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Journal of Integrative Agriculture  2013, Vol. 12 Issue (9): 1522-1529    DOI: 10.1016/S2095-3119(13)60500-6
Crop Genetics · Breeding · Germplasm Resources Advanced Online Publication | Current Issue | Archive | Adv Search |
MicroRNA Primary Transcripts and Promoter Elements Analysis in Soybean (Glycine max L. Merril.)
 LI Jing, LIU Yong-xin, HAN Ying-peng, LI Yong-guang, GUO Mao-zu , LI Wen-bin
1.Key Laboratory of Soybean Biology, Ministry of Education/Northeast Agricultural University, Harbin 150030, P.R.China
2.Department of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, P.R.China
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摘要  The importance of microRNA (miRNA) at the post-transcriptional regulation level has recently been recognized in both animals and plants. In recent years, many studies focused on miRNA target identification and functional analysis. However, little is known about the transcription and regulation of miRNAs themselves. In this study, the transcription start sites (TSSs) for 11 miRNA primary transcripts of soybean from 11 miRNA loci (of 50 loci tested) were cloned by a 5´ rapid amplification of cDNA ends (5´ RACE) procedure using total RNA from 30-d-old seedlings. The features consistent with a RNA polymerase II mechanism of transcription were found among these miRNA loci. A position weight matrix algorithm was used to identify conserved motifs in miRNA core promoter regions. A canonical TATA box motif was identified upstream of the major start site at 8 (76%) of the mapped miRNA loci. Several cis-acting elements were predicted in the 2 kb 5´ to the TSSs. Potential spatial and temporal expression patterns of the miRNAs were found. The target genes for these miRNAs were also predicted and further elucidated for the potential function of the miRNAs. This research provides a molecular basis to explore regulatory mechanisms of miRNA expression, and a way to understand miRNAmediated regulatory pathways and networks in soybean.

Abstract  The importance of microRNA (miRNA) at the post-transcriptional regulation level has recently been recognized in both animals and plants. In recent years, many studies focused on miRNA target identification and functional analysis. However, little is known about the transcription and regulation of miRNAs themselves. In this study, the transcription start sites (TSSs) for 11 miRNA primary transcripts of soybean from 11 miRNA loci (of 50 loci tested) were cloned by a 5´ rapid amplification of cDNA ends (5´ RACE) procedure using total RNA from 30-d-old seedlings. The features consistent with a RNA polymerase II mechanism of transcription were found among these miRNA loci. A position weight matrix algorithm was used to identify conserved motifs in miRNA core promoter regions. A canonical TATA box motif was identified upstream of the major start site at 8 (76%) of the mapped miRNA loci. Several cis-acting elements were predicted in the 2 kb 5´ to the TSSs. Potential spatial and temporal expression patterns of the miRNAs were found. The target genes for these miRNAs were also predicted and further elucidated for the potential function of the miRNAs. This research provides a molecular basis to explore regulatory mechanisms of miRNA expression, and a way to understand miRNAmediated regulatory pathways and networks in soybean.
Keywords:  soybean       miRNA       primary transcript       RACE       TATA box       motif       promoter       cis-acting element  
Received: 14 September 2012   Accepted:
Fund: 

This study was conducted in the Key Laboratory of Soybean Biology of Chinese Education Ministry, Agriculture Research System of China and the Key Laboratory of Northeastern Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, financially supported by the National High-Tech R&D Program of China (2006AA10Z1F1), the National Core Soybean Genetic Engineering Project, China (2011ZX08004-002), the National Natural Science Foundation of China (60932008, 30971810), the National Basic Research Program of China (2009CB118400), the Ministry of Education Innovation Team of Soybean Molecular Design, China and the Innovation Team of the Education Bureau of Heilongjiang Province, China.

Corresponding Authors:  Correspondence LI Wen-bin, Tel: +86-451-55190778, E-mail: wenbinli@neau.edu.cn   
About author:  LI Jing, Mobile: 13936282709, E-mail: lijing_101@126.com;

Cite this article: 

LI Jing, LIU Yong-xin, HAN Ying-peng, LI Yong-guang, GUO Mao-zu , LI Wen-bin. 2013. MicroRNA Primary Transcripts and Promoter Elements Analysis in Soybean (Glycine max L. Merril.). Journal of Integrative Agriculture, 12(9): 1522-1529.

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