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Acta Agron Sin ›› 2010, Vol. 36 ›› Issue (08): 1324-1335.doi: 10.3724/SP.J.1006.2010.01324

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Bioinformatic Prediction of MicroRNAs and Their Target Genes in Maize

ZHANG Zhi-Ming,SONG Rui,PENG Hua,LUO Mao,SHEN Ya-Ou,LIU Li,ZHAO Mao-Jun,PAN Guang-Tang*   

  1. Maize Research Institute,Sichuan Agricultural University,Ya'an 625014,China
  • Received:2009-12-30 Revised:2010-04-16 Online:2010-08-12 Published:2010-05-20
  • Contact: PAN Guang-Tang, E-mail: pangt1956@yahoo.com.cn; Tel: 0835-2882714

Abstract: microRNAs (miRNAs) are an extensive class of endogenous, non-coding, short (19–24 nt) RNA molecules directly involved in regulating gene expression at the post-transcriptional level and played an important role in gene expression regulation. Previous reports have noted that plant miRNAs are highly conserved, which provides the foundation for identification of miRNAs in plant species through homology alignment. With the method of bioinformatic computation, all previously known miRNAs in Arabidopsis, rice, and other plant species were blasted against maize EST (expressed sequence tags) and GSS (genomic survey sequence) sequences to select novel miRNAs in maize by a series of filtering criteria. A total of 23 conserved miRNAs were identified and predicted the target genes by a web-based integrated computing system, WMD 3. Total of 89 miRNA targets were predicted and verified to be involved in maize growth and development, signal transduction, transcriptional regulation, metabolism, and stress responses.

Key words: microRNA, Bioinformatics, Prediction Target genes, Maize

[1]Bartel D P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 2004, 116: 281-297
[2]Jin L-G(金龙国), Wang C(王川), Liu J-Y(刘进元). Plant micro RNA. Chin J Biochem Mol Biol (中国生物化学与分子生物学报), 2006, 22(8): 609-614 (in Chinese with English abstract)
[3]Jones-Rhoades M W, Bartel D P, Bartel B. MicroRNAs and their regulatory roles in plants
[J].Annu Rev Plant Biol
[4]Zhang B, Pan X, Cannon C H, Cobb G P, Anderson T A. Conservation and divergence of plant microRNA genes
[J].Plant J
[5]Arazi T, Talmor-Neiman M, Stav R, Riese M, Huijser P, Baulcombe D C. Cloning and characterization of microRNAs from moss
[J].Plant J
[6]Sunkar R, Zhu J K. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis
[J].Plant Cell
[7]Sunkar R, Girke T, Jain P K, Zhu J K. Cloning and characterization of microRNAs from rice
[J].Plant Cell
[8]Griffiths-Jones S, Grocock R J, van Dongen S, Bateman A, Enright A J. miRBase: microRNA sequences, targets and gene nomenclature
[J].Nucl Acids Res
[9]Lee R C, Feinbaum R L, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 1993, 75: 843-854
[10]Moxon S, Jing R, Szittya G, Schwach F, Rusholme Pilcher R L, Moulton V, Dalmay T. Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening
[J].Genome Res
[11]Qiu D Y, Pan X P, Wilson W I, Li F, Liu M, Teng W, Zhang B. High throughput sequencing technology reveals that the taxoid elicitor methyl jasmonate regulates microRNA expression in Chinese yew (Taxus chinensis). Gene, 2009, 436: 37-44
[12]Jones-Rhoades M W, Bartel D P. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA
[J].Mol Cell
[13]Bonnet E, Wuyts J, Rouzé P, Van de Peer Y. Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important targets
[J].Proc Natl Acad Sci USA
[14]Zhang B H, Pan X P, Wang Q L, Cobb G P, Anderson T A. Identification and characterization of new plant microRNAs using EST analysis
[J].Cell Res
[15]Llave C, Xie Z, Kasschau K D, Carrington J C. Cleavage of scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science, 2002, 297: 2053-2056
[16]Ye M(叶茂), Chen Y-L(陈跃磊), Ming Z-H(明镇寰). Progress in the research of miRNAs (microRNAs) family. Prog Biochem Biophys (生物化学与生物物理进展), 2003, 30(3): 370-374 (in Chinese with English abstract)
[17]Ossowski S, Schwab R, Weigel D. Gene silencing in plants using artificial microRNAs and other small RNAs
[J].Plant J
[18]Ambros V. A uniform system for microRNA annotation. RNA, 2003, 9: 277-279
[19]Zhang Q(张旗), He X-J(何湘君), Pan X-Y(潘秀英). Real-time quantification of microRNAs by RNA-tailing and primer- extension RT-PCR. J Peking Univ (Health Sci), 2007, 39(1): 87-91
[20]Hu X-L(胡晓丽), Li D-Q(李德全). Protein phosphatase 2C in plants and its functions of signal transduction. Plant Physiol Commun (植物生理学通讯), 2007, 43(3): 407-410 (in Chinese with English abstract)
[21]Hu X-B(胡学博), Song F-M(宋凤鸣), Zheng Z(郑重). The structure and function of protein phosphatase 2Cs in higher plants. Chin J Cell Biol (细胞生物学杂志), 2005, 27(): 29-34 (in Chinese with English abstract)
[22]Schweighofer A, Hirt H, Meskiene I. Plant PP2C phosphatases: emerging functions in stress signaling
[J].Trends Plant Sci
[23]Demarco A, Roubelakis-Angelakis K A. Laccase activity could contribute to cell wall reconstitution of regenerating protoplasts
[J].Phytochemistry
[24]Li L, Steffen S J C. Overexpression of polyphenol oxidase in transgenic tomato plants results in enhanced bacterial disease resistance. Planta, 2002, 215: 239-247
[25]Pourcel L, Routaboul J M, Kerhoas L, Caboche M, Lepiniec L, Debeaujon I. Transparent TESTA 10 encodes a laccase-like enzyme involved in oxidative polymerization of flavonoids in arabidopsis seed coat
[J].Plant Cell
[26]Wang G-D(王国栋), Chen X-Y(陈晓亚). The properties, functions, catalytic mechanism and applicability of laccase. Chin Bull Bat (植物学通报), 2003, 20(4): 469-475 (in Chinese with English abstract)
[27]Zhang L F, Chia J, Kumari S, Stein J C, Liu Z J, Narechania A, Maher C A, Guill K, McMullen M D, Ware D. A genome-wide characterization of microRNA genes in maize. PLoS Genet, 2009, 5(11): e1000716
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