A non-coding genetic variant associated with abdominal aortic aneurysm alters ERG gene regulation

Abdominal aortic aneurysm (AAA) is a major cause of sudden death in the elderly. While AAA has some overlapping genetic and environmental risk factors with atherosclerosis, there are substantial differences, and AAA-specific medication is lacking. A recent meta-analysis of genome-wide association studies has identified four novel single-nucleotide polymorphisms (SNPs) specifically associated with AAA. Here, we investigated the gene regulatory function for one of four non-coding SNPs associated with AAA, rs2836411, which is located in an intron of the ERG gene. Rs2836411 resides within a >70 kb super-enhancer that has high levels of H3K27ac and H3K4me1 in vascular endothelial and haematopoietic cell types. Enhancer luciferase assays in cell lines showed that the risk allele significantly alters enhancer activity. The risk allele also correlates with reduced ERG expression in aortic and other vascular tissues. To identify whether rs2836411 directly contacts the promoters of ERG and/or of genes further away, we performed allele-specific circular chromosome conformation capture sequencing. In vascular endothelial cells, which express ERG, the SNP region interacts highly within the super-enhancer, while in vascular smooth muscle cells, which do not express ERG, the interactions are distributed across a wider region that includes neighbouring genes. Furthermore, the risk allele has fewer interactions within the super-enhancer compared to the protective allele. In conclusion, our results indicate that rs2836411 likely affects ERG expression by altering enhancer activity and changing local chromatin interactions. ERG is involved in vascular development, angiogenesis, and inflammation in atherosclerosis; therefore mechanistically, rs2836411 could contribute to AAA by modulating ERG levels.