Epigenomic variation atlas across human tissues and individuals in GTEx

摘要： 基因型-组织表达项目（GTEx）正在扩大初级组织的可用性， 用于研究遗传变异对个体间基因表达的影响的样本， 组织中然而，基因表达水平的个体间差异通常可由以下因素引起： 多种变体的组合效应，其中每一种都可能影响不同调节因子的活性。 区域以复杂的方式，也整合复杂的转录后事件。从而 直接评估序列变异对调控元件的影响，我们建议 对储存的GTEx生物标本进行系统性表观遗传修饰，以增强 基因表达变异分析已经可用，并由GTEx联盟计划。 目标1。我们将使用全基因组亚硫酸氢盐测序（WGBS）来分析DNA甲基化 8个GTEx组织中20个个体基因组中所有28 M CpG的水平。我们将利用这些 鉴定跨细胞类型和跨个体的可变甲基化区域（VMR）， 评估eQTL SNP对邻近CpG的DNA甲基化水平的影响， 识别等位基因特异性甲基化（ASM）区域及其组织特异性。目标2.我们将 系统地分析了250个个体在相同的8个组织中的DNA甲基化水平， 杂交选择亚硫酸氢盐测序（HSBS），用于在 增强子相关、eQTL相关和个体间可变区。我们将会用这些 为了预测每个组织中的甲基化数量性状基因座（meQTL），将这些与GTEx相关， 表达QTL（eQTL）为相同的组织，以提供机制的假设， 个体基因表达变异，并发现没有单一eQTL的基因的meQTL 意义重大目标3。我们将使用染色质免疫沉淀测序（ChIP-Seq）， 6 GTEx脑中增强子和启动子相关组蛋白修饰H3 K27 ac的概况 100个个体的样本，以识别基因型相关的增强子区域， 增强QTL。我们将把这些与相同组织中的eQTL和使用 增强子近端和eQTL近端CpG上的HSBS，以产生用于增强子近端和eQTL近端CpG的机制模型。 与基因型变异相关的调节变化。我们将与GTEx密切合作 分析联盟将GTEx eQTL与我们预测的meQTL、ASM区域和 增强QTL将调控区变异与基因表达变异和全基因组相关 关联研究，以了解组织特异性基因序列变异的作用 调节、基因表达和人类疾病。

Abstract: The Genotype-Tissue Expression project (GTEx) is expanding the availability of primary tissue samples for studying the impact of genetic variation on gene expression across individuals and tissues. However, inter-individual variation in gene expression level can often result from the combined effects of multiple variants, each of which may affect the activity of different regulatory regions in complex ways, and also integrate complex post-transcriptional events. Thus, to directly assess the effect of sequence variants on regulatory elements, we propose to systematic profile epigenetic modifications on stored GTEx biospecimens to enhance the analysis of gene expression variation already available and planned by the GTEx consortium. Aim 1. We will use whole-genome bisulfite sequencing (WGBS) to profile DNA methylation levels for all 28M CpGs in the genome of 20 individuals in 8 GTEx tissues. We will use these to identify variable methylated regions (VMRs) across cell types and across individuals, to evaluate the effects of eQTL SNPs on DNA methylation levels of neighboring CpGs, and to recognize allele-specific methylation (ASM) regions and their tissue specificity. Aim 2. We will systematically profile DNA methylation levels across 250 individuals in the same 8 tissues using hybrid-selection bisulfite sequencing (HSBS) for a subset of 2M regions selected within enhancer-associated, eQTL-associated, and inter-individual variable regions. We will use these to predict methylation quantitative trait loci (meQTLs) in each tissue, relate these to GTEx expression QTLs (eQTLs) for the same tissues to provide mechanistic hypotheses for inter- individual gene expression variation, and to discover meQTLs for genes where no single eQTL is significant. Aim 3. We will use chromatin immunoprecipitation sequencing (ChIP-Seq) to profile enhancer- and promoter-associated histone modification H3K27ac in 6 GTEx brain samples across 100 individuals, to recognize genotype-associated enhancer regions and enhQTLs. We will relate these to eQTLs in the same tissues and meQTLs discovered using HSBS on enhancer-proximal and eQTL proximal CpGs to generate mechanistic models for regulatory changes associated with genotype variation. We will work closely with the GTEx Analysis Consortium to integrate GTEx eQTLs with our predicted meQTLs, ASM regions, and enhQTLs to relate regulatory region variation to gene expression variation and to genome-wide association studies to understand the role of sequence variation in tissue-specific gene regulation, gene expression, and human disease.