2015) Transcriptome-wide investigation of circular RNAs in rice. RNA 21:2076–2087CrossRefGoogle Scholar
  12. 12.
    Ye CY, Zhang X, Chu Q et al (2017) Full-length sequence assembly reveals circular RNAs with diverse non-GT/AG splicing signals in rice. RNA Biol 14:1055–1063CrossRefGoogle Scholar
  13. 13.
    Chen L, Zhang P, Fan Y et al (2018) Circular RNAs mediated by transposons are associated with transcriptomic and phenotypic variation in maize. New Phytol 217:1292–1306CrossRefGoogle Scholar
  14. 14.
    Ghorbani A, Izadpanah K, Peters JR et al (2018) Detection and profiling of circular RNAs in uninfected and maize Iranian mosaic virus-infected maize. Plant Sci 274:402–409CrossRefGoogle Scholar
  15. 15.
    Darbani B, Noeparvar S, Borg S (2016) Identification of circular RNAs from the parental genes involved in multiple aspects of cellular metabolism in barley. Front Plant Sci 7:776CrossRefGoogle Scholar
  16. 16.
    Wang Y, Yang M, Wei S et al (2016) Identification of circular RNAs and their targets in leaves of Triticum aestivum L. under dehydration stress. Front Plant Sci 7:2024PubMedGoogle Scholar
  17. 17.
    Zhang Y, Liang W, Zhang P et al (2017) Circular RNAs: emerging cancer biomarkers and targets. J Exp Clin Cancer Res 36:152CrossRefGoogle Scholar
  18. 18.
    Sablok G, Zhao H, Sun X (2016) Plant circular RNAs (circRNAs): transcriptional regulation beyond miRNAs in plants. Mol Plant 9:192–194CrossRefGoogle Scholar
  19. 19.
    Wang Y, Wang Z (2015) Efficient backsplicing produces translatable circular mRNAs. RNA 21:172–179CrossRefGoogle Scholar
  20. 20.
    Jeck WR, Sorrentino JA, Wang K et al (2013) Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA 19:141–157CrossRefGoogle Scholar
  21. 21.
    Liang D, Wilusz JE (2014) Short intronic repeat sequences facilitate circular RNA production. Genes Dev 28:2233–2247CrossRefGoogle Scholar
  22. 22.
    Zhang P, Fan Y, Sun X et al (2019) A large-scale circular RNA profiling reveals universal molecular mechanisms responsive to drought stress in maize and Arabidopsis. Plant J 98:697.  https://doi.org/10.1111/tpj.14267CrossRefPubMedGoogle Scholar
  23. 23.
    Conn SJ, Pillman KA, Toubia J et al (2015) The RNA binding protein quaking regulates formation of circRNAs. Cell 160:1125–1134CrossRefGoogle Scholar
  24. 24.
    Zhou R, Zhu Y, Zhao J et al (2017) Transcriptome-wide identification and characterization of potato circular RNAs in response to Pectobacterium carotovorum subspecies brasiliense infection. Int J Mol Sci 19:71CrossRefGoogle Scholar
  25. 25.
    Li X, Yang L, Chen LL (2018) The biogenesis, functions, and challenges of circular RNAs. Mol Cell 71:428–442CrossRefGoogle Scholar
  26. 26.
    Tang B, Hao Z, Zhu Y et al (2018) Genome-wide identification and functional analysis of circRNAs in Zea mays. PLoS One 13:e0202375CrossRefGoogle Scholar
  27. 27.
    Xu Y, Ren Y, Lin T et al (2019) Identification and characterization of CircRNAs involved in the regulation of wheat root length. Biol Res 52:19CrossRefGoogle Scholar
  28. 28.
    Jakobi T, Dieterich C (2018) Deep computational circular RNA analytics from RNA-seq data. Methods Mol Biol 1724:9–25CrossRefGoogle Scholar
  29. 29.
    Chu Q, Zhang X, Zhu X et al (2017) PlantcircBase: a database for plant circular RNAs. Mol Plant 10:1126–1128CrossRefGoogle Scholar
  30. 30.
    Ye J, Wang L, Li S et al (2017) AtCircDB: a tissue-specific database for Arabidopsis circular RNAs. Brief Bioinform 20:58.  https://doi.org/10.1093/bib/bbx089CrossRefGoogle Scholar
  31. 31.
    Chen L, Yu Y, Zhang X et al (2016) PcircRNA_finder: a software for circRNA prediction in plants. Bioinformatics 32:3528–3529PubMedPubMedCentralGoogle Scholar
  32. 32.
    Zhang XO, Dong R, Zhang Y et al (2016) Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res 26:1277–1287CrossRefGoogle Scholar
  33. 33.
    Zhang P, Meng X, Chen H, et al (2017) PlantCircNet: a database for plant circRNA–miRNA–mRNA regulatory networks. Database. 2017.  https://doi.org/10.1093/database/bax089
  34. 34.
    Liu YC, Li JR, Sun CH et al (2016) CircNet: a database of circular RNAs derived from transcriptome sequencing data. Nucleic Acids Res 44(D1):D209–D215CrossRefGoogle Scholar
  35. 35.
    Amaral PP, Dinger ME, Mattick JS (2013) Non-coding RNAs in homeostasis, disease and stress responses: an evolutionary perspective. Brief Funct Genomics 12:254–278CrossRefGoogle Scholar
  36. 36.
    Celton JM, Gaillard S, Bruneau M et al (2014) Widespread anti-sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control. New Phytol 203:287–299CrossRefGoogle Scholar
  37. 37.
    Weiberg A, Jin H (2015) Small RNAs—the secret agents in the plant–pathogen interactions. Curr Opin Plant Biol 26:87–94CrossRefGoogle Scholar
  38. 38.
    Zhu B, Yang Y, Li R et al (2015) RNA sequencing and functional analysis implicate the regulatory role of long non-coding RNAs in tomato fruit ripening. J Exp Bot 66:4483–4495CrossRefGoogle Scholar
  39. 39.
    Lai X, Bazin J, Webb S et al (2018) CircRNAs in plants. Adv Exp Med Biol 1087:329–343CrossRefGoogle Scholar
  40. 40.
    Li QF, Zhang YC, Chen YQ et al (2017) Circular RNAs roll into the regulatory network of plants. Biochem Biophys Res Commun 488:382–386CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • Luis M. Vaschetto
    • 1
    • 2
    • 7
  • Celso Gaspar LitholdoJr
    • 3
  • Lorena Noelia Sendín
    • 4
  • Claudia Mabel Terenti Romero
    • 5
  • María Paula Filippone
    • 6
  1. 1.Instituto de Diversidad y Ecología Animal, Consejo Nacional de Investigaciones Científicas y Técnicas (IDEA, CONICET)CórdobaArgentina
  2. 2.Facultad de Ciencias Exactas, Físicas y NaturalesUniversidad Nacional de Córdoba, (FCEFyN, UNC)CórdobaArgentina
  3. 3.Centre National pour la Recherche Scientifique (CNRS)/Université de Perpignan Via Domitia (UPVD)—Laboratoire Génome et Développement des Plantes (LGDP—UMR5096)PerpignanFrance
  4. 4.Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Estación Experimental Agroindustrial Obispo Colombres (EEAOC)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)TucumánArgentina
  5. 5.Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria San Luis (INTA, EEA SAN LUIS)San LuisArgentina
  6. 6.Universidad Nacional de Tucumán, Facultad de Agronomía y Zootecnia, (UNT-FAZ)TucumánArgentina
  7. 7.Agronomy, Horticulture and Plant Science DepartmentSouth Dakota State UniversitySDUSA

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