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

Authors: WANG, XIAOWEI - Ningxia University; ZHOU, XIAONAN - Ningxia University; LI, CHENGLONG - Ningxia University; QU, CHANG - Ningxia University; SHI, YUANGANG - Ningxia University; Li, Congjun - Cj; KANG, XIAOLONG - Ningxia University

Submitted to: Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/4/2024
Publication Date: 11/9/2024
Citation: Wang, X., Zhou, X., Li, C., Qu, C., Shi, Y., Li, C., Kang, X. 2024. 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. Genomics. 116(6):110959. https://doi.org/10.1016/j.ygeno.2024.110959.
DOI: https://doi.org/10.1016/j.ygeno.2024.110959

Interpretive Summary: Butyric acid is a short-chain fatty acid which is a product of digestion of feed in the rumen by microbial metabolism. Butyrate is known to have specific effects on histones which in turn result in changing cell functions due to gene expression patterns. Butyrate can also alter DNA structure again resulting in changed cell functions in some tissues. However, the impact of butyrate on the DNA structure of bovine skeletal muscle satellite cells (SMSCs) remains unclear. Here, we report that treatment of SMSCs with sodium butyrate significantly changes the expression of two groups of enzymes involved in DNA structure modification. The changes in these two groups of enzymes' expression induced changes in DNA structure which resulted in changes in DNA function without changing the DNA sequence (e.g., epigenetic regulation). This study provides new insights into butyrate as a modifier that affects DNA structure and gene function with a new pathway. These findings offer valuable insight into the molecular mechanisms underlying butyric acid regulation of bovine SMSC proliferation and differentiation.

Technical Abstract: Butyric acid, 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, primarily by inhibiting histone deacetylation. This process is a significant molecular regulatory mechanism. 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 WGBS and RNA-seq data revealed a total of 130 overlapping genes, including MDFIC, CREBBP, and DMD. 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. It enhances our understanding of butyrate as an epigenetic modifier beyond its role in acetylation.