Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants (ChIP-seq)

Chromatin-based functional genomic analyses and genomewide association studies (GWASs) together implicate enhancers as critical elements influencing gene expression and risk for common diseases. Here, we performed systematic chromatin and transcriptome pro- filing in human pancreatic islets. Integrated analysis of islet data with those generated by the ENCODE project in nine cell types identified specific and significant enrichment of type 2 diabetes and related quantitative trait GWAS variants in islet enhancers. Our integrated chromatin maps reveal that most enhancers are short (median = 0.8 kb). Each cell type also contains a substantial number of more extended (=3 kb) enhancers. Interestingly, these stretch enhancers are often tissue-specific and overlap locus control regions, suggesting that they are important chromatin regulatory beacons. Indeed, we show that (i) tissue specificity of enhancers and nearby gene expression increase with enhancer length; (ii) neighborhoods containing stretch enhancers are enriched for important cell type– specific genes; and (iii) GWAS variants associated with traits rele- vant to a particular cell type are more enriched in stretch enhancers compared with short enhancers. Reporter constructs containing stretch enhancer sequences exhibited tissue-specific activity in cell culture experiments and in transgenic mice. These results suggest that stretch enhancers are critical chromatin elements for coordinating cell type–specific regulatory programs and that sequence variation in stretch enhancers affects risk of major common human diseases. Overall design: Integrated analysis of islet chromatin modification and transcriptome data with those generated by the ENCODE project. NISC Comparative Sequencing Program

基于染色质的功能基因组分析与全基因组关联研究（Genome-Wide Association Studies, GWAS）共同证实，增强子是影响基因表达与常见疾病发病风险的关键调控元件。本研究在人类胰岛中开展了系统性染色质与转录组谱分析。将胰岛数据与ENCODE计划在9种细胞类型中生成的数据进行整合分析后，我们发现2型糖尿病及相关数量性状的GWAS变异位点在胰岛增强子中呈现显著且特异性的富集。我们的整合染色质图谱显示，大多数增强子长度较短（中位数为0.8 kb），而每种细胞类型中亦存在大量长度≥3 kb的延长型增强子。有趣的是，这类延长型增强子通常具有组织特异性，且与位点控制区域存在重叠，提示其为重要的染色质调控标记。本研究验证表明：其一，增强子的组织特异性及其邻近基因的表达水平随增强子长度增加而提升；其二，携带延长型增强子的基因组区域显著富集细胞类型特异性的关键基因；其三，与特定细胞类型相关性状关联的GWAS变异位点，在延长型增强子中的富集程度显著高于短长度增强子。包含延长型增强子序列的报告基因构建体，在细胞培养实验与转基因小鼠模型中均表现出组织特异性的调控活性。上述结果表明，延长型增强子是协调细胞类型特异性调控程序的关键染色质元件，其序列变异可影响人类主要常见疾病的发病风险。实验整体设计：将胰岛染色质修饰与转录组数据，与ENCODE计划生成的数据进行整合分析。NISC比较测序计划