Interaction between genetic and epigenetic variation defines gene expression patterns at the asthma-associated locus 17q12-q21 in lymphoblastoid cell lines.

Soizik Berlivet,Abeer Al Tuwaijri,Dominique J Verlaan,Sanny Moussette,Tony Kwan,Manon Ouimet,Tomi Pastinen,Anna K Naumova,Daniel Sinnett,Vonda Koka

doi:10.1007/s00439-012-1142-x

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.Electronic supplementary materialThe online version of this article (doi:10.1007/s00439-012-1142-x) contains supplementary material, which is available to authorized users.

Highlights

Phenotypic variation is largely dependent on variation in gene expression levels
To determine to what extent allelic diVerences in gene expression levels in the 17q12-q21 region were deWned by genetic polymorphisms within gene promoters, the activity of annotated promoter regions of zona pellucida binding protein 2 (ZPBP2), gasdermin B (GSDMB) and ORMDL3 was tested in in vitro transfection assays in Wve diVerent cell types (Table 1; Fig. 1c)
We demonstrate that another common SNP, rs4795397 that is part of the cisregulatory haplotype and is located within the promoter region of the ZPBP2 is a putative functional polymorphism that shows allele-speciWc nucleosome occupancy and in vitro promoter activity

Summary

Introduction

Phenotypic variation is largely dependent on variation in gene expression levels. To identify the genetic determinants of phenotypic variation (including complex disease) in the human population, several genome-wide studies of genetically deWned diVerences in gene expression levels succeeded to map cis-regulatory polymorphisms for a proportion of genes with variable expression (Dixon et al 2007; Ge et al 2009; Goring et al 2007; Pastinen et al 2004; Verlaan et al 2009b; Yan et al 2002). DiVerences in the expression of three genes: zona pellucida binding protein 2 (ZPBP2), ORM1-like 3 (S. cerevisiae) (ORMDL3) and gasdermin B (GSDMB) located in 17q12-q21 (Fig. 1a) This genomic interval is associated with predisposition to early onset asthma, Crohn disease, ulcerative colitis and rheumatoid arthritis (Anderson et al 2011; Barrett et al 2008; MoVatt et al 2007, 2011; Stahl et al 2010). Elucidation of the regulatory mechanism that underlies the eVect of common polymorphisms on gene regulation is essential for the understanding of pathogenesis of asthma and other autoimmune diseases; a search for functional cisregulatory polymorphisms was undertaken This search identiWed SNP rs12936231 that modiWes a CTCF-binding site and inXuences nucleosome occupancy (Verlaan et al 2009a). To further elucidate the transcriptional control of this asthma-associated locus, we focused on the interaction between genetic and epigenetic factors in the promoter regions of the three genes whose expression depends upon the cis-regulatory haplotype

Methods

Results

Conclusion