赵春丽1, 2,李先恩2,都晓伟1*,孙 鹏2*.地黄microRNAs和靶基因的生物信息学预测及验证[J].中草药,2014,45():
地黄microRNAs和靶基因的生物信息学预测及验证
Bioinformatic prediction and validation of conserved microRNAs and their target genes in Rehmannia glutinosa
  
DOI:
中文关键词:  地黄  microRNA  靶基因  生物信息学  PCR检测
英文关键词:Rehmannia glutinosa Libosch  microRNA  target gene  bioinformatics  PCR detection
基金项目:国家自然科学基金资助项目(30901969)
作者单位
赵春丽1, 2,李先恩2,都晓伟1*,孙 鹏2* 1. 黑龙江中医药大学黑龙江 哈尔滨 150040 2. 中国医学科学院 北京协和医学院 药用植物研究所北京 100193 
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中文摘要:
      目的 microRNAs(miRNA)是一类非编码的单链小分子RNA,在植物的生长发育、逆境适应和代谢调控等过程中发挥着至关重要的作用。本研究拟利用地黄EST数据通过生物信息学手段预测新的地黄miRNA,为今后地黄miRNA的生物学研究奠定基础。方法 本研究根据miRNA 家族在不同物种中的保守性,将miRBase数据库中的已知植物miRNA与通过高通量测序获得的93172条地黄EST序列进行同源比对,按照miRNA前体应具备的标准进行筛选。结果 预测到分属于8个家族的8条潜在地黄miRNA序列,并通过实时荧光定量PCR对8条预测的miRNA进行了检测,证实8条miRNA在地黄中真实存在。随后利用软件对8条地黄miRNA的靶基因进行预测,发现其靶基因主要编码与地黄生长发育、代谢以及胁迫响应等过程相关的蛋白。结论 新预测的地黄miRNA及其靶基因为今后研究它们在地黄中的生物学功能奠定了基础。
英文摘要:
      Objective MicroRNAs (miRNA) are a class of small non-coding RNA molecules, playing vital roles in plant growth and development, stress adaption, and metabolic pathway regulation. In order to establish the material basis for future studies on the biological function of miRNAs, we aimed to predict novel miRNAs from EST sequences of Rehmannia glutinosa by using bioinformatic strategies. Methods Since most of the plant miRNAs were conserved in plant species, all plant miRNAs deposited in miRNase were aligned to the 93 172 EST sequences generated by next generation high-throughput RNA sequencing technology and the putative miRNA precursors were screened according to serious criteria. Results Eight novel rehmannia miRNAs were identified that belonged to eight different families, which were further validated by real-time PCR analysis. Then the eight rehmannia miRNAs were subjected to target prediction analysis, and the results showed that the target genes encoded the proteins related to root growth, metabolism, stress responses, and other processes. Conclusion The miRNAs and their target genes identified in this study will provide clues to their biological functions in R. glutinosa.
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