Integrative analysis of whole genome bisulfite and transcriptome sequencing reveals the effect of sodium butyrate on DNA methylation in the differentiation of bovine skeletal muscle satellite cells

• Published in: Genomics (San Diego, Calif.) Calif.), 2024-11, Vol.116 (6), p.110959, Article 110959
• Main Authors: Wang, Xiaowei, Zhou, Xiaonan, Li, Chenglong, Qu, Chang, Shi, Yuangang, Li, Cong-Jun, Kang, Xiaolong
• Format: Article
• Language: English
• Subjects: acetylation; Animals; bisulfites; Bovine skeletal muscle satellite cells; Butyrate; butyric acid; Butyric Acid - pharmacology; Cattle; Cell differentiation; Cell Differentiation - drug effects; Cells, Cultured; Demethylases; DNA methylation; DNA Methylation - drug effects; DNA methyltransferase; DNA methyltransferases; Epigenesis, Genetic - drug effects; epigenetics; gene expression; genome; genomics; growth and development; histones; metabolites; muscle development; muscles; RNA; Satellite Cells, Skeletal Muscle - cytology; Satellite Cells, Skeletal Muscle - drug effects; Satellite Cells, Skeletal Muscle - metabolism; sequence analysis; skeletal muscle; sodium butyrate; Sulfites - pharmacology; Transcriptome; Transcriptome - drug effects; Whole Genome Sequencing
• ISSN: 0888-7543; 1089-8646; 1089-8646
• DOI: 10.1016/j.ygeno.2024.110959

Butyric acid as a short-chain fatty acid (SCFA) is one of the key microbial metabolites of ruminants. Numerous studies indicate that butyrate is crucial in muscle growth and development, and plays an important molecular regulatory role mainly by inhibiting histone deacetylation. DNA methylation, a major epigenetic modification, is involved in cell differentiation. Butyrate, in addition to its role in acetylation modifications, can alter the DNA methylation status of cells. However, the impact of butyrate on the DNA methylation of bovine skeletal muscle satellite cells (SMSCs) remains unclear. In this study, we developed a differentiation model of SMSCs and employed RNA sequencing (RNA-seq) alongside whole genome bisulfite sequencing (WGBS) to explore the effects of butyrate treatment on DNA methylation status and its relationship with gene expression. Treatment of SMSCs with sodium butyrate (NaB) at 1.0 mM for 2 days significantly inhibited the expression of DNA methyltransferases (DNMT1, DNMT2, DNMT3A) at the mRNA and protein levels while promoting the expression of demethylases (TET1, TET2, TET3) at mRNA levels. WGBS identified 4292 differentially methylated regions (DMRs), comprising 2294 hypermethylated and 1998 hypomethylated regions. These DMRs were significantly enriched in the MAPK, cAMP, and Wnt signaling pathways, all of which are implicated in myogenesis and development. Combining RNA-seq and WGBS data revealed a total of 130 overlapping genes, including MDFIC, CREBBP, DMD, LTBP2 and KLF4. These genes are predominantly involved in regulating the FoxO, MAPK, PI3K-Akt, and Wnt signaling pathways. This study provides new insights into the effects of butyrate-mediated DNA methylation on SMSC development and enhances our understanding of butyrate as an epigenetic modifier beyond its role in acetylation. •NaB treatment significantly down-regulated the expression of DNA methyltransferase genes (DNMT1, DNMT2, and DNMT3A) in differentiating bovine SMSCs.•To elucidate the impact of NaB on DNA methylation, we generated a comprehensive methylation profile of NaB-treated bovine SMSCs.•Combined analysis of WGBS and RNA-seq data identified subgroups of genes responsive to NaB treatment and identified differentially expressed genes associated with myoblast differentiation (MDFIC, CREBBP, DMD, LTBP2 and KLF4).