Comparative genome-wide methylation analysis of longissimus dorsi muscles between Japanese black (Wagyu) and Chinese Red Steppes cattle

Abstract

DNA methylation is an important epigenetic mechanism involved in expression of genes in many biological processes including muscle growth and development. Its effects on economically important traits are evinced from reported significant differences in meat quality traits between Japanese black (Wagyu) and Chinese Red Steppes cattle, thus presenting a unique model for analyzing the effects of DNA methylation on these traits. In the present study, we performed whole genome DNA methylation analysis in the two breeds by whole genome bisulfite sequencing (WGBS). Overall, 23150 differentially methylated regions (DMRs) were identified which were located in 8596 genes enriched in 9922 GO terms, of which 1046 GO terms were significantly enriched (p<0.05) including lipid translocation (GO: 0034204) and lipid transport (GO: 0015914). KEGG analysis showed that the DMR related genes were distributed among 276 pathways. Correlation analysis found that 331 DMRs were negatively correlated with the expression levels of differentially expressed genes (DEGs) with 21 DMRs located in promoter regions. Our results identified novel candidate DMRs and DEGs correlated with meat quality traits, which will be valuable for future genomic and epigenomic studies of muscle development and for marker assisted selection of meat quality traits.

Genome-Wide DNA Methylation Analysis of Mammary Gland Tissues From Chinese Holstein Cows With Staphylococcus aureus Induced Mastitis

“…A previous study also reported that S. aureus-positive cattle had significantly more methylation sites on BTA 11 than S. aureusnegative controls (Song et al, 2016), implying a potential regulatory role of DNA methylation in response to S. aureus mastitis. We observed the intergenic and intron regions had more methylation sites (adjusted P < 0.05) compared with other functional gene elements, which is in agreement with previous studies in other cattle breeds (Song et al, 2016;Fang et al, 2017;Chen et al, 2019,a). Similar to results obtained with other mammalian species (Gim et al, 2015;Song et al, 2016;Zhang Y. et al, 2017), the methylation level was DMEGs, the C m CGG differently methylated genes with significantly different gene expression level in the same animal model; BP, biological process; CC, cellular component.…”

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

“…The PI3K-Akt signaling pathway is critical for skeletal muscle protein synthesis and degradation [18]. The calcium signaling pathway is the key pathway exerting allosteric regulation on many proteins, including through ion channel activation or by acting as a secondary messenger, which could directly affect skeletal muscle metabolism [7]. As muscle is a major metabolic tissue, it was not unexpected that metabolic pathways, including carbon metabolism, insulin secretion, and insulin signaling, were enriched in our study.…”

“…The muscle of genome-wide methylation patterns were similar between fetus and adult in functional genomic regions. However, there were differences among the three mC contexts which might be related to differences in the sequences of the different genetic elements [7]. After filtering the WGBS-seq raw data, we obtained 230 million clean reads per sample.…”

“…Genome-wide DNA methylation profiling in skeletal muscle tissues of aging pigs showed that DNA methylation play a key role in improving proteolysis that is related to muscle function [6]. A comparative analysis of whole genome DNA methylation regulation of gene expressionat the level of transcription in muscles of Japanese Black and Chinese Red Steppes cattle identified several genes associated with DMRs that is related to muscle development [7]. These studies indicate DNA methylation play an important roles in muscle development.…”

DNA methylation pattern of the goat &lt;i&gt;PITX1&lt;/i&gt; gene and its effects on milk performance

“…Recently an increasing number of studies have demonstrated that nutritional or environmental changes contribute to changes in inheritable epigenetic modifications, such as DNA methylation (Lan et al, 2013a;Chavatte-Palmer et al, 2018;Kwan et al, 2018;Yuan et al, 2018). As one of the most important and common types of epigenetic modification, DNA methylation plays a significant role in regulating biological processes such as milk production and organ development (Hwang et al, 2017;Fleming et al, 2018;Jessop et al, 2018). In recent years, gene methylation involved in vital biological functions has been wellstudied in animals (Ibeagha-Awemu and Zhao, 2015).…”