Sex-specific DNA methylation and associations with in utero tobacco smoke exposure at nuclear-encoded mitochondrial genes

Sex-linked differences in mitochondrial ATP production, enzyme activities, and reactive oxygen species generation have been reported in multiple tissue and cell types. While the effects of reproductive hormones underlie many of these differences, regulation of sexually dimorphic mitochondrial function has not been fully characterized. We hypothesized that sex-specific DNA methylation contributes to sex-specific expression of nuclear genes that influence mitochondrial function. Herein, we analysed DNA methylation data specifically focused on nuclear-encoded mitochondrial genes in 191 males and 190 females. We found 596 differentially methylated sites (DMSs) (FDR p ATP5G2, encoding subunit C of ATP synthase, contains seven DMSs and exhibits a sex difference in expression (p = 0.04). Finally, we also found that alterations in DNA methylation associated with in utero tobacco smoke exposure were sex-specific in these nuclear-encoded mitochondrial genes. Interestingly, the level of sex differences in DNA methylation at nuclear-encoded mitochondrial genes and the level of methylation changes associated with smoke exposure were less prominent than that of other genes. This suggests more conservative regulation of DNA methylation at these nuclear-encoded mitochondrial genes as compared to others. Overall, our findings suggest that sex-specific DNA methylation may help establish sex differences in expression and function and that sex-specific alterations in DNA methylation in response to exposures could contribute to sex-variable toxicological responses.

已有多项研究在多种组织与细胞类型中发现，线粒体ATP生成、酶活性以及活性氧（reactive oxygen species）的产生存在性别相关差异。尽管生殖激素的作用是这类差异的重要基础，但目前对于线粒体功能性别二态性的调控机制尚未完全阐明。本研究提出假设：性别特异性DNA甲基化（DNA methylation）可能参与调控影响线粒体功能的核基因的性别特异性表达。本研究针对191名男性和190名女性的样本，分析了聚焦于核编码线粒体基因的DNA甲基化数据。我们在这些核编码线粒体基因中，共发现596个呈现性别偏倚甲基化的差异甲基化位点（differentially methylated sites, DMSs），经错误发现率（FDR）校正的p值<0.001。在这些差异甲基化位点中，28%（167/596）在女性样本中呈高甲基化状态，72%（429/596）在男性样本中呈高甲基化状态。编码ATP合酶（ATP synthase）亚基C的ATP5G2基因包含7个差异甲基化位点，且其表达存在性别差异（p=0.04）。此外，本研究还发现，与宫内（in utero）烟草暴露相关的DNA甲基化改变，在这些核编码线粒体基因中也存在性别特异性。值得注意的是，核编码线粒体基因的DNA甲基化性别差异程度，以及与烟草暴露相关的甲基化改变程度，均弱于其他基因。这表明相较于其他基因，核编码线粒体基因的DNA甲基化调控更为保守。综上，本研究结果表明，性别特异性DNA甲基化可能参与塑造基因表达与功能的性别差异；而暴露因素诱导的DNA甲基化性别特异性改变，或可导致毒性应答的性别差异。