Abstract
Long noncoding RNAs (lncRNAs) have been shown to play important roles in various organisms, including plant species. Several tools and pipelines have emerged for lncRNA identification, including reference-based transcriptome assembly pipelines and various coding potential calculating tools. In this protocol, we have integrated some of the most updated computational tools and described the procedures step-by-step for identifying lncRNAs from plant strand-specific RNA-sequencing datasets. We will start from clean RNA-sequencing reads, followed by reference-based transcriptome assembly, filtering of known genes, and lncRNA prediction. At the end point, users will obtain a set of predicted lncRNAs for downstream use.
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References
Marchese FP, Raimondi I, Huarte M (2017) The multidimensional mechanisms of long noncoding RNA function. Genome Biol 18(1):206
Bazin J, Bailey-Serres J (2015) Emerging roles of long non-coding RNA in root developmental plasticity and regulation of phosphate homeostasis. Front Plant Sci 6:400
Chekanova JA (2015) Long non-coding RNAs and their functions in plants. Curr Opin Plant Biol 27:207–216
Zhao J, He Q, Chen G et al (2016) Regulation of non-coding RNAs in heat stress responses of plants. Front Plant Sci 7:1213
Liu J, Jung C, Xu J et al (2012) Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 24(11):4333–4345
Wang H, Chung PJ, Liu J et al (2014) Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis. Genome Res 24(3):444–453
Wang T-Z, Liu M, Zhao M-G et al (2015) Identification and characterization of long non-coding RNAs involved in osmotic and salt stress in Medicago truncatula using genome-wide high-throughput sequencing. BMC Plant Biol 15(1):131
Zhang Y, Huang H, Zhang D et al (2017) A review on recent computational methods for predicting noncoding RNAs. Biomed Res Int 2017:1–14
Johnsson P, Lipovich L, Grandér D et al (2014) Evolutionary conservation of long non-coding RNAs; sequence, structure, function. Biochim Biophys Acta 1840(3):1063–1071
Han S, Liang Y, Li Y et al (2016) Long noncoding RNA identification: comparing machine learning based tools for long noncoding transcripts discrimination. Biomed Res Int 2016:1–14
Pertea M, Kim D, Pertea GM et al (2016) Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc 11(9):1650–1667
Wucher V, Legeai F, Hédan 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):gkw1306
Parkhomchuk D, Borodina T, Amstislavskiy V et al (2009) Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 37(18):e123
Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12(4):357–360
Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078–2079
Pertea M, Pertea GM, Antonescu CM et al (2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol 33(3):290–295
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120
Bolser DM, Staines DM, Perry E et al (2017) Ensembl plants: integrating tools for visualizing, mining, and analyzing plant genomic data. Methods Mol Biol 1374:115–140
Lagesen K, Hallin P, Rødland EA et al (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35(9):3100–3108
Schattner P, Brooks AN, Lowe TM (2005) The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33(Web Server issue):W686–W689
Nawrocki EP, Eddy SR (2013) Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29(22):2933–2935
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
Acknowledgments
This work was supported by grants from the Hong Kong Research Grants Council Area of Excellence Scheme (AoE/M-403/16); CUHK VC Discretionary Fund (VCF2014004); National Key Research and Development Program–Key Innovative and Collaborative Science and Technology Scheme for Hong Kong, Macau, and Taiwan (2017YFE0191100); CUHK Direct Grant (3132782); and the Lo Kwee-Seong Biomedical Research Fund to H.-M.L.
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Lin, X., Ni, M., Xiao, Z., Chan, TF., Lam, HM. (2019). Reference-Based Identification of Long Noncoding RNAs in Plants with Strand-Specific RNA-Sequencing Data. In: Chekanova, J.A., Wang, HL.V. (eds) Plant Long Non-Coding RNAs. Methods in Molecular Biology, vol 1933. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9045-0_14
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DOI: https://doi.org/10.1007/978-1-4939-9045-0_14
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-9044-3
Online ISBN: 978-1-4939-9045-0
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