microRNA (miRNA)是一类具有20~24 nt 核苷酸长度的非蛋白质编码的内源小分子RNA, 它在植物生长发育和逆境胁迫响应等过程中发挥着重要作用。文章利用基于Illumina/Solexa原理的小分子RNA深度测序技术, 结合生物信息学的方法对玉米根系和叶片中已知miRNA的类型、丰度及靶基因进行了分析。研究发现, 在根系中共检测到92个已知的miRNA, 分别属于18个miRNA家族, 其表达丰度在1~105 943之间; 在叶片中, 共发现86个已知的miRNA, 分别属于17个miRNA家族, 其表达丰度在1~85 973之间。靶基因预测结果表明, 根系中的18个miRNA家族共靶向54个蛋白, 进一步的功能预测发现, 这些基因涉及了转录调控、物质能量代谢、电子传递、胁迫响应和信号转导等过程。以上研究结果表明, 就已知的miRNA而言, 无论是miRNA的类型还是表达丰度, 在玉米根系和叶片中都存在较大差异。
microRNA (miRNAs) is a newly identified class of 20~24 nt non-protein-coding and endogenous small RNA, which plays an important role in plant growth, development and response to environmental stresses. Combined with bioinformatic method, the types, abundance, and targets of known miRNAs in root and leaf of maize (Zea mays L.) were analyzed by small RNA deep sequencing technology, which was based on Illumina/Solexa principium. The results indicated that 92 known miRNAs were detected in maize root, which were attributed to 18 miRNA families and their abundance ranged from 1 to 105 943 reads. Synchronously, 86 known miRNAs were detected in maize leaf, which were attributed to 17 miRNA families and their abundance ranged from 1 to 85 973 reads. The target gene prediction showed that 54 putative target genes as these known miRNAs were predicted. Some of them were involved in the following processes, such as tran-scription regulation, substance and energy metabolism, electron transport, stress response, and signal transduction through further function prediction. In conclusion, there were obvious differences in both types and abundance of known miRNAs between root and leaf in maize.
[1] Lee RC, Feinbaum RL, Ambros V. The C. elegans hetero-chronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 1993, 75(5): 843–854.
[2] Sunkar R, Zhu JK. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell, 2004, 16(8): 2001–2019.
[3] Reddy AM, Zheng Y, Jagadeeswaran G, Macmil SL, Gra-ham WB, Roe BA, Desilva U, Zhang WX, Sunkar R. Cloning, characterization and expression analysis of por-cine microRNAs. BMC Genomics, 2009, 10: 65, 1–15.
[4] Arazi T, Talmor-Neiman M, Stav R, Riese M, Huijser P, Baulcombe DC. Cloning and characterization of mi-cro-RNAs from moss. Plant Journal, 2005, 43(6): 837–848.
[5] Sunkar R, Girke T, Jain P K and Zhu JK. Cloning and characterization of microRNAs from rice. Plant Cell, 2005, 17(5): 1397–1411.
[6] Erica M, Luca G, Mario E P. Characterization of five mi-croRNA families in maize. J Exp Bot, 2006, 57(11): 2601–2612.
[7] Yao YY, Guo GG, Ni ZF, Sunkar R, Du JK, Zhu JK, Sun QX. Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). Genome Biol, 2007, 8(6): R96.1–15.
[8] Lu SF, Sun YH, Shi R, Clark C, Li LG, Chiang VL. Novel and mechanical stress–responsive microRNAs in populus trichocarpa that are absent from arabidopsis. Plant Cell, 2005, 17(8): 2186–2203.
[9] Carrington JC, Ambros V. Role of microRNAs in plant and animal development. Science, 2003, 301(5631): 336–338.
[10] Bartel DP. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell, 2004, 116(2): 281–297.
[11] Jones-Rhoades MW, Bartel DP. Computational identifica-tion of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell, 2004, 14(6): 787–799.
[12] Sunkar R, Kapoor A, Zhu JK. Posttranscriptional induc-tion of two Cu/Zn superoxide dismutase genes in Arabi-dopsis is mediated by downregulation of miR398 and im-portant for oxidative stress tolerance. Plant Cell, 2006, 18(8): 2051–2065.
[13] Bernstein E, Caudy AA, Hammond SM and Hannon GJ. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 2001, 409(6818): 363–366.
[14] Jones-Rhoades MW, Bartel DP, Bartel B. MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol, 2006, 57: 19–53.
[15] Axtell MJ, Bartel DP. Antiquity of microRNAs and their targets in land plants. Plant Cell, 2005, 17(6): 1658–1673.
[16] Zhang BH, Pan XP, Wang QL, Cobb GP and Anderson TA. Identification and characterization of new plant microR-NAs using EST analysis. Cell Res, 2005, 15(5): 336–360.
[17] Glazov EA, Cottee PA, Barris WC, Moore RJ, Dalrymple BP, Tizard ML. A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res, 2008, 18(6): 957–964.
[18] Moxon S, Jing RC, Szittya G, Schwach F, Rusholme Pil-cher RL, Moulton V, Dalmay T. Deep sequencing of to-mato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res, 2008, 18(10): 1602–1609.
[19] Wei B, Cai T, Zhang RZ, Li AL, Huo NX, Li S, Gu YQ, Vogel J, Jia JZ, Qi YJ, Mao L. Novel microRNAs uncov-ered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv. Funct Integr Genomics, 2009, 9(4): 499–511.
[20] Wang JW, Wang LJ, Mao YB, Cai WJ, Xue HW, Chen XY. Control of root cap formation by microRNA-targeted auxin response factors in Arabidopsis. Plant Cell, 2005, 17(8): 2204–2216.
[21] Palatnik JF, Allen E, Wu XL, Schommer C, Schwab R, Carrington JC, Weigel D. Control of leaf morphogenesis by microRNAs. Nature, 2003, 425(6955): 257–263.
[22] Schwab R, Palatnik J, Riester M, Schommer C, Schmid M, Weigel D. Specific
