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

Abstract

38Transcriptome wide changes in human skeletal muscle after acute (anabolic) and chronic resistance exercise 39 (RE) induced hypertrophy have been extensively determined in the literature. We have also recently 40 undertaken DNA methylome analysis (850,000 + CpG sites) in human skeletal muscle after acute and 41 chronic RE, detaining and retraining, where we identified an association between DNA methylation in an 42 epigenetic memory of exercise induced skeletal muscle hypertrophy. However, it is currently unknown as to 43 whether all the genes identified in the transcriptome studies to date are also epigenetically regulated at the 44 DNA level after acute, chronic or repeated RE exposure. We therefore aimed to undertake large scale 45 bioinformatical analysis by pooling the publicly available transcriptome data after acute (110 samples) and 46 chronic RE (181 samples) and comparing these large data sets with our genome-wide DNA methylation 47 analysis in human skeletal muscle after acute and chronic RE, detraining and retraining. Indeed, after acute 48 RE we identified 866 up-and 936 down-regulated genes at the expression level, with 270 (out of the 866 up-49 regulated) identified as being hypomethylated, and 216 (out of 936 downregulated) as hypermethylated. 50After chronic RE we identified 2,018 up-and 430 down-regulated genes with 592 (out of 2,018 upregulated) 51 identified as being hypomethylated and 98 (out of 430 genes downregulated) as hypermethylated. After 52 KEGG pathway analysis, genes associated with 'cancer' pathways were significantly enriched in both 53 bioinformatic analysis of the pooled transcriptome and methylome data after both acute and chronic RE. 54 This resulted in 23 (out of 69) and 28 (out of 49) upregulated and hypomethylated and 12 (out of 37) and 2 55 (out of 4) downregulated and hypermethylated 'cancer' genes following acute and chronic RE respectively. 56Within skeletal muscle tissue, these 'cancer' genes predominant functions were associated with matrix/ actin 57 structure and remodelling, mechano-transduction (including PTK2/Focal Adhesion Kinase and 58 Phospholipase D-following chronic RE only), TGF-beta signalling and protein synthesis (GSK3B after 59 acute RE only). Interestingly, 51 genes were also identified to be up/downregulated in both the acute and 60 chronic RE pooled transcriptome analysis as well as significantly hypo/hypermethylated after acute RE, 61 chronic RE, detraining and retraining. Five genes; FLNB, MYH9, SRGAP1, SRGN, ZMIZ1 demonstrated 62 increased gene expression in the acute and chronic RE transcriptome and also demonstrated 63 hypomethylation in these conditions. Importantly, these 5 genes demonstrated retained hypomethylation 64 even during detraining (following training induced hypertrophy) when exercise was ceased and lean mass 65 returned to baseline (pre-training) levels, identifying them as potential epigenetic memory genes. 66 Importantly, for the first time across the transcriptome and epigenome combined, this study identifies novel 67 diffe...

Knockdown of the E3 Ubiquitin ligase UBR5 and its role in skeletal muscle anabolism

“…A recent study also supported the role of UBR5 as being essential for muscle growth through RNAi screening in Drosophila larvae, where UBR5 inhibition led to smaller sized larvae (Hunt et al, 2019). Finally, unpublished data from our lab in bioengineered mouse SkM also demonstrated that UBR5 was the most significantly upregulated transcript after loading, amongst a selection of genes that are known to be regulated across the human transcriptome and methylome after acute RE (Seaborne et al, 2018b;Turner et al, 2019b). Collectively, these data support the notion that UBR5 is involved in load-induced anabolism and hypertrophy, in contrast with the well-known MuRF1 and MAFbx E3 ligases that are associated with muscle atrophy.…”

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

“…Human muscle cells were isolated from the vastus lateralis biopsies of three healthy young adult males (28 ± 11 years, 73.00 ± 0.91 kg, 177.2 ± 4.3 cm, mean ± SD) that were recreationally active but had never undergone a period of supervised chronic aerobic or resistance exercise. The full biopsy procedure and the primary cell isolation procedures have been described previously (Seaborne et al 2018a;Seaborne et al 2018b;Turner et al 2019a;Turner et al 2019b). Ethical approval was granted by the NHS West Midlands Black Country, UK, Research Ethics Committee (NREC approval no.…”

Associations of combined genetic and epigenetic scores with muscle size and muscle strength: a pilot study in older women

“…We shared one CpG site in each of the loading and unloading phase, with both CpGs located in the intergenic region ( Table S5A). We further compared our CpGs with those identified by Turner et al ., 34 who analysed transcriptome and methylome associations after acute/chronic resistance training, but no common CpG was found. Notably, Turner et al .…”