BACKGROUND Genome-wide association studies (GWASs) have identified single-nucleotide polymorphisms (SNPs) that may be genetic factors underlying Alzheimer's disease (AD). However, how these AD-associated SNPs (AD SNPs) contribute to the pathogenesis of this disease is poorly understood because most of them are located in non-coding regions, such as introns and intergenic regions. Previous studies reported that some disease-associated SNPs affect regulatory elements including enhancers. We hypothesized that non-coding AD SNPs are located in enhancers and affect gene expression levels via chromatin loops. METHODS To characterize AD SNPs within non-coding regions, we extracted 406 AD SNPs with GWAS p-values of less than 1.00 × 10- 6 from the GWAS catalog database. Of these, we selected 392 SNPs within non-coding regions. Next, we checked whether those non-coding AD SNPs were located in enhancers that typically regulate gene expression levels using publicly available data for enhancers that were predicted in 127 human tissues or cell types. We sought expression quantitative trait locus (eQTL) genes affected by non-coding AD SNPs within enhancers because enhancers are regulatory elements that influence the gene expression levels. To elucidate how the non-coding AD SNPs within enhancers affect the gene expression levels, we identified chromatin-chromatin interactions by Hi-C experiments. RESULTS We report the following findings: (1) nearly 30% of non-coding AD SNPs are located in enhancers; (2) eQTL genes affected by non-coding AD SNPs within enhancers are associated with amyloid beta clearance, synaptic transmission, and immune responses; (3) 95% of the AD SNPs located in enhancers co-localize with their eQTL genes in topologically associating domains suggesting that regulation may occur through chromatin higher-order structures; (4) rs1476679 spatially contacts the promoters of eQTL genes via CTCF-CTCF interactions; (5) the effect of other AD SNPs such as rs7364180 is likely to be, at least in part, indirect through regulation of transcription factors that in turn regulate AD associated genes. CONCLUSION Our results suggest that non-coding AD SNPs may affect the function of enhancers thereby influencing the expression levels of surrounding or distant genes via chromatin loops. This result may explain how some non-coding AD SNPs contribute to AD pathogenesis.

中文翻译：

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与阿尔茨海默病相关的增强子变异通过染色质环影响基因表达。

背景全基因组关联研究（GWAS）已经鉴定出单核苷酸多态性（SNP）可能是阿尔茨海默病（AD）的遗传因素。然而，人们对这些 AD 相关 SNP（AD SNP）如何促成这种疾病的发病机制知之甚少，因为它们大多数位于非编码区域，例如内含子和基因间区域。先前的研究报告称，一些与疾病相关的 SNP 会影响包括增强子在内的调控元件。我们假设非编码 AD SNP 位于增强子中并通过染色质环影响基因表达水平。方法 为了表征非编码区域内的 AD SNP，我们从 GWAS 目录数据库中提取了 406 个 GWAS p 值小于 1.00 × 10-6 的 AD SNP。其中，我们选择了非编码区域内的 392 个 SNP。接下来，我们利用在 127 种人体组织或细胞类型中预测的增强子的公开数据，检查了这些非编码 AD SNP 是否位于通常调节基因表达水平的增强子中。我们寻找增强子内受非编码 AD SNP 影响的表达数量性状基因座 (eQTL) 基因，因为增强子是影响基因表达水平的调控元件。为了阐明增强子内的非编码 AD SNP 如何影响基因表达水平，我们通过 Hi-C 实验鉴定了染色质-染色质相互作用。结果我们报告了以下发现：（1）近30%的非编码AD SNP位于增强子中；(2) 增强子内受非编码 AD SNP 影响的 eQTL 基因与 β 淀粉样蛋白清除、突触传递和免疫反应相关；(3) 增强子中 95% 的 AD SNP 与拓扑关联域中的 eQTL 基因共定位，表明调节可能通过染色质高级结构发生；(4) rs1476679通过CTCF-CTCF相互作用在空间上接触eQTL基因的启动子；(5) 其他 AD SNP（例如 rs7364180）的影响可能至少部分是通过转录因子的调节间接产生的，而转录因子反过来又调节 AD 相关基因。结论 我们的结果表明，非编码 AD SNP 可能影响增强子的功能，从而通过染色质环影响周围或远处基因的表达水平。这一结果可以解释一些非编码 AD SNP 如何促进 AD 发病机制。