Analysis of DNA methylation profiles during sheep skeletal muscle development using whole-genome bisulfite sequencing

Abstract

Background: DNA methylation is an epigenetic regulatory form that plays an important role in regulating the gene expression and the tissues development.. However, DNA methylation regulators involved in sheep muscle development remain unclear. To explore the functional importance of genome-scale DNA methylation during sheep muscle growth, this study systematically investigated the genome-wide DNA methylation profiles at key stages of Hu sheep developmental (fetus and adult) using deep whole-genome bisulfite sequencing (WGBS). Results: Our study found that the expression levels of DNA methyltransferase (DNMT)-related genes were lower in fetal muscle than in the muscle of adults. The methylation levels in the CG context were higher than those in the CHG and CHH contexts, and methylation levels were highest in introns, followed by exons and downstream regions. Subsequently, we identified 48,491, 17, and 135 differentially methylated regions (DMRs) in the CG, CHG, and CHH sequence contexts and 11,522 differentially methylated genes (DMGs). The results of bisulfite sequencing PCR (BSP) correlated well with the WGBS-Seq data. Moreover, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation analysis revealed that some DMGs were involved in regulating skeletal muscle development and fatty acid metabolism. By combining the WGBS-Seq and previous RNA-Seq data, a total of 159 overlap genes were obtained between differentially expressed genes (DEGs) and DMGs (FPKM > 10 and fold change > 4). Finally, we found that 9 DMGs were likely to be involved in muscle growth and metabolism of Hu sheep. Conclusions: We systemically studied the global DNA methylation patterns of fetal and adult muscle development in Hu sheep, which provided new insights into a better understanding of the epigenetic regulation of sheep muscle development.

Genome-wide DNA methylation analysis in Chinese Chenghua and Yorkshire pigs

“…Bismark methylation extractor outputs read coverage and methylation percentage of detected methylated or unmethylated reads at one genomic position. The R package methyKit v1.14.2 [ 44 ] was used to identify DMRs (window size = 500 bp, qvalue< 0.01, methylation difference > =0.25) based on the Bismark coverage file. The R package Rldeogram v0.2.2 [ 45 ] was used to visualize the distribution of DMR.…”

Key Genes Regulating Skeletal Muscle Development and Growth in Farm Animals

“…Based on analysis of gene expression profiles in ovine skeletal muscle from five Spanish meat breeds, candidate genes related to muscle contraction, including actin α1 ( ACTA1 ), myosin light chain phosphorylatable fast skeletal muscle ( MYLPF ), myosin heavy chains 2 ( MYH2 ) and 7 ( MYH7 ), tropomyosin 2 ( TPM2 ), and titin ( TTN ), were identified [ 130 ]. Fan et al [ 131 ] employed whole-genome bisulfite sequencing to examine genome-wide DNA methylation profiles in Hu sheep and identified many important differentially methylated genes associated with muscle growth and metabolism ( Figure 3 ). Based on network analysis, they identified nine candidate genes ( ADIPOQ , CCNA2 , ITGA2 , MYOG , MAPT , DIAPH1 , NR4A1 , DLK1 , and COL1A2 ) that may be associated with muscle cell proliferation and differentiation and determined that their regulation across DNA methylation can control differential muscle development.…”

“… The network of differentially methylated genes associated with muscle development in sheep. Darker lines indicate higher confidence levels [ 131 ]. …”

Impacts of Epigenetic Processes on the Health and Productivity of Livestock

“…DNA methylation is one of the most studied epigenetic mechanisms involved in the regulation of gene expression related to muscle development ( Table 2 ; Baik et al, 2014 ; Gotoh, 2015 ; Chen Z. et al, 2019 ). The genome-wide DNA methylation profiles of longissimus dorsi muscles from different breeds of sheep provided insight on the epigenetic regulatory mechanisms modulating the expression of genes involved in the regulation of muscle development, such as DLK1 , NR4A1 , TGFB3 , ACSL1 , RYR1 , ACOX2 , PPARG2 , NTN1 , and MAPRE1 ( Couldrey et al, 2014 ; Cao et al, 2017 ; Fan et al, 2020 ). Meanwhile, a number of DMRs on genes associated with important biological processes such as lipid translocation and lipid transport were identified in latissimus dorsi muscle from different breeds of beef cattle with diverse meat quality traits ( Fang et al, 2017 ).…”