Post-GWAS methodologies for localisation of functional non-coding variants: ANGPTL3

Area of Science:

• Genetics
• Molecular Biology
• Cardiovascular Disease Research

Background:

• Genome-wide association studies (GWAS) link non-coding ANGPTL3 gene variants to coronary artery disease (CAD) and lipid levels.
• Linkage disequilibrium at the ANGPTL3 locus complicates identification of causal variants.

Purpose of the Study:

• To identify functional non-coding variants impacting the ANGPTL3 regulome and their association with CAD risk factors.
• To investigate the regulatory mechanisms underlying ANGPTL3 expression and lipid metabolism.

Main Methods:

• Integration of ENCODE regulatory annotations with functional assays (allele-specific formaldehyde-assisted isolation of regulatory elements, electrophoretic mobility shift assay, luciferase reporter assays).
• Statistical analyses including expression quantitative trait loci (eQTL) and lipid colocalization.
• Examination of 253 variants associated with ANGPTL3 mRNA expression and/or lipid traits.

Main Results:

• Identified 46 potentially functional variants within liver regulatory elements.
• rs10889352 demonstrated allele-specific effects on DNA-protein interactions, reporter gene expression, and chromatin accessibility.
• These effects correlated with altered low-density lipoprotein cholesterol (LDL-C) levels and ANGPTL3 mRNA expression.

Conclusions:

• The study successfully localized a functional non-coding variant (rs10889352) affecting ANGPTL3 regulation and lipid metabolism.
• This variant, located within non-coding regions of DOCK7, suggests complex long-range regulatory effects on ANGPTL3 gene expression.
• The findings provide a model for analyzing regulatory variants identified through GWAS.