Exercise training alters DNA methylation patterns in genes related to muscle growth and differentiation in mice

Abstract

The adaptive response of skeletal muscle to exercise training is tightly controlled and therefore requires transcriptional regulation. DNA methylation is an epigenetic mechanism known to modulate gene expression, but its contribution to exercise-induced adaptations in skeletal muscle is not well studied. Here, we describe a genome-wide analysis of DNA methylation in muscle of trained mice ( n = 3). Compared with sedentary controls, 2,762 genes exhibited differentially methylated CpGs ( P < 0.05, meth diff >5%, coverage >10) in their putative promoter regions. Alignment with gene expression data ( n = 6) revealed 200 genes with a negative correlation between methylation and expression changes in response to exercise training. The majority of these genes were related to muscle growth and differentiation, and a minor fraction involved in metabolic regulation. Among the candidates were genes that regulate the expression of myogenic regulatory factors ( Plexin A2) as well as genes that participate in muscle hypertrophy ( Igfbp4) and motor neuron innervation ( Dok7). Interestingly, a transcription factor binding site enrichment study discovered significantly enriched occurrence of CpG methylation in the binding sites of the myogenic regulatory factors MyoD and myogenin. These findings suggest that DNA methylation is involved in the regulation of muscle adaptation to regular exercise training.

Small-Magnitude Effect Sizes in Epigenetic End Points are Important in Children’s Environmental Health Studies: The Children’s Environmental Health and Disease Prevention Research Center’s Epigenetics Working Group

“…Different individuals have different baselines, and intrapersonal changes may be masked by interpersonal differences when using case–control design. Mouse models such as the one by Kanzleiter et al (2015) have also demonstrated longitudinal methylomic differences in skeletal muscle cells in response to exercise training. The authors reported 2,762 differentially methylated genes associated with exercise training, and that ~ 13% of these methylomic differences also were associated with differential expression of the corresponding genes.…”

Genome-wide methylation analysis reveals differentially methylated loci that are associated with an age-dependent increase in bovine fibroblast response to LPS

“…DNA was diluted to 40 ng/μl and a total of 2 μg was sent to Zymo Research (Irvine, CA) for Methyl-MiniSeq TM RRBS library preparation. Libraries were generated with 200–500 ng of DNA as previously described [28]. Briefly, DNA was sequentially digested with 60 units of TaqαI and 30 units of MSP I (NEB, Ipswich, MA) which recognizes CCGG as a cut site and cleaves after the first cytosine, creating DNA products with CG dinucleotides on both ends of the DNA and enriching for CG rich regions.…”

Skeletal muscle DNMT3A plays a necessary role in endurance exercise by regulating oxidative capacity of red muscles

“…Exercise significantly alters the DNA methylation profile of skeletal muscle [29][30][31][32][33][34][35][36][37]. DNA methylation, a reversible epigenetic mark that usually occurs on a cytosine residue followed by a guanine (CpG), is mediated by a member of the DNA methyltransferase (DNMT) family [38].…”

“…The resultant potassium influx into the matrix lowers the mitochondrial membrane potential, which causes mitochondrial swelling, opening of permeability transition pores, and elevated ROS production [23][24][25]. In addition, NOX-derived ROS causes leakage of Ca2+ from the sarcoplasmic reticulum or entry of extracellular Ca2+, resulting in mitochondrial Ca2+ overload and mitochondrial ROS emission, which ultimately results in muscle fatigue and dysfunction [13,[17][18][19][26][27][28].Exercise significantly alters the DNA methylation profile of skeletal muscle [29][30][31][32][33][34][35][36][37]. DNA methylation, a reversible epigenetic mark that usually occurs on a cytosine residue followed by a guanine (CpG), is mediated by a member of the DNA methyltransferase (DNMT) family [38].…”

“…Methylation prevents the binding of transcriptional machinery that requires interaction with cytosine, usually resulting in transcriptional silencing [39]. Acute and chronic forms of exercise induce both hyper-and hypo-CpG methylation of target loci [29][30][31][32][33][34][35][36][37], and some of these modifications are inversely correlated with gene expression [29,34,37,40]. For example, a single bout of aerobic endurance exercise in human subjects transiently induces promoter hypomethylation in important mitochondria-related transcripts (e.g., PPARGC1A, PDK4, TFAM, and PPARD), followed by an increase in their expression [29].…”