Identification of a regulatory variant that binds FOXA1 and FOXA2 at the CDC123/CAMK1D type 2 diabetes GWAS locus.
Identification of a regulatory variant that binds FOXA1 and FOXA2 at the CDC123/CAMK1D type 2 diabetes GWAS locus.
复制标题
DOI：
10.1371/journal.pgen.1004633
复制
发表时间：
2014-09
期刊：
影响因子：
4.5
通讯作者：
Mohlke KL
中科院分区：
文献类型：
--
作者：
Fogarty MP;Cannon ME;Vadlamudi S;Gaulton KJ;Mohlke KL
通过全基因组关联研究确定的许多2型糖尿病位点定位于非蛋白编码内含子和基因间区域，并且可能包含调节基因转录的变体。10号染色体上的CDC 123/CAMK 1D 2型糖尿病相关信号跨越CDC 123和CAMK 1D之间的基因间区域，并且也与CDC 123 3 3′UTR重叠。为了深入了解相关信号的分子机制，我们使用了来自2型糖尿病相关细胞类型的开放染色质、组蛋白修饰和转录因子ChIP-seq数据集来鉴定与预测调控区重叠的SNP。使用荧光素酶报告基因测定法测试含有2型糖尿病相关变体的两个区域的增强子活性。一个SNP，rs 11257655，在832/13和MIN 6胰岛素瘤细胞以及人HepG 2肝细胞癌细胞中显示转录增强子活性的等位基因差异。rs 11257655的风险等位基因T显示更大的转录活性比非风险等位基因C在所有测试的细胞类型。使用电迁移率偏移和超偏移分析，我们证明了rs 11257655风险等位基因表现出等位基因特异性结合FOXA 1和FOXA 2。我们在人类胰岛中使用等位基因特异性ChIP验证了在rs 11257655风险等位基因处的FOXA 1和FOXA 2富集。这些结果表明，rs 11257655通过改变包括FOXA 1和FOXA 2的蛋白复合物的结合来影响转录活性，从而在该GWAS位点提供了潜在的分子机制。GWAS已经确定了1200多个与疾病风险相关的基因座，其中包括70多个与2型糖尿病相关的基因座。随着大多数相关变异定位于基因组的非编码区，焦点已经转移到识别解释关联信号的功能变异。变体可能起作用的一种机制是影响调节靶基因表达的增强子元件的活性。在这项研究中，我们利用人类调控元件的全基因组注释的最新进展，优先考虑CDC 123/CAMK 1D基因座的候选功能变体。我们确定了两个T2 D相关的变体，重叠预测的调控增强子元件。我们证明了一个变体，rs 11257655，在与2型糖尿病相关的哺乳动物细胞系中显示等位基因特异性转录增强子活性。我们还显示了差异蛋白质-DNA结合，表明rs 11257655 2型糖尿病风险等位基因通过结合包括FOXA 1和FOXA 2的蛋白质复合物增加转录活性。这项研究表明，全基因组调控元件的地图是一个有用的资源，以指导识别差异影响转录活性的变体，并提供深入了解T2 D易感基因座的分子机制。
Many of the type 2 diabetes loci identified through genome-wide association studies localize to non-protein-coding intronic and intergenic regions and likely contain variants that regulate gene transcription. The CDC123/CAMK1D type 2 diabetes association signal on chromosome 10 spans an intergenic region between CDC123 and CAMK1D and also overlaps the CDC123 3′UTR. To gain insight into the molecular mechanisms underlying the association signal, we used open chromatin, histone modifications and transcription factor ChIP-seq data sets from type 2 diabetes-relevant cell types to identify SNPs overlapping predicted regulatory regions. Two regions containing type 2 diabetes-associated variants were tested for enhancer activity using luciferase reporter assays. One SNP, rs11257655, displayed allelic differences in transcriptional enhancer activity in 832/13 and MIN6 insulinoma cells as well as in human HepG2 hepatocellular carcinoma cells. The rs11257655 risk allele T showed greater transcriptional activity than the non-risk allele C in all cell types tested. Using electromobility shift and supershift assays we demonstrated that the rs11257655 risk allele showed allele-specific binding to FOXA1 and FOXA2. We validated FOXA1 and FOXA2 enrichment at the rs11257655 risk allele using allele-specific ChIP in human islets. These results suggest that rs11257655 affects transcriptional activity through altered binding of a protein complex that includes FOXA1 and FOXA2, providing a potential molecular mechanism at this GWAS locus. GWAS have identified more than 1200 loci contributing to risk of disease, including more than 70 loci associated with type 2 diabetes. With a majority of associated variants localized to non-coding regions of the genome, focus has moved to identifying the functional variants explaining the association signals. One mechanism by which variants may act is to affect activity of enhancer elements regulating target gene expression. In this study, we take advantage of recent advances in genome-wide annotation of human regulatory elements to prioritize candidate functional variants at the CDC123/CAMK1D locus. We identify two T2D-associated variants that overlap predicted regulatory enhancer elements. We demonstrate that one variant, rs11257655, shows allele-specific transcriptional enhancer activity in mammalian cell lines relevant to type 2 diabetes. We also show differential protein-DNA binding suggesting that the rs11257655 type 2 diabetes- risk allele increased transcriptional activity through binding a protein complex that includes FOXA1 and FOXA2. This study demonstrates that genome-wide maps of regulatory elements are a useful resource to guide identification of variants differentially affecting transcriptional activity and provides insight into molecular mechanisms underlying a T2D susceptibility locus.
登录
查看更多内容
影响因子：
9.8
作者：
ENCODE Project Consortium
通讯作者：
ENCODE Project Consortium
影响因子：
3.7
作者：
Haney S;Zhao J;Tiwari S;Eng K;Guey LT;Tien E
通讯作者：
Tien E
影响因子：
64.8
作者：
Heintzman, Nathaniel D.;Hon, Gary C.;Hawkins, R. David;Kheradpour, Pouya;Stark, Alexander;Harp, Lindsey F.;Ye, Zhen;Lee, Leonard K.;Stuart, Rhona K.;Ching, Christina W.;Ching, Keith A.;Antosiewicz-Bourget, Jessica E.;Liu, Hui;Zhang, Xinmin;Green, Roland D.;Lobanenkov, Victor V.;Stewart, Ron;Thomson, James A.;Crawford, Gregory E.;Kellis, Manolis;Ren, Bing
通讯作者：
Ren, Bing
遗传和分子洞察力对Prox1在葡萄糖代谢中的作用。
影响因子：
7.7
作者：
Lecompte S;Pasquetti G;Hermant X;Grenier-Boley B;Gonzalez-Gross M;De Henauw S;Molnar D;Stehle P;Béghin L;Moreno LA;Amouyel P;Dallongeville J;Meirhaeghe A
通讯作者：
Meirhaeghe A
人类胰岛中的开放染色质图。
影响因子：
30.8
作者：
Gaulton, Kyle J.;Nammo, Takao;Pasquali, Lorenzo;Simon, Jeremy M.;Giresi, Paul G.;Fogarty, Marie P.;Panhuis, Tami M.;Mieczkowski, Piotr;Secchi, Antonio;Bosco, Domenico;Berney, Thierry;Montanya, Eduard;Mohlke, Karen L.;Lieb, Jason D.;Ferrer, Jorge
通讯作者：
Ferrer, Jorge