Title | Multiple variant enhancers modulate its cardiac gene expression and the QT interval. |
Publication Type | Journal Article |
Year of Publication | 2019 |
Authors | Kapoor A, Lee D, Zhu L, Soliman EZ, Grove ML, Boerwinkle E, Arking DE |
Secondary Authors | Chakravarti A |
Journal | Proc Natl Acad Sci U S A |
Volume | 116 |
Issue | 22 |
Pagination | 10636-10645 |
Date Published | 2019 05 28 |
ISSN | 1091-6490 |
Keywords | Alleles, Animals, Cell Line, Electrocardiography, Gene Expression Regulation, Genetic Variation, Genome-Wide Association Study, Heart, Humans, Mice, Myocardium, NAV1.5 Voltage-Gated Sodium Channel, Quantitative Trait Loci, Regulatory Sequences, Nucleic Acid |
Abstract | The rationale for genome-wide association study (GWAS) results is sequence variation in -regulatory elements (CREs) modulating a target gene's expression as the major cause of trait variation. To understand the complete molecular landscape of one of these GWAS loci, we performed in vitro reporter screens in cardiomyocyte cell lines for CREs overlapping nearly all common variants associated with any of five independent QT interval (QTi)-associated GWAS hits at the - locus. We identified 13 causal CRE variants using allelic reporter activity, cardiomyocyte nuclear extract-based binding assays, overlap with human cardiac tissue DNaseI hypersensitive regions, and predicted impact of sequence variants on DNaseI sensitivity. Our analyses identified at least one high-confidence causal CRE variant for each of the five sentinel hits that could collectively predict cardiac gene expression and QTi association. Although all 13 variants could explain gene expression, the highest statistical significance was obtained with seven variants (inclusive of the five above). Thus, multiple, causal, mutually associated CRE variants can underlie GWAS signals. |
DOI | 10.1073/pnas.1808734116 |
Alternate Journal | Proc Natl Acad Sci U S A |
PubMed ID | 31068470 |
PubMed Central ID | PMC6561183 |
Grant List | R01 GM104469 / GM / NIGMS NIH HHS / United States HHSN268201700001I / HL / NHLBI NIH HHS / United States HHSN268201700002I / HL / NHLBI NIH HHS / United States HHSN268201700003I / HL / NHLBI NIH HHS / United States HHSN268201700005I / HL / NHLBI NIH HHS / United States HHSN268201700004I / HL / NHLBI NIH HHS / United States R01 HL086694 / HL / NHLBI NIH HHS / United States U01 HG004402 / HG / NHGRI NIH HHS / United States UL1 RR025005 / RR / NCRR NIH HHS / United States |