title: Post-GWAS methodologies for localisation of functional non-coding variants: ANGPTL3.
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.
authors.affiliation: Department of Cardiovascular Genetics, Institute of Cardiovascular Sciences, University College London, London, UK; Department of Molecular Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
authors.forename: Federico
authors.initials: F
authors.lastname: Oldoni
authors.affiliation: Department of Cardiovascular Genetics, Institute of Cardiovascular Sciences, University College London, London, UK.
authors.forename: Jutta
authors.initials: J
authors.lastname: Palmen
authors.affiliation: UCL Genetics Institute, University College London, London, UK.
authors.forename: Claudia
authors.initials: C
authors.lastname: Giambartolomei
authors.affiliation: Department of Cardiovascular Genetics, Institute of Cardiovascular Sciences, University College London, London, UK.
authors.forename: Philip
authors.initials: P
authors.lastname: Howard
authors.affiliation: Department of Cardiovascular Genetics, Institute of Cardiovascular Sciences, University College London, London, UK.
authors.forename: Fotios
authors.initials: F
authors.lastname: Drenos
authors.affiliation: UCL Genetics Institute, University College London, London, UK.
authors.forename: Vincent
authors.initials: V
authors.lastname: Plagnol
authors.affiliation: Department of Cardiovascular Genetics, Institute of Cardiovascular Sciences, University College London, London, UK.
authors.forename: Steve E
authors.initials: SE
authors.lastname: Humphries
authors.affiliation: Department of Cardiovascular Genetics, Institute of Cardiovascular Sciences, University College London, London, UK.
authors.forename: Philippa J
authors.initials: PJ
authors.lastname: Talmud
authors.affiliation: Department of Cardiovascular Genetics, Institute of Cardiovascular Sciences, University College London, London, UK. Electronic address: Andrew.J.P.Smith@ucl.ac.uk.
authors.forename: Andrew J P
authors.initials: AJ
authors.lastname: Smith
mesh_terms: D000091303:Angiopoietin-Like Protein 3; D000075802:Angiopoietin-like Proteins; D042682:Angiopoietins / Q000235:genetics* / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly; D019295:Computational Biology; D003324:Coronary Artery Disease / Q000175:diagnosis / Q000453:epidemiology / Q000235:genetics* / Q000378:metabolism; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D056945:Hep G2 Cells; D006801:Humans; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D013997:Time Factors; D014162:Transfection
chemical_list: C479896:ANGPTL3 protein, human; D000091303:Angiopoietin-Like Protein 3; D000075802:Angiopoietin-like Proteins; D042682:Angiopoietins
keywords: ANGPTL3; Chromatin; FAIRE; Functional polymorphism; Genome-wide; LDL-C; Polymorphism; Regulation