Institute for Health and Sport (iHeS), Victoria University, PO Box 14428, Melbourne, VIC, 8001, Australia.
Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia.
Clin Epigenetics. 2021 Nov 3;13(1):202. doi: 10.1186/s13148-021-01188-1.
Nearly all human complex traits and diseases exhibit some degree of sex differences, with epigenetics being one of the main contributing factors. Various tissues display sex differences in DNA methylation; however, this has not yet been explored in skeletal muscle, despite skeletal muscle being among the tissues with the most transcriptomic sex differences. For the first time, we investigated the effect of sex on autosomal DNA methylation in human skeletal muscle across three independent cohorts (Gene SMART, FUSION, and GSE38291) using a meta-analysis approach, totalling 369 human muscle samples (222 males and 147 females), and integrated this with known sex-biased transcriptomics. We found 10,240 differentially methylated regions (DMRs) at FDR < 0.005, 94% of which were hypomethylated in males, and gene set enrichment analysis revealed that differentially methylated genes were involved in muscle contraction and substrate metabolism. We then investigated biological factors underlying DNA methylation sex differences and found that circulating hormones were not associated with differential methylation at sex-biased DNA methylation loci; however, these sex-specific loci were enriched for binding sites of hormone-related transcription factors (with top TFs including androgen (AR), estrogen (ESR1), and glucocorticoid (NR3C1) receptors). Fibre type proportions were associated with differential methylation across the genome, as well as across 16% of sex-biased DNA methylation loci (FDR < 0.005). Integration of DNA methylomic results with transcriptomic data from the GTEx database and the FUSION cohort revealed 326 autosomal genes that display sex differences at both the epigenome and transcriptome levels. Importantly, transcriptional sex-biased genes were overrepresented among epigenetic sex-biased genes (p value = 4.6e-13), suggesting differential DNA methylation and gene expression between male and female muscle are functionally linked. Finally, we validated expression of three genes with large effect sizes (FOXO3A, ALDH1A1, and GGT7) in the Gene SMART cohort with qPCR. GGT7, involved in antioxidant metabolism, displays male-biased expression as well as lower methylation in males across the three cohorts. In conclusion, we uncovered 8420 genes that exhibit DNA methylation differences between males and females in human skeletal muscle that may modulate mechanisms controlling muscle metabolism and health.
几乎所有的人类复杂特征和疾病都表现出一定程度的性别差异，表观遗传学是主要的影响因素之一。不同组织的 DNA 甲基化存在性别差异；然而，这在骨骼肌中尚未得到探索，尽管骨骼肌是转录组性别差异最大的组织之一。我们首次使用荟萃分析方法，在三个独立的队列（Gene SMART、FUSION 和 GSE38291）中，研究了性对人类骨骼肌常染色体 DNA 甲基化的影响，共分析了 369 个人类肌肉样本（222 名男性和 147 名女性），并将其与已知的性别偏向转录组学相结合。我们发现了 10240 个差异甲基化区域（DMR），在 FDR<0.005 时，94%的区域在男性中呈低甲基化状态，基因集富集分析表明，差异甲基化基因参与肌肉收缩和底物代谢。然后，我们研究了 DNA 甲基化性别差异的生物学基础，发现循环激素与性别偏向的 DNA 甲基化位点的差异甲基化无关；然而，这些性别特异性的位点富含激素相关转录因子的结合位点（顶级 TF 包括雄激素（AR）、雌激素（ESR1）和糖皮质激素（NR3C1）受体）。纤维类型比例与全基因组以及 16%的性别偏向 DNA 甲基化位点（FDR<0.005）的差异甲基化有关。将 DNA 甲基组学结果与 GTEx 数据库和 FUSION 队列的转录组学数据整合，揭示了 326 个常染色体基因，这些基因在表观基因组和转录组水平上都存在性别差异。重要的是，转录组性别偏向基因在表观基因组性别偏向基因中过度表达（p 值=4.6e-13），这表明男性和女性肌肉之间的差异 DNA 甲基化和基因表达在功能上是相关的。最后，我们用 qPCR 在 Gene SMART 队列中验证了三个具有大效应量的基因（FOXO3A、ALDH1A1 和 GGT7）的表达。GGT7 参与抗氧化代谢，在三个队列中均表现出男性偏倚表达和男性甲基化程度降低。总之，我们发现了 8420 个在人类骨骼肌中男性和女性之间存在 DNA 甲基化差异的基因，这些基因可能调节控制肌肉代谢和健康的机制。
