Epigenomic variation atlas across human tissues and individuals in GTEx

描述（由申请人提供）：基因型-组织表达项目（GTEx）正在扩大原代组织样本的可用性，以研究遗传变异对个体和组织基因表达的影响。然而，基因表达水平的个体间变异通常是由多个变体的联合作用引起的，每个变体都可能以复杂的方式影响不同调控区域的活性，并且还整合复杂的转录后事件。因此，为了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生物标本进行系统的表观遗传修饰，以增强GTEx联盟已经提供和计划的基因表达变异分析。目标1。我们将使用全基因组亚硫酸氢盐测序（WGBS）来分析8个GTEx组织中20个个体基因组中所有28 M CpG的DNA甲基化水平。我们将使用这些来识别跨细胞类型和跨个体的可变甲基化区域（VMR），以评估eQTL SNP对相邻CpG的DNA甲基化水平的影响，并识别等位基因特异性甲基化（ASM）区域及其组织特异性。目标二。我们将系统地分析250个个体的DNA甲基化水平， 使用杂交选择亚硫酸氢盐测序（HSBS）对在增强子相关、eQTL相关和个体间可变区内选择的2 M区域的子集对相同的8个组织进行测序。我们将使用这些来预测每个组织中的甲基化数量性状基因座（meQTL），将这些与相同组织的GTEx表达QTL（eQTL）相关联，以提供个体间基因表达变异的机制假设，并发现没有单个eQTL显著的基因的meQTL。目标3。我们将使用染色质免疫沉淀测序（ChIP-Seq）来分析100个个体的6个GTEx脑样本中增强子和启动子相关的组蛋白修饰H3 K27 ac，以识别基因型相关的增强子区域和enhQTL。我们将把这些与相同组织中的eQTL和使用HSBS在增强子近端和eQTL近端CpG上发现的meQTL相关联，以生成与基因型变异相关的调控变化的机制模型。我们将与GTEx分析联盟密切合作，将GTEx eQTL与我们预测的meQTL、ASM区域和enhQTL整合，将调控区域变异与基因表达变异和全基因组关联研究联系起来，以了解序列变异在组织特异性基因调控、基因表达和人类疾病中的作用。

DESCRIPTION (provided by applicant): 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.