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Open Access Research article

Identification and profiling of conserved and novel microRNAs from Chinese Qinchuan bovine longissimus thoracis

Jiajie Sun1, Mijie Li1, Zhuanjian Li1, Jing Xue1, Xianyong Lan1, Chunlei Zhang2, Chuzhao Lei1 and Hong Chen1*

Author Affiliations

1 College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, China

2 Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China

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BMC Genomics 2013, 14:42  doi:10.1186/1471-2164-14-42

Published: 18 January 2013

Abstract

Background

MicroRNAs (miRNAs) are a family of ~22 nucleotide small RNA molecules that regulate gene expression by fully or partially binding to their complementary sequences. Recently, a large number of miRNAs and their expression patterns have been identified in various species. However, to date no miRNAs have been reported to modulate muscle development in beef cattle.

Results

Total RNAs from the Chinese Qinchuan bovine longissimus thoracis at fetal and adult stages were used to construct small RNA libraries for Solexa SBS technology sequencing. A total of 15,454,182 clean reads were obtained from the fetal bovine library and 13,558,164 clean reads from the adult bovine library. In total, 521 miRNAs including 104 novel miRNA candidates were identified. Furthermore, the nucleotide bias, base edit and family of the known miRNAs were also analyzed. Based on stem-loop qPCR, 25 high-read miRNAs were detected, and the results showed that bta-miRNA-206, miRNA-1, miRNA-133, miRNAn12, and miRNAn17 were highly expressed in muscle-related tissue or organs, suggesting that these miRNAs may play a role in the development of bovine muscle tissues.

Conclusions

This study confirmed the authenticity of 417 known miRNAs, discovered 104 novel miRNAs in bos taurus, and identified five muscle-specific miRNAs. The identification of novel miRNAs significantly expanded the repertoire of bovine miRNAs and could contribute to further studies on the muscle development of cattle.

Keywords:
Bovine; Deep sequencing technology; microRNA; Muscle; Proliferation; Differentiation