Abstract
Phenotypic variation results from variation in gene expression, which is modulated by genetic and/or epigenetic factors. To understand the molecular basis of human disease, interaction between genetic and epigenetic factors needs to be taken into account. The asthma-associated region 17q12-q21 harbors three genes, the zona pellucida binding protein 2 (
ZPBP2
), gasdermin B (
GSDMB)
and ORM1-like 3 (
ORMDL3
), that show allele-specific differences in expression levels in lymphoblastoid cell lines (LCLs) and CD4+ T cells. Here, we report a molecular dissection of allele-specific transcriptional regulation of the genes within the chromosomal region 17q12-q21 combining in vitro transfection, formaldehyde-assisted isolation of regulatory elements, chromatin immunoprecipitation and DNA methylation assays in LCLs. We found that a single nucleotide polymorphism rs4795397 influences the activity of
ZPBP2
promoter in vitro in an allele-dependent fashion, and also leads to nucleosome repositioning on the asthma-associated allele
.
However, variable methylation of exon 1 of
ZPBP2
masks the strong genetic effect on
ZPBP2
promoter activity in LCLs. In contrast, the
ORMDL3
promoter is fully unmethylated, which allows detection of genetic effects on its transcription. We conclude that the
cis
-regulatory effects on 17q12-q21 gene expression result from interaction between several regulatory polymorphisms and epigenetic factors within the
cis
-regulatory haplotype region.