Journal
AMERICAN JOURNAL OF HUMAN GENETICS
Volume 97, Issue 6, Pages 801-815Publisher
CELL PRESS
DOI: 10.1016/j.ajhg.2015.10.016
Keywords
-
Categories
Funding
- NIH [T32HL069768, T32GM007092, R01DK072193, R21DA027040, R01DK093757, T32GM067553, R01DK062370, K99HL121172, P01HL28481]
- National Human Genome Research Institute Division of Intramural Research [Z01HG000024]
- American Heart Association [13PRE16930025]
- Academy of Finland [77299, 124243]
- Finnish Heart Foundation
- Finnish Diabetes Foundation
- Finnish Funding Agency for Technology and Innovation (TEKES) [1510/31/06]
- Commission of the European Community [HEALTH-F2-2007-201681]
- University of Oulu
- British Heart Foundation
- Wellcome Trust
- Medical Research Council
- MRC [MC_UU_12013/1] Funding Source: UKRI
- Medical Research Council [MC_UU_12013/1] Funding Source: researchfish
- Academy of Finland (AKA) [77299, 77299] Funding Source: Academy of Finland (AKA)
Ask authors/readers for more resources
Genome-wide association studies (GWASs) have identified more than 150 loci associated with blood lipid and cholesterol levels; however, the functional and molecular mechanisms for many associations are unknown. We examined the functional regulatory effects of candidate variants at the GALNT2 locus associated with high-density lipoprotein cholesterol (HDL-C). Fine-mapping and conditional analyses in the METSIM study identified a single locus harboring 25 noncoding variants (r(2) > 0.7 with the lead GWAS variants) strongly associated with total cholesterol in medium-sized HDL (e.g., rs17315646, p = 3.5 x 10(-12)). We used luciferase reporter assays in HepG2 cells to test all 25 variants for allelic differences in regulatory enhancer activity. rs2281721 showed allelic differences in transcriptional activity (75-fold [T] versus 27-fold [C] more than the empty-vector control), as did a separate 780-bp segment containing rs4846913, rs2144300, and rs6143660 (49-fold [AT(-) haplotype] versus 16-fold [CC+ haplotype] more). Using electrophoretic mobility shift assays, we observed differential CEBPB binding to rs4846913, and we confirmed this binding in a native chromatin context by performing chromatin-immunoprecipitation (ChIP) assays in HepG2 and Huh-7 cell lines of differing genotypes. Additionally, sequence reads in HepG2 DNase-I-hypersensitivity and CEBPB ChIP-seq signals spanning rs4846913 showed significant allelic imbalance. Allelic-expression-imbalance assays performed with RNA from primary human hepatocyte samples and expression-quantitative-trait-locus (eQTL) data in human subcutaneous adipose tissue samples confirmed that alleles associated with increased HDL-C are associated with a modest increase in GALNT2 expression. Together, these data suggest that at least rs4846913 and rs2281721 play key roles in influencing GALNT2 expression at this HDL-C locus.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available