Post-GWAS methodologies for localisation of functional non-coding variants: ANGPTL3. (March 2016)

• Record Type: Journal Article
• Authors: Oldoni, Federico; Palmen, Jutta; Giambartolomei, Claudia; Howard, Philip; Drenos, Fotios; Plagnol, Vincent; Humphries, Steve E.; Talmud, Philippa J.; Smith, Andrew J.P.
• Is Part Of: Atherosclerosis. Volume 246(2016)
• Page Start: 193
• Page End: 201
• Publication Date: 2016-03
• Subjects: ANGPTL3 -- Polymorphism -- Regulation -- Chromatin -- Genome-wide -- Functional polymorphism -- FAIRE -- LDL-C; GWAS genome-wide association study -- LDL-C low density lipoprotein cholesterol -- HDL-C high density lipoprotein cholesterol -- TG triglycerides -- EMSA electrophoretic mobility shift assay -- SNP single nucleotide polymorphism; Arteriosclerosis -- Periodicals; Electronic journals; 616.136
• DOI: 10.1016/j.atherosclerosis.2015.12.009
• Languages: English
• ISSNs: 0021-9150

Abstract

Abstract: Genome-wide association studies have confirmed the involvement of non-coding angiopoietin-like 3 ( ANGPTL3 ) gene variants with coronary artery disease, levels of low-density lipoprotein cholesterol (LDL-C), triglycerides and ANGPTL3 mRNA transcript. Extensive linkage disequilibrium at the locus, however, has hindered efforts to identify the potential functional variants. Using regulatory annotations from ENCODE, combined with functional in vivo assays such as allele-specific formaldehyde-assisted isolation of regulatory elements, statistical approaches including eQTL/lipid colocalisation, and traditional in vitro methodologies including electrophoretic mobility shift assay and luciferase reporter assays, variants affecting the ANGPTL3 regulome were examined. From 253 variants associated with ANGPTL3 mRNA expression, and/or lipid traits, 46 were located within liver regulatory elements and potentially functional. One variant, rs10889352, demonstrated allele-specific effects on DNA-protein interactions, reporter gene expression and chromatin accessibility, in line with effects on LDL-C levels and expression of ANGPTL3 mRNA. The ANGPTL3 gene lies within DOCK7, although the variant is within non-coding regions outside of ANGPTL3, within DOCK7, suggesting complex long-range regulatory effects on gene expression. This study illustrates the power of combining multiple genome-wide datasets with laboratory data to localise functional non-coding variation and provides a model for analysis of regulatory variants from GWAS. Highlights: Over 200 variants exist in strong linkage disequilibrium with the lead ANGPTL3 SNP locus. rs10889352 affects DNA-protein interactions from liver nuclear extract. rs10889352 affects reporter gene expression in liver cells. rs10889352 is associated with chromatin accessibility. Effects on ANGPTL3 gene expression and lipid levels is likely due to rs10889352.