Comparative Transcriptome and Methylome Analysis in Human Skeletal Muscle Anabolism, Hypertrophy and Epigenetic Memory

Abstract

Transcriptome wide changes in human skeletal muscle after acute (anabolic) and chronic resistance exercise (RE) induced hypertrophy have been extensively determined in the literature. We have also recently undertaken DNA methylome analysis (850,000 + CpG sites) in human skeletal muscle after acute and chronic RE, detraining and retraining, where we identified an association between DNA methylation and epigenetic memory of exercise induced skeletal muscle hypertrophy. However, it is currently unknown as to whether all the genes identified in the transcriptome studies to date are also epigenetically regulated at the DNA level after acute, chronic or repeated RE exposure. We therefore aimed to undertake large scale bioinformatical analysis by pooling the publicly available transcriptome data after acute (110 samples) and chronic RE (181 samples) and comparing these large data sets with our genome-wide DNA methylation analysis in human skeletal muscle after acute and chronic RE, detraining and retraining. Indeed, after acute RE we identified 866 up- and 936 down-regulated genes at the expression level, with 270 (out of the 866 up-regulated) identified as being hypomethylated, and 216 (out of 936 downregulated) as hypermethylated. After chronic RE we identified 2,018 up- and 430 down-regulated genes with 592 (out of 2,018 upregulated) identified as being hypomethylated and 98 (out of 430 genes downregulated) as hypermethylated. After KEGG pathway analysis, genes associated with ‘cancer’ pathways were significantly enriched in both bioinformatic analysis of the pooled transcriptome and methylome datasets after both acute and chronic RE. This resulted in 23 (out of 69) and 28 (out of 49) upregulated and hypomethylated and 12 (out of 37) and 2 (out of 4) downregulated and hypermethylated ‘cancer’ genes following acute and chronic RE respectively. Within skeletal muscle tissue, these ‘cancer’ genes predominant functions were associated with matrix/actin structure and remodelling, mechano-transduction (e.g. PTK2/Focal Adhesion Kinase and Phospholipase D- following chronic RE), TGF-beta signalling and protein synthesis (e.g. GSK3B after acute RE). Interestingly, 51 genes were also identified to be up/downregulated in both the acute and chronic RE pooled transcriptome analysis as well as significantly hypo/hypermethylated after acute RE, chronic RE, detraining and retraining. Five genes; FLNB, MYH9, SRGAP1, SRGN, ZMIZ1 demonstrated increased gene expression in the acute and chronic RE transcriptome and also demonstrated hypomethylation in these conditions. Importantly, these 5 genes demonstrated retained hypomethylation even during detraining (following training induced hypertrophy) when exercise was ceased and lean mass returned to baseline (pre-training) levels, identifying them as genes associated with epigenetic memory in skeletal muscle. Importantly, for the first time across the transcriptome and epigenome combined, this study identifies novel differentially methylated genes associated with human skeletal muscle anaboli...

Impact of a diet and activity health promotion intervention on regional patterns of DNA methylation

“…Yet, in comparing our results to the current literature, we identified no studies that examined a combined lifestyle intervention among healthy adults with DNA methylation pathway analysis. However, a recent study by Turner et al examined the impact of chronic versus acute resistance exercise on DNA methylation pathways in the skeletal muscle [55]. Even though this study only used the KEGG pathway database, the results identified several significant pathways related to cancer including those related to proteoglycans, transcriptional regulation, colorectal cancer, and small cell lung cancer.…”

UBR5 is a novel E3 ubiquitin ligase involved in skeletal muscle hypertrophy and recovery from atrophy

“…; Turner et al . ). Ethical approval was granted by the NHS West Midlands Black Country, UK, Research Ethics Committee (NREC approval no.…”

Adaptive responses of histone modifications to resistance exercise in human skeletal muscle

“…Recently, it has been reported that DNA methylation is also affected by RE in human skeletal muscles [8,9]. Seaborne et al [8] reported that the frequency of genome-wide hypomethylation at the CpG sites in human skeletal muscle was increased after chronic RE training (9,153 sites), maintained during the detraining period (8,891 sites), and further enhanced in response to reloading (18,816 sites).…”

“…Seaborne et al [8] reported that the frequency of genome-wide hypomethylation at the CpG sites in human skeletal muscle was increased after chronic RE training (9,153 sites), maintained during the detraining period (8,891 sites), and further enhanced in response to reloading (18,816 sites). Turner et al [9] further reported that the expression of 592 of 5,262 genes that were hypomethylated at their CpG sites after chronic RE training was up-regulated. These results indicate that RE training altered the status of genes activation, in agreement with our present results which show an enhancement of the hallmarks of active transcription in histone distributions after RE training.…”

“…This indicates that endurance exercise training stimulated the turnover of histones [7], but it is currently unclear how RE affects the distribution of histones and their modification patterns in animal models. Furthermore, even less research has been conducted on the epigenetic response to RE in human skeletal muscle [8][9][10][11]. Therefore, the present study is built upon the animal model literature, and aims to investigate the response of gene expression profiles and histone modifications in human muscle before and after acute RE and chronic RE training, respectively.…”