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Current Bioinformatics

Author(s): Youhuang Bai, Xiaozhuan Dai, Tiantian Ye, Peijing Zhang, Xu Yan, Xiaonan Gong, Siliang Liang and Ming Chen*

DOI: 10.2174/1574893614666190131161002

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PlncRNADB: A Repository of Plant lncRNAs and lncRNA-RBP Protein Interactions

Page: [621 - 627] Pages: 7

  • * (Excluding Mailing and Handling)

Abstract

Background: Long noncoding RNAs (lncRNAs) are endogenous noncoding RNAs, arbitrarily longer than 200 nucleotides, that play critical roles in diverse biological processes. LncRNAs exist in different genomes ranging from animals to plants.

Objective: PlncRNADB is a searchable database of lncRNA sequences and annotation in plants.

Methods: We built a pipeline for lncRNA prediction in plants, providing a convenient utility for users to quickly distinguish potential noncoding RNAs from protein-coding transcripts.

Results: More than five thousand lncRNAs are collected from four plant species (Arabidopsis thaliana, Arabidopsis lyrata, Populus trichocarpa and Zea mays) in PlncRNADB. Moreover, our database provides the relationship between lncRNAs and various RNA-binding proteins (RBPs), which can be displayed through a user-friendly web interface.

Conclusion: PlncRNADB can serve as a reference database to investigate the lncRNAs and their interaction with RNA-binding proteins in plants. The PlncRNADB is freely available at http://bis.zju.edu.cn/PlncRNADB/.

Keywords: Plant lncRNA prediction, RNA-protein interaction, lncRNA database, Arabidopsis thaliana, Populus trichocarpa, Zea mays.

Graphical Abstract

[1]
Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell 2009; 136: 629-41.
[2]
Pang KC, Frith MC, Mattick JS. Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genet 2006; 22: 1-5.
[3]
Rinn JL, Chang HY. Genome regulation by long noncoding RNAs. Annu Rev Biochem 2012; 81: 145-66.
[4]
Liu J, Jung C, Xu J, et al. Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 2012; 24: 4333-45.
[5]
Wang H, Chung PJ, Liu J, et al. Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis. Genome Res 2014; 24: 444-53.
[6]
Zhu QH, Stephen S, Taylor J, Helliwell CA, Wang MB. Long noncoding RNAs responsive to Fusarium oxysporum infection in Arabidopsis thaliana. New Phytol 2014; 201: 574-84.
[7]
Li L, Eichten SR, Shimizu R, et al. Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biol 2014; 15: R40.
[8]
Ma X, Shao C, Jin Y, Wang H, Meng Y. Long non-coding RNAs: a novel endogenous source for the generation of Dicer-like 1-dependent small RNAs in Arabidopsis thaliana. RNA Biol 2014; 11: 373-90.
[9]
Wu HJ, Wang ZM, Wang M, Wang XJ. Widespread long noncoding RNAs as endogenous target mimics for microRNAs in plants. Plant Physiol 2013; 161: 1875-84.
[10]
Guttman M, Rinn JL. Modular regulatory principles of large non-coding RNAs. Nature 2012; 482: 339-46.
[11]
Nagano T, Fraser P. No-nonsense functions for long noncoding RNAs. Cell 2011; 145: 178-81.
[12]
Wang KC, Chang HY. Molecular mechanisms of long noncoding RNAs. Mol Cell 2011; 43: 904-14.
[13]
Gupta RA, Shah N, Wang KC, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010; 464: 1071-6.
[14]
Morey C, Avner P. The demoiselle of X-inactivation: 50 years old and as trendy and mesmerising as ever. PLoS Genet 2011; 7e1002212
[15]
Wang KC, Yang YW, Liu B, et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 2011; 472: 120-4.
[16]
Gomez JA, Wapinski OL, Yang YW, et al. The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-gamma locus. Cell 2013; 152: 743-54.
[17]
Yang YW, Flynn RA, Chen Y, et al. Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency. eLife 2014; 3e02046
[18]
Campalans A, Kondorosi A, Crespi M. Enod40, a short open reading frame-containing mRNA, induces cytoplasmic localization of a nuclear RNA binding protein in Medicago truncatula. Plant Cell 2004; 16: 1047-59.
[19]
Bardou F, Ariel F, Simpson CG, et al. Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. Dev Cell 2014; 30: 166-76.
[20]
Bai Y, Dai X, Harrison AP, Chen M. RNA regulatory networks in animals and plants: a long noncoding RNA perspective. Brief Funct Genomics 2015; 14: 91-101.
[21]
Burge SW, Daub J, Eberhardt R, et al. Rfam 11.0: 10 years of RNA families. Nucleic Acids Res 2013; 41: D226-32.
[22]
Xie C, Yuan J, Li H, et al. NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res 2014; 42: D98-D103.
[23]
Quek XC, Thomson DW, Maag JL, et al. lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. Nucleic Acids Res 2015; 43: D168-73.
[24]
Chen G, Wang Z, Wang D, et al. LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res 2013; 41: D983-6.
[25]
Liao Q, Xiao H, Bu D, et al. ncFANs: a web server for functional annotation of long non-coding RNAs. Nucleic Acids Res 2011; 39W118-24
[26]
Jin J, Liu J, Wang H, Wong L, Chua NH. PLncDB: plant long non-coding RNA database. Bioinformatics 2013; 29: 1068-71.
[27]
Andreu Paytuví Gallart, Antonio Hermoso Pulido, Irantzu Anzar Martínez de Lagrán, Walter Sanseverino, Riccardo Aiese Cigliano. GREENC: a Wiki-based database of plant lncRNAs. Nucleic Acids Res 2016; 44: D1161-6.
[28]
Szczesniak MW, Rosikiewicz W, Makalowska I. CANTATAdb: A Collection of Plant Long Non-Coding RNAs. Plant Cell Physiol 2016; 57: e8
[29]
Wang L, Park HJ, Dasari S, et al. CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res 2013; 41e74
[30]
Goodstein DM, Shu S, Howson R, et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 2012; 40: D1178-86.
[31]
Gan X, Stegle O, Behr J, et al. Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 2011; 477: 419-23.
[32]
Luo C, Sidote DJ, Zhang Y, et al. Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production. Plant J 2013; 73: 77-90.
[33]
Kurihara Y, Schmitz RJ, Nery JR, et al. Surveillance of 3′ Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis. G3 2012; 2: 487-98.
[34]
Wang J, Tao F, Marowsky NC, Fan C. Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes. Plant Physiol 2016; 172: 427-40.
[35]
Trapnell C, Roberts A, Goff L, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012; 7: 562-78.
[36]
Bussotti G, Raineri E, Erb I, et al. BlastR--fast and accurate database searches for non-coding RNAs. Nucleic Acids Res 2011; 39: 6886-95.
[37]
Kin T, Yamada K, Terai G, et al. fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. Nucleic Acids Res 2007; 35: D145-8.
[38]
Shuai P, Liang D, Tang S, et al. Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa. J Exp Bot 2014; 65: 4975-83.
[39]
Doroshenk KA, Crofts AJ, Morris RT, Wyrick JJ, Okita TW. RiceRBP: A Resource for Experimentally Identified RNA Binding Proteins in Oryza sativa. Front Plant Sci 2012; 3: 90.
[40]
Hao Y, Wu W, Li H, et al. NPInter v3.0: an upgraded database of noncoding RNA-associated interactions. Database 2016 2016.
[41]
Bellucci M, Agostini F, Masin M, Tartaglia GG. Predicting protein associations with long noncoding RNAs. Nat Methods 2011; 8: 444-5.
[42]
Agostini F, Zanzoni A, Klus P, et al. catRAPID omics: a web server for large-scale prediction of protein-RNA interactions. Bioinformatics 2013; 29: 2928-30.
[43]
Buels R, Yao E, Diesh CM, et al. JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol 2016; 17: 66.
[44]
Ono K, Demchak B, Ideker T. Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. F1000 Res 2014; 3: 143.
[45]
Cirillo D, Agostini F, Klus P, et al. Quantitative predictions of protein-RNA interactions. RNA 2013; 19: 129-40.