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Updated: May 3, 2026
A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants
Published on: January 21, 2020
Analysis of promoters of microRNAs from a Glycine max degradome library
Yi-qiang Han1, Zheng Hu, Dian-feng Zheng
1College 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.
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.
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