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Open Access Highly Accessed Research article

Identification of differences in microRNA transcriptomes between porcine oxidative and glycolytic skeletal muscles

Yingkai Liu1, Mingzhou Li1, Jideng Ma1, Jie Zhang1, Chaowei Zhou1, Tao Wang1, Xiaolian Gao2 and Xuewei Li1*

Author Affiliations

1 Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Ya’an, Sichuan, China

2 Department of Biology & Biochemistry, University of Houston, Houston, TX, USA

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BMC Molecular Biology 2013, 14:7  doi:10.1186/1471-2199-14-7

Published: 18 February 2013

Abstract

Background

MicroRNAs (miRNAs) are a type of non-coding small RNA ~22 nucleotides in length that regulate the expression of protein coding genes at the post-transcriptional level. Glycolytic and oxidative myofibers, the two main types of skeletal muscles, play important roles in metabolic health as well as in meat quality and production in the pig industry. Previous expression profile studies of different skeletal muscle types have focused on these aspects of mRNA and proteins; nonetheless, an explanation of the miRNA transcriptome differences between these two distinct muscles types is long overdue.

Results

Herein, we present a comprehensive analysis of miRNA expression profiling between the porcine longissimus doris muscle (LDM) and psoas major muscle (PMM) using a deep sequencing approach. We generated a total of 16.62 M (LDM) and 18.46 M (PMM) counts, which produced 15.22 M and 17.52 M mappable sequences, respectively, and identified 114 conserved miRNAs and 89 novel miRNA*s. Of 668 unique miRNAs, 349 (52.25%) were co-expressed, of which 173 showed significant differences (P < 0.01) between the two muscle types. Muscle-specific miR-1-3p showed high expression levels in both libraries (LDM, 32.01%; PMM, 20.15%), and miRNAs that potentially affect metabolic pathways (such as the miR-133 and -23) showed significant differences between the two libraries, indicating that the two skeletal muscle types shared mainly muscle-specific miRNAs but expressed at distinct levels according to their metabolic needs. In addition, an analysis of the Gene Ontology (GO) terms and KEGG pathway associated with the predicted target genes of the differentially expressed miRNAs revealed that the target protein coding genes of highly expressed miRNAs are mainly involved in skeletal muscle structural development, regeneration, cell cycle progression, and the regulation of cell motility.

Conclusion

Our study indicates that miRNAs play essential roles in the phenotypic variations observed in different muscle fiber types.

Keywords:
microRNA; Deep sequencing; Longissimus doris muscle; Psoas major muscle; Pig