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Published on: August 29, 2018
MicroRNA identity and abundance in porcine skeletal muscles determined by deep sequencing
M Nielsen1, J H Hansen, J Hedegaard
1Department of Genetics and Biotechnology, Aarhus University, DK-Tjele, Denmark.
Abstract:
MicroRNAs (miRNA) are short single-stranded RNA molecules that regulate gene expression post-transcriptionally by binding to complementary sequences in the 3' untranslated region (3' UTR) of target mRNAs. MiRNAs participate in the regulation of myogenesis, and identification of the complete set of miRNAs expressed in muscles is likely to significantly increase our understanding of muscle growth and development. To determine the identity and abundance of miRNA in porcine skeletal muscle, we applied a deep sequencing approach. This allowed us to identify the sequences and relative expression levels of 212 annotated miRNA genes, thereby providing a thorough account of the miRNA transcriptome in porcine muscle tissue. The expression levels displayed a very large range, as reflected by the number of sequence reads, which varied from single counts for rare miRNAs to several million reads for the most abundant miRNAs. Moreover, we identified numerous examples of mature miRNAs that were derived from opposite sides of the same predicted precursor stem-loop structures, and also observed length and sequence heterogeneity at the 5' and 3' ends. Furthermore, KEGG pathway analysis suggested that highly expressed miRNAs are involved in skeletal muscle development and regeneration, signal transduction, cell-cell and cell-extracellular matrix communication and neural development and function.
Insights
This study identifies 212 microRNAs (miRNAs) in porcine skeletal muscle using deep sequencing. These muscle-specific miRNAs are crucial for understanding muscle growth, development, and regeneration processes.
Area of Science:
- Molecular Biology
- Genomics
- Animal Science
Background:
- MicroRNAs (miRNAs) are key post-transcriptional regulators of gene expression.
- MiRNAs play a significant role in myogenesis, influencing muscle growth and development.
- Comprehensive identification of muscle-specific miRNAs is essential for advancing our understanding of muscle biology.
Purpose of the Study:
- To identify and quantify the microRNA transcriptome in porcine skeletal muscle.
- To characterize the diversity and expression levels of miRNAs in muscle tissue.
- To explore the functional implications of identified miRNAs in muscle physiology.
Main Methods:
- Deep sequencing technology was employed to analyze miRNA profiles.
- Bioinformatic analysis was used to identify miRNA sequences and determine their relative abundance.
- KEGG pathway analysis was performed to infer the functional roles of highly expressed miRNAs.
Main Results:
- A total of 212 annotated miRNA genes were identified in porcine skeletal muscle.
- Expression levels of miRNAs varied significantly, ranging from rare to highly abundant.
- Analysis revealed mature miRNAs derived from both arms of precursor stem-loops, along with length and sequence heterogeneity.
- KEGG pathway analysis indicated involvement of highly expressed miRNAs in muscle development, regeneration, signaling, and neural functions.
Conclusions:
- Deep sequencing provides a comprehensive view of the porcine muscle miRNA transcriptome.
- The identified miRNAs are implicated in critical muscle biological processes, including development and regeneration.
- This study offers valuable insights into the regulatory roles of miRNAs in skeletal muscle.
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