背景:将通过全基因组关联研究(GWAS)鉴定的遗传风险基因座与其因果基因联系起来仍然是一个重大挑战。疾病相关的遗传变异集中在含有调节DNA元件的区域,如启动子和增强子。尽管研究人员之前已经发表了肾小管细胞和肾小球内皮细胞这些调控区域的DNA图谱,足细胞和系膜细胞的地图尚未获得。
方法:我们从主要由足细胞和肾小球系膜细胞组成的人肾小球的原代生长培养物中生成了调控DNA图谱(DNase-seq)和配对基因表达谱(RNA-seq)。我们从肾皮质培养物中产生了类似的数据集,与肾小球文化进行比较。因为调节DNA元件可以在较大的基因组距离上作用于靶基因,我们还从新鲜分离的人肾小球中生成了染色质构象图谱。
结果:我们发现了数千种独特的DNA调控元件,许多位于转录因子基因附近,肾小球和皮质样本以不同的水平表达。我们发现与肾脏疾病(GWAS)相关的遗传变异和肾脏表达数量性状基因座在调节DNA区域中富集。通过结合GWAS,表观基因组,和染色质构象数据,我们在功能上注释了46个肾病基因。
结论:通过利用独特的调节DNA图谱和整合的表观基因组和遗传分析,我们证明了一种将肾脏疾病/性状相关基因座与其靶基因功能连接的强大方法。此过程可应用于其他肾脏细胞类型,并将增强我们对基因组调控及其对肾脏疾病中基因表达的影响的理解。
BACKGROUND: Linking genetic risk loci identified by genome-wide association studies (GWAS) to their causal genes remains a major challenge. Disease-associated genetic variants are concentrated in regions containing regulatory DNA elements, such as promoters and enhancers. Although researchers have previously published DNA maps of these regulatory regions for kidney tubule cells and glomerular endothelial cells, maps for podocytes and mesangial cells have not been available.
METHODS: We generated regulatory DNA maps (DNase-seq) and paired gene expression profiles (RNA-seq) from primary outgrowth cultures of human glomeruli that were composed mainly of podocytes and mesangial cells. We generated similar datasets from renal cortex cultures, to compare with those of the glomerular cultures. Because regulatory DNA elements can act on target genes across large genomic distances, we also generated a chromatin conformation map from freshly isolated human glomeruli.
RESULTS: We identified thousands of unique regulatory DNA elements, many located close to transcription factor genes, which the glomerular and cortex samples expressed at different levels. We found that genetic variants associated with kidney diseases (GWAS) and kidney expression quantitative trait loci were enriched in regulatory DNA regions. By combining GWAS, epigenomic, and chromatin conformation data, we functionally annotated 46 kidney disease genes.
CONCLUSIONS: We demonstrate a powerful approach to functionally connect kidney disease-/trait-associated loci to their target genes by leveraging unique regulatory DNA maps and integrated epigenomic and genetic analysis. This process can be applied to other kidney cell types and will enhance our understanding of genome regulation and its effects on gene expression in kidney disease.