茄子microRNAs与其靶基因的生物信息学预测

doi:10.3724/SP.J.1005.2011.00776

遗传 ›› 2011, Vol. 33 ›› Issue (7): 776-784.doi: 10.3724/SP.J.1005.2011.00776

茄子microRNAs与其靶基因的生物信息学预测

张磊^1,2, 晁江涛¹, 崔萌萌¹, 陈雅琼^1,2, 宗鹏^1,2, 孙玉合¹

1. 中国农业科学院烟草研究所, 中国农业科学院烟草遗传改良与生物技术重点开放实验室, 青岛 266101 2. 中国农业科学院研究生院, 北京 100081

收稿日期:2011-03-27 修回日期:2011-04-27 出版日期:2011-07-20 发布日期:2011-07-25
通讯作者: 孙玉合 E-mail:yhsun@163.com
基金资助:
国家烟草专卖局重点科技项目(编号：110200701021)资助

Bioinformatic prediction of conserved microRNAs and their target genes in eggplant (Solanum melongena L.)

ZHANG Lei^1,2, CHAO Jiang-Tao¹, CUI Meng-Meng¹, CHEN Ya-Qiong^1,2, ZONG Peng^1,2, SUN Yu-He¹

1. Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Chinese Academy of Agricultural Sciences, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China 2. Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China

Received:2011-03-27 Revised:2011-04-27 Online:2011-07-20 Published:2011-07-25

摘要/Abstract

摘要： microRNAs(miRNAs)是一类在真核生物中发现的长度为21 nt左右、非编码、内源性的单链小分子RNA, 通过与靶基因的互补发挥转录后水平的负调控作用。目前, 已在许多物种中报道了miRNAs的存在, 然而还未见关于茄子miRNAs的报道。根据miRNAs在植物中的高度保守性及其前体的二级结构特征, 文章通过同源预测的方法, 将已知植物的miRNAs与茄子EST数据库比对, 经过一系列的筛选, 最终预测到12个家族的16条茄子miRNAs, 其中包括3个miRNA家族的正义/反义miRNAs, 而miR390和miR399家族的正义/反义miRNAs属于第一次发现。文章还通过在线软件psRNATarget预测到15条茄子miRNAs的71个靶基因, 这些靶基因主要编码与茄子生长发育、新陈代谢以及胁迫响应等过程相关的蛋白。

关键词: microRNAs(miRNAs), 靶基因, 生物信息学, EST, 茄子

Abstract: MicroRNAs (miRNAs), a recently discovered class of small (~21nt), non-coding, endogenous, single-stranded RNAs in eukaryotes, regulate gene expression negatively at the post-transcriptional levels depending on the extent of com-plementation between miRNA and mRNA. To date, a large number of miRNAs have been reported in many species, but none for eggplant (Solanum melongena L.). In this paper, a computational homology search approach based on the conservation of miRNA sequences and the stem-loop hairpin secondary structures of miRNAs was adopted. The search was started with the known plant miRNAs compared to eggplant expressed sequence tags (EST) databases to find potential miRNAs. Following a range of filtering criteria, a total of 16 potential miRNAs belonging to 12 families were identified. Three pairs of sense and antisense strand eggplant miRNAs belonging to three different miRNA families were also found. Furthermore, miR390 and miR399 sense/antisense pairs are identified for the first time in plants. Using online software psRNATarget, we further predicted the target genes of these 16 miRNAs and got 71 potential targets genes on base of 15 eggplant miRNAs. Most of these target genes were predicted to encode proteins that play key role in eggplant growth, de-velopment, metabolism, and stress responses.

Key words: target gene, bioinformatics, EST, eggplant(Solanum melongena L.), microRNAs (miRNAs)

张磊，晁江涛，崔萌萌，陈雅琼，宗鹏，孙玉合. 茄子microRNAs与其靶基因的生物信息学预测[J]. 遗传, 2011, 33(7): 776-784.

ZHANG Lei, CHAO Jiang-Chao, CUI Meng-Meng, CHEN Ya-Qiong, ZONG Feng, SUN Yu-Ge. Bioinformatic prediction of conserved microRNAs and their target genes in eggplant (Solanum melongena L.)[J]. HEREDITAS, 2011, 33(7): 776-784.

参考文献

[1] Bartel DP. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell, 2004, 116(2): 281-297.
[2] Zhang BH, Pan XP, Cobb GP, Anderson TA. Plant microRNA: A small regulatory molecule with big impact. Dev Biol, 2006, 289(1): 3-16.
[3] Chen XM. MicroRNA biogenesis and function in plants. FEBS Lett, 2005, 579(26): 5923-5931.
[4] Taylor PF, Zhang BH. Identification of plant microRNAs using expressed sequence tag analysis. Methods Mol Biol, 2011, 678: 13-25.
[5] Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 1993, 75(5): 843-854.
[6] Baker CC, Sieber P, Wellmer F, Meyerowitz EM. The early extra petals1 mutant uncovers a role for microRNA miR164c in regulating petal number in Arabidopsis. Curr Biol, 2005, 15(4): 303-315.
[7] Jones-Rhoades MW, Bartel DP, Bartel B. MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol, 2006, 57(1): 19-53.
[8] 卫波, 张荣志, 李爱丽, 毛龙. 利用高通量测序技术发现植物小分子RNA研究进展. 中国农业科学, 2009, 42(11): 3755-3764.
[9] Zhang BH, Pan XP, Cannon CH, Cobb GP, Anderson TA. Conservation and divergence of plant microRNA genes. Plant J, 2006, 46(2): 243-259.
[10] Floyd SK, Bowman JL. Gene regulation: ancient mi-croRNA target sequences in plants. Nature, 2004, 428(6982): 485-486.
[11] Wang JF, Zhou H, Chen YQ, Luo QJ, Qu LH. Identification of 20 microRNAs from Oryza sativa. Nucleic Acids Res, 2004, 32(5): 1688-1695.
[12] Jones-Rhoades MW, Bartel DP. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell, 2004, 14(6): 787-799.
[13] Zhang BH, Pan XP, Wang QL, Cobb GP, Anderson TA. Identification and characterization of new plant microR-NAs using EST analysis. Cell Res, 2005, 15(5): 336-360.
[14] Yin ZJ, Li CH, Han XL, Shen FF. Identification of con-served microRNAs and their target genes in tomato (Lycopersicon esculentum). Gene, 2008, 414(1-2): 60-66.
[15] Zhang BH, Wang QL, Wang KB, Pan XP, Liu F, Gou TL, Cobb GP, Anderson TA. Identification of cotton microR-NAs and their targets. Gene, 2007, 397(1-2): 26-37.
[16] Zhang BH, Pan XP, Anderson TA. Identification of 188 conserved maize microRNAs and their targets. FEBS Lett, 2006, 580(15): 3753-3762.
[17] Lang QL, Jin CZ, Lai LY, Feng JL, Chen SN, Chen JH. Tobacco microRNAs prediction and their expression infected with Cucumber mosaic virus and Potato virus X. Mol Biol Rep, 2010, 38(3): 1523-1531.
[18] Frazier TP, Xie FL, Freistaedter A, Burklew CE, Zhang BH. Identification and characterization of microRNAs and their target genes in bobacco (Nicotiana tabacum). Planta, 2010, 232(6): 1289-1308.
[19] Daunay MC, Lester RN. The usefulness of taxonomy for Solanaceae breeders, with special reference to the genus Solanum and to Solanum melongena L. (eggplant). Capsicum Newslett, 1988, (7): 70-79.
[20] Griffiths-Jones S, Saini HK, Dongen SV, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res, 2008, 36(S1): D154-D158.
[21] Song CN, Fang JG, Wang C, Guo L, Nicholas KK, Ma ZQ. MiR-RACE, a new efficient approach to determine the precise sequences of computationally identied trifoliate orange (Poncirus trifoliata) microRNAs. PLoS ONE, 2010, 5(6): e10861.
[22] Dsouza M, Larsen N, Overbeek R. Searching for patterns in genomic data. Trends Genet, 1997, 13(12): 497-498.
[23] Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P. Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie, 1994, 125(2): 167-188.
[24] Dai XB, Zhuang ZH, Zhao PX. Computational analysis of miRNA targets in plants: current status and challenges. Brief

编辑推荐

Metrics

www.chinagene.cn
备案号：京ICP备09063187号-4
总访问:,今日访问:,当前在线:

茄子microRNAs与其靶基因的生物信息学预测

Bioinformatic prediction of conserved microRNAs and their target genes in eggplant (Solanum melongena L.)

PDF (PC)

可视化

被引次数

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

[1]	王姗姗, 赵琬怡, 吴慧潇, 舒梦, 袁嘉欣, 方丽, 徐潮. 特发性低促性腺激素性性腺功能减退症FGFR1与CEP290基因变异研究[J]. 遗传, 2022, 44(10): 937-949.
[2]	向虹, 阳小胡, 艾亮霞, 潘燕平, 胡勇. 脱发相关差异表达基因的生物信息学分析[J]. 遗传, 2020, 42(2): 172-182.
[3]	吕红强, 郝乐乐, 刘二虎, 吴志芳, 韩九强, 刘源. 基于生物信息学的Hi-C研究现状与发展趋势[J]. 遗传, 2020, 42(1): 87-99.
[4]	卢涣滋,王迪侃,王智. HPV阳性口咽癌患者预后与T细胞浸润和新抗原负荷相关性分析[J]. 遗传, 2019, 41(8): 725-735.
[5]	黄子莹, 李龙, 李倩倩, 刘向东, 李长春. lncRNA TCONS_00815878对猪骨骼肌卫星细胞分化的影响[J]. 遗传, 2019, 41(12): 1119-1128.
[6]	张源笙,夏琳,桑健,李漫,刘琳,李萌伟,牛广艺,曹佳宝,滕徐菲,周晴,章张. 生命与健康大数据中心资源[J]. 遗传, 2018, 40(11): 1039-1043.
[7]	李俊涛,赵薇,李丹丹,冯静,巴贵,宋天增,张红平. miR-101a靶向EZH2促进山羊骨骼肌卫星细胞的分化[J]. 遗传, 2017, 39(9): 828-836.
[8]	向小华, 吴新儒, 晁江涛, 杨明磊, 杨帆, 陈果, 刘贯山, 王元英. 普通烟草WRKY基因家族的鉴定及表达分析[J]. 遗传, 2016, 38(9): 840-856.
[9]	徐妙云, 朱佳旭, 张敏, 王磊. 植物miR169/NF-YA调控模块研究进展[J]. 遗传, 2016, 38(8): 700-706.
[10]	李晓旭, 刘成, 李伟, 张增林, 高晓明, 周慧, 郭永峰. 番茄WOX转录因子家族的鉴定及其进化、表达分析[J]. 遗传, 2016, 38(5): 444-460.
[11]	吴骏,张俊红,黄蒙慧,朱敏慧,童再康. 光皮桦miR164及其靶基因NAC1在低氮胁迫中的表达分析[J]. 遗传, 2016, 38(2): 155-162.
[12]	周学, 杜宜兰, 金萍, 马飞. 癌症相关microRNA与靶基因的生物信息学分析[J]. 遗传, 2015, 37(9): 855-864.
[13]	方翔, 李宁求, 付小哲, 李凯彬, 林强, 刘礼辉, 石存斌, 吴淑勤. 基于“天河二号”的水产病原生物信息分析平台构建及其在水产病原分析中的应用[J]. 遗传, 2015, 37(7): 702-710.
[14]	邱红梅，郝文媛，高淑芹，马晓萍，郑宇宏，孟凡凡，范旭红，王洋，王跃强，王曙明. 大豆含硫氨基酸相关酶基因发掘[J]. 遗传, 2014, 36(9): 934-942.
[15]	施杨, 徐筱, 李昊阳, 徐倩, 徐吉臣. 水稻扩展蛋白家族的生物信息学分析[J]. 遗传, 2014, 36(8): 809-820.