Advertisement

Identification of Novel lincRNA and Co-Expression Network Analysis Using RNA-Sequencing Data in Plants

  • Song Qi
  • Shamima Akter
  • Song LiEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1933)

Abstract

Long intergenic noncoding RNA (lincRNA) plays important biological functions in plants. Identification and annotation of lincRNA in plants largely rely on RNA sequencing followed by computational analysis. In this protocol, we describe a multistep computational pipeline for lincRNA identification using RNA-sequencing data. This pipeline can also construct co-expression network that is made of both lincRNA and mRNA genes. The co-expression network generated by this pipeline can be used to provide putative annotation of lincRNAs that have no known biological functions.

Key words

Co-expression network lincRNA Noncoding RNA Plant 

Notes

Acknowledgment

This work is supported by the Virginia Agricultural Experiment Station (Blacksburg) and the National Institute of Food and Agriculture, US Department of Agriculture (Washington, DC).

References

  1. 1.
    Li S, Yamada M, Han X et al (2016) High resolution expression map of the Arabidopsis root reveals alternative splicing and lincRNA regulation. Dev Cell 39(4):508–522CrossRefGoogle Scholar
  2. 2.
    Ulitsky I, Bartel DP (2013) lincRNAs: genomics, evolution, and mechanisms. Cell 154:26–46CrossRefGoogle Scholar
  3. 3.
    Shuai P, Liang D, Tang S et al (2014) Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa. J Exp Bot 65(17):4975–4983CrossRefGoogle Scholar
  4. 4.
    Liu J, Jung C, Xu J et al (2012) Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 24:4333–4345CrossRefGoogle Scholar
  5. 5.
    Shen Y, Zhou Z, Wang Z et al (2014) Global dissection of alternative splicing in paleopolyploid soybean. Plant Cell 26:996–1008CrossRefGoogle Scholar
  6. 6.
    Thatcher SR, Danilevskaya ON, Meng X et al (2016) Genome-wide analysis of alternative splicing during development and drought stress in maize. Plant Physiol 170:586–599CrossRefGoogle Scholar
  7. 7.
    Zhang W, Han Z, Guo Q et al (2014) Identification of maize long non-coding RNAs responsive to drought stress. PLoS One 9:e98958CrossRefGoogle Scholar
  8. 8.
    Aghamirzaie D, Batra D, Heath LS et al (2015) Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos. BMC Genomics 16:928CrossRefGoogle Scholar
  9. 9.
    Dobin A, Davis CA, Schlesinger F et al (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21CrossRefGoogle Scholar
  10. 10.
    Liao Y, Smyth GK, Shi W (2014) FeatureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923–930CrossRefGoogle Scholar
  11. 11.
    Pertea M, Pertea GM, Antonescu CM et al (2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol 33:290–295CrossRefGoogle Scholar
  12. 12.
    Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:1–34CrossRefGoogle Scholar
  13. 13.
    Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140CrossRefGoogle Scholar
  14. 14.
    Leinonen R, Sugawara H, Shumway M (2011) International nucleotide sequence database collaboration. The sequence read archive. Nucleic Acids Res 39:D19–D21CrossRefGoogle Scholar
  15. 15.
    Gentleman RC, Carey VJ, Bates DM et al (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5:R80CrossRefGoogle Scholar
  16. 16.
    Krishnakumar V, Hanlon MR, Contrino S et al (2015) Araport: the Arabidopsis information portal. Nucleic Acids Res 43:D1003–D1009CrossRefGoogle Scholar
  17. 17.
    Cheng CY, Krishnakumar V, Chan AP et al (2017) Araport11: a complete reannotation of the Arabidopsis thaliana reference genome. Plant J 89:789–804CrossRefGoogle Scholar
  18. 18.
    Smoot ME, Ono K, Ruscheinski J et al (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27:431–432CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Ph.D. Program in Genetics, Bioinformatics and Computational BiologyVirginia Polytechnic Institute and State UniversityBlacksburgUSA
  2. 2.Department of Crop & Soil Environmental SciencesVirginia Polytechnic Institute and State UniversityBlacksburgUSA

Personalised recommendations