Comparative analysis of miRNAs and their targets across four plant species

BMC Research Notes

Dirk Walther³  Patrick May²  Dorina Lenz¹ 

[1] LGC Genomics GmbH, Ostendstrasse 25, 12459 Berlin, Germany;Institute for Systems Biology, Seattle, WA, USA;Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany

关键词: next generation sequencing;    conservation;    miRNA targets;    miRNA;    plants;   

Others  :  1166972
DOI  :  10.1186/1756-0500-4-483

 received in 2011-07-05, accepted in 2011-11-08,  发布年份 2011

【 摘 要 】

Background

MicroRNA (miRNA) mediated regulation of gene expression has been recognized as a major posttranscriptional regulatory mechanism also in plants. We performed a comparative analysis of miRNAs and their respective gene targets across four plant species: Arabidopsis thaliana (Ath), Medicago truncatula(Mtr), Brassica napus (Bna), and Chlamydomonas reinhardtii (Cre).

Results

miRNAs were obtained from mirBase with 218 miRNAs for Ath, 375 for Mtr, 46 for Bna, and 73 for Cre, annotated for each species respectively. miRNA targets were obtained from available database annotations, bioinformatic predictions using RNAhybrid as well as predicted from an analysis of mRNA degradation products (degradome sequencing) aimed at identifying miRNA cleavage products. On average, and considering both experimental and bioinformatic predictions together, every miRNA was associated with about 46 unique gene transcripts with considerably variation across species. We observed a positive and linear correlation between the number miRNAs and the total number of transcripts across different plant species suggesting that the repertoire of miRNAs correlates with the size of the transcriptome of an organism. Conserved miRNA-target pairs were found to be associated with developmental processes and transcriptional regulation, while species-specific (in particular, Ath) pairs are involved in signal transduction and response to stress processes. Conserved miRNAs have more targets and higher expression values than non-conserved miRNAs. We found evidence for a conservation of not only the sequence of miRNAs, but their expression levels as well.

Conclusions

Our results support the notion of a high birth and death rate of miRNAs and that miRNAs serve many species specific functions, while conserved miRNA are related mainly to developmental processes and transcriptional regulation with conservation operating at both the sequence and expression level.

【 授权许可】

   
2010 Walther et al; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Ambros V: The functions of animal microRNAs. Nature 2004, 431:350-355.
• [2]Wienholds E, Plasterk RH: MicroRNA function in animal development. FEBS Lett 2005, 579:5911-5922.
• [3]Stark A, Brennecke J, Bushati N, Russell RB, Cohen SM: Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution. Cell 2005, 123:1133-1146.
• [4]Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA: Conservation and divergence of plant microRNA genes. Plant J 2006, 46:243-259.
• [5]Axtell MJ, Bowman JL: Evolution of plant microRNAs and their targets. Trends Plant Sci 2008, 13:343-349.
• [6]Axtell MJ, Bartel DP: Antiquity of microRNAs and their targets in land plants. Plant Cell 2005, 17:1658-1673.
• [7]Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC: High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One 2007, 2:e219.
• [8]Rajagopalan R, Vaucheret H, Trejo J, Bartel DP: A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 2006, 20:3407-3425.
• [9]Fahlgren N, Jogdeo S, Kasschau KD, Sullivan CM, Chapman EJ, Laubinger S, Smith LM, Dasenko M, Givan SA, Weigel D, Carrington JC: MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. Plant Cell 2010, 22:1074-1089.
• [10]Axtell MJ: Evolution of microRNAs and their targets: are all microRNAs biologically relevant? Biochim Biophys Acta 2008, 1779:725-734.
• [11]Pant BD, Musialak-Lange M, Nuc P, May P, Buhtz A, Kehr J, Walther D, Scheible WR: Identification of nutrient-responsive Arabidopsis and rapeseed microRNAs by comprehensive real-time polymerase chain reaction profiling and small RNA sequencing. Plant Physiol 2009, 150:1541-1555.
• [12]Devers EA, Branscheid A, May P, Krajinski F: Stars and symbiosis: microRNA- and microRNA*-mediated transcript cleavage involved in arbuscular mycorrhizal symbiosis. Plant Physiol 2011.
• [13]German MA, Pillay M, Jeong DH, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis LA, Nobuta K, German R, De Paoli E, Lu C, Schroth G, Meyers BC, Green PJ: Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 2008, 26:941-946.
• [14]Addo-Quaye C, Miller W, Axtell MJ: CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics 2009, 25:130-131.
• [15]Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ: miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, 36:D154-158.
• [16]Huala E, Dickerman AW, Garcia-Hernandez M, Weems D, Reiser L, LaFond F, Hanley D, Kiphart D, Zhuang M, Huang W, Mueller LA, Bhattacharyya D, Bhaya D, Sobral BW, Beavis W, Meinke DW, Town CD, Somerville C, Rhee SY: The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res 2001, 29:102-105.
• [17]Hsieh LC, Lin SI, Shih AC, Chen JW, Lin WY, Tseng CY, Li WH, Chiou TJ: Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiol 2009, 151:2120-2132.
• [18]Myers EW, Miller W: Optimal alignments in linear space. Comput Appl Biosci 1988, 4:11-17.
• [19]Alves L Jr, Niemeier S, Hauenschild A, Rehmsmeier M, Merkle T: Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana. Nucleic Acids Res 2009, 37:4010-4021.
• [20]Gustafson AM, Allen E, Givan S, Smith D, Carrington JC, Kasschau KD: ASRP: the Arabidopsis Small RNA Project Database. Nucleic Acids Res 2005, 33:D637-640.
• [21]Devers E, Branscheid P, May P, Kranjinski F: Stars and symbiosis: microRNA- and microRNA*-mediated transcript cleavage involved in arbuscular mycorrhizal symbiosis. Plant Physiology 2011, 111. 172627
• [22]Kruger J, Rehmsmeier M: RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res 2006, 34:W451-454.
• [23]Benjamini Y, Hochberg Y: Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological 1995, 57:289-300.
• [24]Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP: Prediction of plant microRNA targets. Cell 2002, 110:513-520.
• [25]Johnston JS, Pepper AE, Hall AE, Chen ZJ, Hodnett G, Drabek J, Lopez R, Price HJ: Evolution of genome size in Brassicaceae. Ann Bot 2005, 95:229-235.
• [26]Misumi O, Yoshida Y, Nishida K, Fujiwara T, Sakajiri T, Hirooka S, Nishimura Y, Kuroiwa T: Genome analysis and its significance in four unicellular algae, Cyanidioschyzon [corrected] merolae, Ostreococcus tauri, Chlamydomonas reinhardtii, and Thalassiosira pseudonana. J Plant Res 2008, 121:3-17.
• [27]Gutierrez MV, Vaz Patto MC, Huguet T, Cubero JI, Moreno MT, Torres AM: Cross-species amplification of Medicago truncatula microsatellites across three major pulse crops. Theor Appl Genet 2005, 110:1210-1217.