Abstract
Long non-coding RNAs (lncRNAs) are a class of potent regulators of gene expression that are found in a wide array of eukaryotes; however, our knowledge about these molecules in plants is very limited. In particular, a number of plant species with important roles in biotechnology, agriculture and basic research still lack comprehensively identified and annotated sets of lncRNAs. To address these shortcomings, we previously created a database of lncRNAs in 10 model species, called CANTATAdb, and now we are expanding this online resource to encompass 39 species, including three algae. The lncRNAs were identified computationally using publicly available RNA sequencing (RNA-Seq) data. Expression values, coding potential calculations and other types of information were used to provide annotations for the identified lncRNAs. The data are freely available for searching, browsing and downloading from an online database called CANTATAdb 2.0 (http://cantata.amu.edu.pl, http://yeti.amu.edu.pl/CANTATA/).
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Zhao Y, Li H, Fang S, Kang Y, Wu W, Hao Y et al (2016) NONCODE 2016: an informative and valuable data source of long non-coding RNAs. Nucleic Acids Res 44:D203–D208
Zerbino DR, Achuthan P, Akanni W, Amode MR, Barrell D, Bhai J et al (2018) Ensembl 2018. Nucleic Acids Res 46:D754–D761
Paytuvi Gallart A, Hermoso Pulido A, Anzar Martinez de Lagran I, Sanseverino W, Aiese Cigliano R (2016) GREENC: a Wiki-based database of plant lncRNAs. Nucleic Acids Res 44:D1161–D1166
Szczesniak MW, Rosikiewicz W, Makalowska I (2016) CANTATAdb: a collection of plant long non-coding RNAs. Plant Cell Physiol 57:e8
Kim DH, Xi Y, Sung S (2017) Modular function of long noncoding RNA, COLDAIR, in the vernalization response. PLoS Genet 13:e1006939
Zhang YC, Liao JY, Li ZY, Yu Y, Zhang JP, Li QF et al (2014) Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice. Genome Biol 15:512
Wang Y, Li J, Deng XW, Zhu D (2017) Arabidopsis noncoding RNA modulates seedling greening during deetiolation. Sci China Life Sci 61:199. https://doi.org/10.1007/s11427-017-9187-9
Yuan J, Zhang Y, Dong J, Sun Y, Lim BL, Liu D et al (2016) Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana. BMC Genomics 17:655
Zhang J, Wang C, Ke N, Bliesath J, Chionis J, He QS et al (2007) A more efficient RNAi inducible system for tight regulation of gene expression in mammalian cells and xenograft animals. RNA 13:1375–1383
Ben Amor B, Wirth S, Merchan F, Laporte P, d'Aubenton-Carafa Y, Hirsch J et al (2009) Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Res 19:57–69
Deng F, Zhang X, Wang W, Yuan R, Shen F (2018) Identification of Gossypium hirsutum long non-coding RNAs (lncRNAs) under salt stress. BMC Plant Biol 18:23
Bardou F, Ariel F, Simpson CG, Romero-Barrios N, Laporte P, Balzergue S et al (2014) Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. Dev Cell 30:166–176
Bazin J, Baerenfaller K, Gosai SJ, Gregory BD, Crespi M, Bailey-Serres J (2017) Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation. Proc Natl Acad Sci U S A 114:E10018–E10027
Bolser DM, Staines DM, Perry E, Kersey PJ (2017) Ensembl plants: integrating tools for visualizing, mining, and analyzing plant genomic data. Methods Mol Biol 1533:1–31
Kodama Y, Shumway M, Leinonen R (2012) The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res 40:D54–D56
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S et al (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21
Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL (2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol 33:290–295
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ et al (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511–515
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J et al (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8:1494–1512
Kong L, Zhang Y, Ye Z, Liu X, Zhao S, Wei L et al (2007) CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res 35:W345–W349
Kalvari I, Argasinska J, Quinones-Olvera N, Nawrocki EP, Rivas E, Eddy SR, Bateman A et al (2018) Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Res 46:D335–D342
Sun L, Luo H, Bu D, Zhao G, Yu K, Zhang C et al (2013) Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res 41:e166
The UniProt Consortium (2017) UniProt: the universal protein knowledgebase. Nucleic Acids Res 45:D158–D169
Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C (2017) Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods 14:417–419
Yi X, Zhang Z, Ling Y, Xu W, Su Z (2015) PNRD: a plant non-coding RNA database. Nucleic Acids Res 43:D982–D989
Xuan H, Zhang L, Liu X, Han G, Li J, Li X et al (2015) PLNlncRbase: a resource for experimentally identified lncRNAs in plants. Gene 573:328–332
Acknowledgments
This work was supported by the National Science Centre (grant No. 2014/15/D/NZ2/00525 to M.W.S); the KNOW Poznan RNA Centre (grant No. 01/KNOW2/2014); the Polish Ministry of Science and Higher Education (decision No. 1268/MOB/IV/2015/0 to M.W.S - Mobility Plus project).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Szcześniak, M.W., Bryzghalov, O., Ciomborowska-Basheer, J., Makałowska, I. (2019). CANTATAdb 2.0: Expanding the Collection of Plant Long Noncoding RNAs. 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_26
Download citation
DOI: https://doi.org/10.1007/978-1-4939-9045-0_26
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-9044-3
Online ISBN: 978-1-4939-9045-0
eBook Packages: Springer Protocols