短串联靶标模拟技术及其在植物miRNA功能研究中的应用

doi:10.13560/j.cnki.biotech.bull.1985.2020-0257

摘要/Abstract

摘要：

MicroRNA（miRNA）作为一类大小长约21-24个核苷酸的内源非编码RNA,通过影响靶基因mRNA的稳定性或者翻译过程调控基因的表达。随着现代分子生物学技术的发展,越来越多的研究表明miRNA在植物的生长和发育过程中发挥着重要的作用。但是,miRNA功能研究缺乏有效的、适用性广的方法。介绍了一种可以特异地靶标miRNA方法,即短串联靶标模拟（Short tandem target mimic,STTM）,并对STTM的基本特点和作用机制、与其他类似技术的比较以及其在植物中miRNA功能研究中的应用等方面进行了总结,有望为今后植物miRNA的功能研究提供技术参考。

关键词: 植物, 短串联靶标模拟, miRNA, 调控机制

Abstract:

MicroRNA（miRNA）,a class of endogenous non-coding RNAs in about 21-24 nucleotides length,regulates gene expression by affecting the stability of target mRNA or by regulating the process of translation. With the development of modern molecular biology technology,more and more studies demonstrated that miRNAs play an important role in the growth and development of plants. However,in the miRNA function research,more effective and widely applicable methods are needed. Here,a specific miRNA targeting method is introduced,namely Short Tandem Target Mimic（STTM）. The basic characteristics,function mechanism of STTM,comparison with other similar technologies,and its application in the study of miRNA function in plants are described,which may provide a technical reference for the study of plant miRNA function in the future.

Key words: plant, STTM, miRNA, regulatory mechanism

郑文清, 张倩, 杜亮. 短串联靶标模拟技术及其在植物miRNA功能研究中的应用[J]. 生物技术通报, 2020, 36(12): 256-264.

ZHENG Wen-qing, ZHANG Qian, DU Liang. Short Tandem Target Mimic and Its Application in Analyzing Plant miRNA Functions[J]. Biotechnology Bulletin, 2020, 36(12): 256-264.

图/表 4

参考文献 60

[1]	Brosnan CA, Voinnet O. The long and the short of noncoding RNAs[J]. Current Opinion Cell Biology, 2009,21(3):416-425.
[2]	Ghildiyal M, Zamore PD[J]. Small silencing RNAs:an expanding universe[J]. Nature Reviews Genetics, 2009,10(2):94-108. URL pmid: 19148191
[3]	Matzke M, Kanno T, Daxinger L, et al. RNA-mediated chromatin-based silencing in plants[J]. Current Opinion Cell Biology, 2009,21(3):367-376.
[4]	Simon SA, Meyers BC. Small RNA-mediated epigenetic modifications in plants[J]. Current Opinion Plant Biology, 2011,14(2):148-155.
[5]	Jones-rhoades MW, Bartel DP, Bartel B. MicroRNA_S and their regulatory roles in plants[J]. Annual Review of Plant Biology, 2006,57:19-53. URL pmid: 16669754
[6]	Sam GJ, Harpreet Kaur S, Stijn VD, et al. MiRBase:tools for microRNA genomics[J]. Nucleic Acids Research, 2008,36:D154-D158. URL pmid: 17991681
[7]	Kan N, Mccormick K, Nakano M, et al. Bioinformatics analysis of small RNAs in plants using next generation sequencing technologies[J]. Methods in Molecular Biology, 2010,592:89-106. URL pmid: 19802591
[8]	Till BJ, Reynolds SH, Greene EA, et al. Large-scale discovery of induced point mutations with high-throughput TILLING[J]. Genome Research, 2003,13(3):524-530. doi: 10.1101/gr.977903 URL pmid: 12618384
[9]	Baker CC, Patrick S, Frank W, et al. The early extra petals1 mutant uncovers a role for microRNA miR164c in regulating petal number in Arabidopsis[J]. Current Biology:CB, 2005,15(4):303-315. URL pmid: 15723790
[10]	Sha a, Zhao J, Yin K, et al. Virus-based microRNA silencing in plants[J]. Plant Physiology, 2014,164(1):36-47. URL pmid: 24296072
[11]	Franco-Zorrilla JM, Valli A, Todesco M, et al. Target mimicry provides a new mechanism for regulation of microRNA activity[J]. Nature Genetics, 2007,39(8):1033-1037. URL pmid: 17643101
[12]	Ebert MS, Neilson JR, Sharp PA. MicroRNA sponges:competitive inhibitors of small RNAs in mammalian cells[J]. Nature Methods, 2007,4(9):721-726. URL pmid: 17694064
[13]	Ebert MS, Sharp PA. MicroRNA sponges:progress and possibilities[J]. RNA, 2010,16(11):2043-2050. URL pmid: 20855538
[14]	Ebert MS, Sharp PA. Emerging roles for natural microRNA sponges[J]. Current Biology, 2010,20(19):858-861.
[15]	Kluiver J, Slezak-Prochazka I, Smigielska-Czepiel K, et al. Generation of miRNA sponge constructs[J]. Methods, 2012,58(2):113-117. doi: 10.1016/j.ymeth.2012.07.019 URL pmid: 22836127
[16]	Haraguchi T, Ozaki Y, Iba H. Vectors expressing efficient RNA decoys achieve the long-term suppression of specific microRNA activity in mammalian cells[J]. Nucleic Acids Research, 2009,37(6):e43.
[17]	Xie J, Ameres S L, Friedline R, et al. Long-term, efficient inhibition of microRNA function in mice using rAAV vectors[J]. Nature Methods, 2012,9(4):403-409. URL pmid: 22388288
[18]	Yan J, Gu Y, Jia X, et al. Effective small RNA destruction by the expression of a short tandem target mimic in Arabidopsis[J]. Plant Cell, 2012,24(2):415-427. URL pmid: 22345490
[19]	Wong J, Gao L, Yang Y, et al. Roles of small RNAs in soybean defense against Phytophthora sojae infection[J]. Plant Journal, 2014,79(6):928-940.
[20]	Cao D, Wang J, Ju Z, et al. Regulations on growth and development in tomato cotyledon, flower and fruit via destruction of miR396 with short tandem target mimic[J]. Plant Science, 2016,247:1-12. URL pmid: 27095395
[21]	Gu Z, Huang C, Li F, Zhou X. A versatile system for functional analysis of genes and microRNAs in cotton[J]. Plant Biotechnology Journal, 2014,12(5):638-649. doi: 10.1111/pbi.12169 URL pmid: 24521483
[22]	Jiao J, Wang Y, Selvaraj JN, et al. Barley stripe mosaic virus(BSMV)induced microRNA silencing in common wheat(Triticum aestivum L.)[J]. PLoS One, 2015,10(5):e0126621. URL pmid: 25955840
[23]	李赵杰, 简超, 刘香利, 等. Tae-miR9677小串联模拟靶标(STTM)表达载体构建及小麦的遗传转化研究[J]. 麦类作物学报, 2016,36(4):404-408.
	Li ZJ, Jian C, Liu XL, et al. Construction of expression vector of Tae-miR9677 short tandem target mimic(STTM)and transformation in Wheat[J]. Journal of Triticeae Crops, 2016,36(4):404-408.
[24]	Zhang H, Zhang J, Yan J, et al. Short tandem target mimic rice lines uncover functions of miRNAs in regulating important agronomic traits[J]. Proceedings of the National Academy of Sciences, 2017,114(20):5277-5282.
[25]	Peng T, Qiao M, Liu H, et al. A Resource for inactivation of microRNAs using short tandem target mimic technology in model and crop plants[J]. Molecular Plant, 2018,11:1400-1417. doi: 10.1016/j.molp.2018.09.003 URL pmid: 30243763
[26]	Tang G, Yan J, Gu Y, et al. Construction of short tandem target mimic(STTM)to block the functions of plant and animal microRNAs[J]. Methods, 2012,58(2):118-125. URL pmid: 23098881
[27]	Tang , G . siRNA and miRNA:an insight into RISCs[J]. Trends in Biochemical Sciences, 2005,30(2):106-114. URL pmid: 15691656
[28]	Takeshi H, Yuka O, Hideo I. Vectors expressing efficient RNA decoys achieve the long-term suppression of specific microRNA activity in mammalian cells[J]. Nucleic Acids Research, 2009,37(6):e43. URL pmid: 19223327
[29]	Yanli W, Stefan J, Haitao L, et al. Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex[J]. Nature, 2009,456(7224):921-926. URL pmid: 19092929
[30]	Ramachandran V, Chen X. Degradation of microRNAs by a family of exoribonucleases in Arabidopsis[J]. Science, 2008,321(5895):1490-1492. URL pmid: 18787168
[31]	Todesco M, Rubio-Somoza I, Paz-Ares J, et al. A collection of target mimics for comprehensive analysis of microRNA function in Arabidopsis thaliana[J]. PLoS Genetics, 2010,6(7):e1001031. URL pmid: 20661442
[32]	Tang G, Tang X. Short tandem target mimic:a long journey to the engineered molecular landmine for selective destruction/blockage of microRNAs in plants and animals[J]. Journal of Genetics and Genomics, 2013,40(6):291-296. doi: 10.1016/j.jgg.2013.02.004 URL pmid: 23790628
[33]	Reichel M, Li Y, Li J, et al. Inhibiting plant microRNA activity:molecular SPONGEs, target MIMICs and STTMs all display variable efficacies against target micro RNAs[J]. Plant Biotechnology Journal, 2015,13(7):915-926. URL pmid: 25600074
[34]	杨天啸. 利用 STTM 技术分析拟南芥 miR160 和 miR165/166的互作网络及玉米 miR166 的初步功能[D]. 郑州:河南农业大学, 2018.
	Yang TX. Dissecting the molecular mechanism of miR160 and miR165/166 interaction in Arabidopsis and miR166 functions in maize[D]. Zhengzhou:Henan Agricultural University, 2018.
[35]	Rhoades MW, Reinhart BJ, Lim LP, et al. Prediction of plant microRNA targets[J]. Cell, 2002,110(4):513-520. doi: 10.1016/s0092-8674(02)00863-2 URL pmid: 12202040
[36]	Prigge MJ, Denichiro O, Alonso JM, et al. Class III homeodomain-leucine zipper gene family members have overlapping, antagonistic, and distinct roles in Arabidopsis development[J]. Plant Cell, 2005,17(1):61-76. URL pmid: 15598805
[37]	Guiliang T, Reinhart B J, Bartel DP, et al. A biochemical framework for RNA silencing in plants[J]. Genes & Development, 2003,17(1):49-63. URL pmid: 12514099
[38]	Kim J, Jung JH, Reyes JL, et al. MicroRNA-directed cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems[J]. The Plant Journal, 2005,42(1):84-94. doi: 10.1111/j.1365-313X.2005.02354.x URL pmid: 15773855
[39]	Leor W, Grigg SP, Mingtang X, et al. Regulation of Arabidopsis shoot apical meristem and lateral organ formation by microRNA miR166g and its AtHD-ZIP target genes[J]. Development, 2005,132(16):3657-3668. doi: 10.1242/dev.01942 URL pmid: 16033795
[40]	Jae-Hoon J, Chung-Mo P. MIR166/165 genes exhibit dynamic expression patterns in regulating shoot apical meristem and floral development in Arabidopsis[J]. Planta, 2007,225(6):1327-1338. doi: 10.1007/s00425-006-0439-1 URL pmid: 17109148
[41]	Mallory A, Reinhart BR, Mw Tang G, et al. MicroRNA control of PHABULOSA in leaf development:importance of pairing to the microRNA 5'region[J]. EMBO J, 2014,23(16):3356-3364. doi: 10.1038/sj.emboj.7600340 URL pmid: 15282547
[42]	Sakaguchi J, Watanabe Y. MiR165/166 and the development of land plants[J]. Development Growth & Differentiation, 2012,54(1):93-99.
[43]	Otsuga D, Deguzman B, Prigge MJ, et al. REVOLUTA regulates meristem initiation at lateral positions[J]. Plant Journal, 2010,25(2):223-236.
[44]	Yang T, Wang Y, Teotia S, et al. The Interaction between miR160 and miR165/166 in the control of leaf development and drought tolerance in Arabidopsis[J]. Scientific Reports, 2019,9(1):2832. doi: 10.1038/s41598-019-39397-7 URL pmid: 30808969
[45]	Zhang J, Zhang H, Srivastavaa K, et al. Knockdown of rice microRNA166 confers drought resistance by causing leaf rolling and altering stem xylem development[J]. Plant Physiology, 2018,176(3):2082-2094. URL pmid: 29367235
[46]	王慧杰, 杨杨, 严孙艺, 等. STTM165/166转化水稻的初步研究[J]. 杂交水稻, 2017,32(5):56-60.
	Wang HJ, Yang Y, Yan SY, et al. A preliminary study on transformation of STTM165/166 into rice[J]. Hybrid Rice, 2017,32(5):56-60.
[47]	Jia X, Ding N, Fan W, et al. Functional plasticity of miR165/166 in plant development revealed by small tandem target mimic[J]. Plant Science, 2015,233:11-21. doi: 10.1016/j.plantsci.2014.12.020 URL pmid: 25711809
[48]	Gu Z, Huang C, Li F, et al. A versatile system for functional analysis of genes and microRNA s in cotton[J]. Plant Biotechnology Journal, 2014,12:638-649. URL pmid: 24521483
[49]	Liu X, Liu S, Wang R, et al. Analyses of MiRNA functions in maize using a newly developed ZMBJ-CMV-2b N81-STTM vector[J]. Frontiers in Plant Science, 2019,10:1277. doi: 10.3389/fpls.2019.01277 URL pmid: 31681375
[50]	曹东艳. miR396在番茄果实生长发育中的功能研究[D]. 北京:中国农业大学, 2018.
	Cao DY. Functional identification of miR396 on tomato fruit growth and development[D]. Beijing:China Agricultural University, 2018.
[51]	Jiang N, Meng J, Cui J, et al. Function identification of miR482b, a negative regulator during tomato resistance to Phytophthora infestans[J]. Horticulture Research, 2018,5:9. doi: 10.1038/s41438-018-0017-2 URL pmid: 29507733
[52]	Canto-Pastor A, Santos B, Valli A, et al. Enhanced resistance to bacterial and oomycete pathogens by short tandem target mimic RNAs in tomato[J]. Proceedings of the National Academy of Sciences, 2019,116(7):2755-2760.
[53]	Guo G, Liu X, Sun F, et al. Wheat miR9678 affects seed germination by generating phased siRNAs and modulating abscisic acid/gibberellin signaling[J]. Plant Cell, 2018,30(4):796-814. URL pmid: 29567662
[54]	Proust H, Bazin J, Sorin C, et al. Stable inactivation of microRNAs in Medicago truncatula[J]. Methods Molecular Biology, 2018,1822:123-132.
[55]	Wong J, Gao L, Yang Y, et al. Roles of small RNAs in soybean defense against Phytophthora sojae infection[J]. Plant Journal, 2014,79:928-940. doi: 10.1111/tpj.12590 URL
[56]	Bao D, Ganbaatar O, Cui X, et al. Down-regulation of genes coding for core RNAi components and disease resistance proteins via corresponding microRNAs might be correlated with successful soybean mosaic virus infection in soybean[J]. Molecular Plant Pathology, 2018,19:948-960. URL pmid: 28695996
[57]	Su Y, Li H, Wang Y, et al. Poplar miR472a targeting NBS-LRRs is involved in effective defense response to necrotrophic fungus Cytospora chrysosperma[J]. Journal Experimental Botany, 2018,69(22):5519-5530.
[58]	梁澜. PtrmiR164a在杨树次生细胞壁合成过程中的功能研究[D]. 重庆:西南大学, 2017.
	Liang L. Functional characterization of PtrmiR164a invoved in the regulation of secondary cell wall in Populus[D]. Chongqing:Southwest University, 2017.
[59]	Sosa-Valencia G, Palomar M, Covarrubias A, et al. The legume miR1514a modulates a NAC transcription factor transcript to trigger phasiRNA formation in response to drought[J]. Journal Experimental Botany, 2017,68:2013-2026.
[60]	Liu J, Cheng X, Liu D, et al. The miR9863 family regulates distinct Mla alleles in barley to attenuate NLR receptor-triggered disease resistance and cell-death signaling[J]. PLoS Genetics, 2014,10(12):e1004755. doi: 10.1371/journal.pgen.1004755 URL pmid: 25502438

技术	结构	作用机制	优点	缺点
TM	1个结合位点无连接序列3个碱基的错配	RISC-RNA interaction	构建较容易	不适用于有多个成员的miRNA家族
SP	4-15个结合位点连接序列4 nt2个碱基的错配	RISC-RNA interaction	在动物中沉默效果较好	构建困难
STTM	2个结合位点连接序列48-88 nt3个碱基的错配	RISC-RNA interaction SDN-mediated degradation	构建较容易,效率高特异性强,表型稳定	不适用于低表达丰度的miRNA家族

技术	结构	作用机制	优点	缺点
TM	1个结合位点无连接序列3个碱基的错配	RISC-RNA interaction	构建较容易	不适用于有多个成员的miRNA家族
SP	4-15个结合位点连接序列4 nt2个碱基的错配	RISC-RNA interaction	在动物中沉默效果较好	构建困难
STTM	2个结合位点连接序列48-88 nt3个碱基的错配	RISC-RNA interaction SDN-mediated degradation	构建较容易,效率高特异性强,表型稳定	不适用于低表达丰度的miRNA家族