MicroRNA Primary Transcripts and Promoter Elements Analysis in Soybean (Glycine max L. Merril.)

doi:10.1016/S2095-3119(13)60500-6

Journal of Integrative Agriculture ›› 2013, Vol. 12 ›› Issue (9): 1522-1529.DOI: 10.1016/S2095-3119(13)60500-6

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

收稿日期:2012-09-14 出版日期:2013-09-01 发布日期:2013-09-15
通讯作者: Correspondence LI Wen-bin, Tel: +86-451-55190778, E-mail: wenbinli@neau.edu.cn
作者简介:LI Jing, Mobile: 13936282709, E-mail: lijing_101@126.com;
基金资助:
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.

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

Received:2012-09-14 Online:2013-09-01 Published:2013-09-15
Contact: 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;
Supported by:
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.

摘要/Abstract

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.

关键词: soybean , miRNA , primary transcript , RACE , TATA box , motif , promoter , cis-acting element

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.

Key words: soybean , miRNA , primary transcript , RACE , TATA box , motif , promoter , cis-acting element

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

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MicroRNA Primary Transcripts and Promoter Elements Analysis in Soybean (Glycine max L. Merril.)

MicroRNA Primary Transcripts and Promoter Elements Analysis in Soybean (Glycine max L. Merril.)

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