Osteoarthritis is highly heritable and genome-wide studies have identified single nucleotide polymorphisms (SNPs) associated with the disease. One such locus is marked by SNP rs11732213 (T > C). Genotype at rs11732213 correlates with the methylation levels of nearby CpG dinucleotides (CpGs), forming a methylation quantitative trait locus (mQTL). This study investigated the regulatory activity of the CpGs to identify a target gene of the locus. Nucleic acids were extracted from the articular cartilage of osteoarthritis patients. Samples were genotyped, and DNA methylation was quantified by pyrosequencing at 14 CpGs within a 259-bp interval. CpGs were tested for enhancer effects in immortalised chondrocytes using a reporter gene assay. DNA methylation at the locus was altered using targeted epigenome editing, with the impact on gene expression determined using quantitative polymerase chain reaction. rs11732213 genotype correlated with DNA methylation at nine CpGs, which formed a differentially methylated region (DMR), with the osteoarthritis risk allele T corresponding to reduced levels of methylation. The DMR acted as an enhancer and demethylation of the CpGs altered expression of TMEM129. Allelic imbalance in TMEM129 expression was identified in cartilage, with under-expression of the risk allele. TMEM129 is a target of osteoarthritis genetic risk at this locus. Genotype at rs11732213 impacts DNA methylation at the enhancer, which, in turn, modulates TMEM129 expression. TMEM129 encodes an enzyme involved in protein degradation within the endoplasmic reticulum, a process previously implicated in osteoarthritis. TMEM129 is a compelling osteoarthritis susceptibility target.

中文翻译：

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鉴定编码泛素蛋白连接酶的 TMEM129 作为骨关节炎遗传风险的效应基因

骨关节炎具有高度遗传性，全基因组研究已确定与该疾病相关的单核苷酸多态性 (SNP)。一个这样的基因座由 SNP rs11732213 (T > C) 标记。rs11732213 的基因型与附近 CpG 二核苷酸 (CpG) 的甲基化水平相关，形成甲基化数量性状基因座 (mQTL)。本研究调查了 CpG 的调节活性，以鉴定该基因座的靶基因。从骨关节炎患者的关节软骨中提取核酸。对样品进行基因分型，并通过焦磷酸测序在 259 bp 间隔内以 14 个 CpG 进行量化。使用报告基因测定法测试 CpG 在永生化软骨细胞中的增强作用。使用靶向表观基因组编辑改变基因座的 DNA 甲基化，使用定量聚合酶链反应确定对基因表达的影响。rs11732213 基因型与 9 个 CpG 的 DNA 甲基化相关，形成差异甲基化区域 (DMR)，骨关节炎风险等位基因 T 对应于甲基化水平降低。DMR 充当增强剂，CpG 的去甲基化改变了 TMEM129 的表达。在软骨中发现 TMEM129 表达的等位基因失衡，风险等位基因表达不足。TMEM129 是该位点骨关节炎遗传风险的目标。rs11732213 的基因型影响增强子的 DNA 甲基化，进而调节 TMEM129 的表达。TMEM129 编码一种参与内质网内蛋白质降解的酶，这一过程以前与骨关节炎有关。