大豆降解组文库中 microRNAs 启动子分析。
Analysis of promoters of microRNAs from a Glycine max degradome library.
机构信息
College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, China; The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing 163319, China.
出版信息
J Zhejiang Univ Sci B. 2014 Feb;15(2):125-32. doi: 10.1631/jzus.B1300179.
OBJECTIVE
MicroRNAs (miRNAs) are genome-encoded, small non-coding RNAs that play important functions in development, biotic and abiotic stress responses, and other processes. Our aim was to explore the regulation of miRNA expression.
METHODS
We used bioinformatics methods to predict the core promoters of 440 miRNAs identified from a soybean (Glycine max) degradome library and to analyze cis-acting elements for 369 miRNAs.
RESULTS
The prediction results showed that 83.86% of the 440 miRNAs contained promoters in their upstream sequences, and 8.64% (38 loci) in their downstream sequences. The distributions of two core promoter elements, TATA-boxes and transcription start sites (TSSs), were similar. The cis-acting elements were examined to provide clues to the function and regulation of spatiotemporal expression of the miRNAs. Analyses of miRNA cis-elements and targets indicated a potential auxin response factor (ARF)- and gibberellin response factor (GARF)-mediated negative feedback loop for miRNA expression.
CONCLUSIONS
The features of miRNAs from a Glycine max degradome library obtained here provide insights into the transcription regulation and functions of miRNAs in soybean.
目的
miRNAs（microRNAs）是基因组编码的小非编码 RNA，在发育、生物和非生物胁迫反应以及其他过程中发挥重要作用。我们的目的是探索 miRNA 表达的调控。
方法
我们使用生物信息学方法预测了从大豆（Glycine max）降解组文库中鉴定的 440 个 miRNA 的核心启动子，并分析了 369 个 miRNA 的顺式作用元件。
结果
预测结果表明，440 个 miRNA 中有 83.86%在其上游序列中含有启动子，8.64%（38 个位点）在其下游序列中含有启动子。两个核心启动子元件（TATA 框和转录起始位点（TSS））的分布相似。顺式作用元件的分析为 miRNA 时空表达的功能和调控提供了线索。miRNA 顺式元件和靶标的分析表明，miRNA 表达可能存在生长素反应因子（ARF）和赤霉素反应因子（GARF）介导的负反馈环。
结论
本研究中获得的大豆降解组文库 miRNA 的特征为大豆中 miRNA 的转录调控和功能提供了新的见解。
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