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Genome-Wide Identification and Functional Characterization of Noncoding RNAs (ncRNAs) Differentially Expressed During Insect Development

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RNAi Strategies for Pest Management

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2360))

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Abstract

MicroRNAs (miRNAs) are important regulatory noncoding RNAs (ncRNAs) at the posttranscriptional level of gene expression. Linear long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) can function as competing endogenous RNAs (ceRNAs) of miRNAs and regulate the expression of protein-coding genes. This chapter presents a procedure for the bioinformatic analysis of these three ncRNAs that are differentially expressed during insect development. In the first step, lncRNAs and circRNAs are identified based on RNA-sequencing data. In the second step, miRNAs are identified based on small RNA-sequencing data and combined with the two ncRNAs from the previous step for functional characterization.

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References

  1. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10(1):57–63. https://doi.org/10.1038/nrg2484

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Friedlander MR, Chen W, Adamidi C et al (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 26(4):407–415. https://doi.org/10.1038/nbt1394

    Article  CAS  PubMed  Google Scholar 

  3. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359. https://doi.org/10.1038/nmeth.1923

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Dobin A, Davis CA, Schlesinger F et al (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29(1):15–21. https://doi.org/10.1093/bioinformatics/bts635

    Article  CAS  PubMed  Google Scholar 

  5. Kovaka S, Zimin AV, Pertea GM et al (2019) Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biol 20(1):278. https://doi.org/10.1186/s13059-019-1910-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Sun L, Luo HT, Bu DC et al (2013) Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res 41(17):e166. https://doi.org/10.1093/nar/gkt646

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Wang L, Park HJ, Dasari S et al (2013) CPAT: coding-potential assessment tool using an alignment-free logistic regression model. Nucleic Acids Res 41(6):e74. https://doi.org/10.1093/nar/gkt006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Wucher V, Legeai F, Hedan B et al (2017) FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome. Nucleic Acids Res 45(8):e57. https://doi.org/10.1093/nar/gkw1306

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Zhang XO, Dong R, Zhang Y et al (2016) Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res 26(9):1277–1287. https://doi.org/10.1101/gr.202895.115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Westholm JO, Miura P, Olson S et al (2014) Genome-wide analysis of Drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation. Cell Rep 9(5):1966–1980. https://doi.org/10.1016/j.celrep.2014.10.062

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Enright AJ, John B, Gaul U et al (2003) MicroRNA targets in Drosophila. Genome Biol 5(1):R1. https://doi.org/10.1186/gb-2003-5-1-r1

    Article  PubMed  PubMed Central  Google Scholar 

  12. Kruger J, Rehmsmeier M (2006) RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res 34:W451–W454. https://doi.org/10.1093/nar/gkl243

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Ibanez-Ventoso C, Vora M, Driscoll M (2008) Sequence relationships among C. elegans, D. melanogaster and human microRNAs highlight the extensive conservation of microRNAs in biology. PLoS One 3(7):e2818. https://doi.org/10.1371/journal.pone.0002818

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Asgari S (2011) Role of microRNAs in insect host-microorganism interactions. Front Physiol 2:48. https://doi.org/10.3389/fphys.2011.00048

    Article  PubMed  PubMed Central  Google Scholar 

  15. Asgari S (2013) MicroRNA functions in insects. Insect Biochem Mol Biol 43(4):388–397. https://doi.org/10.1016/j.ibmb.2012.10.005

    Article  CAS  PubMed  Google Scholar 

  16. Fullaondo A, Lee SY (2012) Identification of putative miRNA involved in Drosophila melanogaster immune response. Dev Comp Immunol 36(2):267–273. https://doi.org/10.1016/j.dci.2011.03.034

    Article  CAS  PubMed  Google Scholar 

  17. Legeai F, Derrien T (2015) Identification of long non-coding RNAs in insects genomes. Curr Opin Insect Sci 7:37–44. https://doi.org/10.1016/j.cois.2015.01.003

    Article  PubMed  Google Scholar 

  18. Zhang Y, Yang L, Chen LL (2014) Life without a tail: new formats of long noncoding RNAs. Int J Biochem Cell Biol 54:338–349. https://doi.org/10.1016/j.biocel.2013.10.009

    Article  CAS  PubMed  Google Scholar 

  19. Cesana M, Cacchiarelli D, Legnini I et al (2011) A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147(2):358–369. https://doi.org/10.1016/j.cell.2011.09.028

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Wang Y, Xu Z, Jiang J et al (2013) Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal. Dev Cell 25(1):69–80. https://doi.org/10.1016/j.devcel.2013.03.002

    Article  CAS  PubMed  Google Scholar 

  21. Feng K, Liu J, Wei P et al (2020) lincRNA_Tc13743.2-miR-133-5p-TcGSTm02 regulation pathway mediates cyflumetofen resistance in Tetranychus cinnabarinus. Insect Biochem Mol Biol 123:103413. https://doi.org/10.1016/j.ibmb.2020.103413

    Article  CAS  PubMed  Google Scholar 

  22. Cortes-Lopez M, Miura P (2016) Emerging functions of circular RNAs. Yale J Biol Med 89(4):527–537

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Kalvari I, Argasinska J, Quinones-Olvera N et al (2018) Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Res 46(D1):D335–D342. https://doi.org/10.1093/nar/gkx1038

    Article  CAS  PubMed  Google Scholar 

  24. Kim D, Salzberg SL (2011) TopHat-fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol 12(8):R72. https://doi.org/10.1186/Gb-2011-12-8-R72

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

This work was supported by the National Key R&D Program of China (2017YFD0200400), Natural Science Foundation of Fujian Province (2019J01369), and Special Key Project of Fujian Province in China (2018NZ0002).

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Authors and Affiliations

  1. State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China

    Yue Wang, Minsheng You & Weiyi He

  2. International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China

    Yue Wang, Minsheng You & Weiyi He

  3. Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China

    Yue Wang, Minsheng You & Weiyi He

Authors
  1. Yue Wang
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  2. Minsheng You
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  3. Weiyi He
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Corresponding author

Correspondence to Weiyi He .

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Editors and Affiliations

  1. Oncativo, Argentina

    Luis María Vaschetto

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Wang, Y., You, M., He, W. (2022). Genome-Wide Identification and Functional Characterization of Noncoding RNAs (ncRNAs) Differentially Expressed During Insect Development. In: Vaschetto, L.M. (eds) RNAi Strategies for Pest Management. Methods in Molecular Biology, vol 2360. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1633-8_1

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  • DOI: https://doi.org/10.1007/978-1-0716-1633-8_1

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1632-1

  • Online ISBN: 978-1-0716-1633-8

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