Journal of Zhejiang University

Journal of Zhejiang University SCIENCE B 2014 Vol.15 No.2 P.125-132

Analysis of promoters of microRNAs from a Glycine max degradome library* #

Author(s): Yi-qiang Han¹,Zheng Hu²,Dian-feng Zheng³,Ya-mei Gao¹
Affiliation(s): 1. 1. College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, China more
Corresponding email(s): gaoym800@126.com
Key Words: Glycine max , MicroRNA (miRNA), Promoter, Cis-acting element, Prediction

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Yi-qiang Han, Zheng Hu, Dian-feng Zheng, Ya-mei Gao. Analysis of promoters of microRNAs from a Glycine max degradome library[J]. Journal of Zhejiang University Science B, 2014, 15(2): 125-132.

@article{title="Analysis of promoters of microRNAs from a Glycine max degradome library",
author="Yi-qiang Han, Zheng Hu, Dian-feng Zheng, Ya-mei Gao",
journal="Journal of Zhejiang University Science B",
volume="15",
number="2",
pages="125-132",
year="2014",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.B1300179"
}

%0 Journal Article
%T Analysis of promoters of microRNAs from a Glycine max degradome library
%A Yi-qiang Han
%A Zheng Hu
%A Dian-feng Zheng
%A Ya-mei Gao
%J Journal of Zhejiang University SCIENCE B
%V 15
%N 2
%P 125-132
%@ 1673-1581
%D 2014
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B1300179

TY - JOUR
T1 - Analysis of promoters of microRNAs from a Glycine max degradome library
A1 - Yi-qiang Han
A1 - Zheng Hu
A1 - Dian-feng Zheng
A1 - Ya-mei Gao
J0 - Journal of Zhejiang University Science B
VL - 15
IS - 2
SP - 125
EP - 132
%@ 1673-1581
Y1 - 2014
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.B1300179

Abstract
Chinese Summary
Academic Network
Reviewer Comment

Abstract: 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.

大豆降解组文库microRNAs的启动子分析

研究目的：通过分析miRNA的核心启动子和顺式作用元件为进一步解析大豆（Glycine max）miRNAs表达调控及其功能研究提供重要信息。
创新要点：利用生物信息学方法全面解析了大豆降解组文库miRNA的启动子特征，并依据顺式作用元件及靶基因构建了miRNA的表达与生长素响应因子、赤霉素响应因子之间存在潜在的负反馈调控网络。
研究方法：本研究利用TSSP 程序和PlantCARE数据库预测了来自大豆降解组文库的440个miRNA的核心启动子以及369个miRNAs的顺式作用元件，并依据顺式作用元件及靶基因构建miRNA调控网络。
重要结论：83.86%的miRNA在其上游序列中含有启动子，8.64%的miRNA在其下游序列中含有启动子，21.59%的miRNA包含增强子。核心启动子的TATA盒与转录起始位点（TSSs）的分布相似（见图2）。此外，对转录起始位点5'端的顺式作用元件预测为miRNAs的可能功能和表达的时空性提供了线索。miRNAs的顺式作用元件和靶基因的分析显示，部分miRNA的表达与生长素响应因子、赤霉素响应因子之间存在潜在的负反馈调控（见图3）。

关键词：大豆；MicroRNA（miRNA）；启动子；顺式作用元件；预测