Yi-qiang Han1, Zheng Hu, Dian-feng Zheng, Ya-mei Gao. 1. 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.
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.
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.
Authors: Chui E Wong; Ying-Tao Zhao; Xiu-Jie Wang; Larry Croft; Zhong-Hua Wang; Farzad Haerizadeh; John S Mattick; Mohan B Singh; Bernard J Carroll; Prem L Bhalla Journal: J Exp Bot Date: 2011-04-19 Impact factor: 6.992
Authors: Franceli R Kulcheski; Luiz Fv de Oliveira; Lorrayne G Molina; Maurício P Almerão; Fabiana A Rodrigues; Juliana Marcolino; Joice F Barbosa; Renata Stolf-Moreira; Alexandre L Nepomuceno; Francismar C Marcelino-Guimarães; Ricardo V Abdelnoor; Leandro C Nascimento; Marcelo F Carazzolle; Gonçalo Ag Pereira; Rogério Margis Journal: BMC Genomics Date: 2011-06-10 Impact factor: 3.969