Analysis of promoters of microRNAs from a Glycine max degradome library.
J Zhejiang Univ Sci B, 2014/2;15(2):125-32.
Han YQ[1], Hu Z, Zheng DF, Gao YM
Affiliations
PMID: 24510705DOI: 10.1631/jzus.B1300179
Impact factor: 5.552
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.
MeSH terms
Amino Acid Motifs; Computational Biology; Enhancer Elements, Genetic; Gene Expression Regulation, Plant; Gene Library; MicroRNAs; Promoter Regions, Genetic; RNA, Plant; Glycine max
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