Genetic variation in human RHS7 of the T H 2 locus control region influences DNA methylation and is associated with IgE

Background: Previously, polymorphisms in the T H 2 cytokine locus on chromosome 5q31 showed associations with asthma and IgE (Li X. et al. J Allergy Clin Immunol 2010; 125(2):328-335e11). While the locus contains interleukins (IL) 4, 5 and 13 essential for T H 2 differentiation the strongest association signal mapped to the RAD50 gene. In mice, Rad50 harbors an epigenetic locus control region defined by four Rad50 DNase I hypersensitive sites (RHS4-7) of which RHS7 undergoes the strongest regulatory changes during T H 2 differentiation (Lee G.R. et al. Nat Immunol 2005; 6(1):42-48). We investigated if the human homolog of RHS7 influences T H 2 locus gene expression or DNA methylation and if associations with asthma or IgE exist. Methods: Human RHS7 was fine mapped for polymorphisms based on 1000 Genomes data. Allele-specific changes in transcription factor binding were analyzed with electrophoretic mobility shift assays. Effects on mRNA expression ( RAD50 , IL4 , IL13 ) were measured in whole blood (n=100 adults). Differences in DNA methylation were studied in cord blood (n=73) and at age 4.5 years (n=61) in the PASTURE cohort. Genetic association with childhood asthma or total serum IgE was tested in the MAGICS/ISAAC II population (n=1,145). Results: Fine mapping identified the polymorphism rs2240032 to be located in RHS7. Allele-specific transcription factor binding was observed in EMSA. Furthermore, significant polymorphism effects were present on methylation in the IL13 promoter region (cord blood: p =0.003; age 4.5 years: p =0.032) and on IgE levels ( p =0.023). Conclusion : Polymorphism rs2240032 in the T H 2 cytokine locus influences 5q31 DNA methylation and total IgE levels.