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Genome-wide methylation and transcriptome differential analysis of skeletal muscle in broilers with valgus-varus
1College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China.
British Poultry Science
|November 6, 2024
Summary
Valgus-varus deformity (VVD) in broilers is linked to altered DNA methylation in leg muscles. This study identifies differentially methylated genes and pathways involved in protein degradation, offering new epigenetic insights into VVD pathogenesis.
Area of Science:
- Epigenetics
- Animal Science
- Molecular Biology
Background:
- Valgus-varus deformity (VVD) significantly impairs broiler leg function, with no effective treatments.
- The role of DNA methylation in skeletal muscle development and VVD pathogenesis in broilers remains unexplored.
Purpose of the Study:
- To investigate genome-wide DNA methylation patterns in the leg muscles of VVD-affected and normal broilers.
- To identify differentially methylated genes (DMGs) and associated pathways involved in VVD.
- To explore the epigenetic mechanisms underlying VVD by analyzing DNA methylation and gene expression.
Main Methods:
- Whole genome bisulfite sequencing was employed to analyze DNA methylation in VVD and control broilers.
- Bioinformatic analyses, including identification of differentially methylated regions (DMRs) and genes (DMGs).
- Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on DMGs. Protein-protein interaction networks were analyzed, and the effect of 5-azacytidine (5-AzaC) on gene expression was investigated.
Main Results:
- Approximately 55% methylation rate was observed in the cytosine-phosphoric acid-guanine (CG) sequence environment, with 4,265 DMRs identified.
- GO enrichment highlighted pathways related to protein degradation (e.g., proteasome complex). KEGG analysis revealed enrichment in signaling pathways like proteasome and nitrogen metabolism.
- MYL9 showed a negative correlation between promoter DNA methylation and mRNA expression. 5-AzaC treatment inhibited DNMT1/DNMT3A and promoted MYL9 expression.
Conclusions:
- This study provides a comprehensive analysis of DNA methylation patterns in broiler leg muscle affected by VVD.
- Identified DMGs and enriched pathways offer insights into the molecular mechanisms of muscle growth and development in VVD.
- Epigenetic alterations, particularly DNA methylation, play a significant role in VVD pathogenesis, opening avenues for future therapeutic strategies.
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