title: Role of DNA methylation in expression control of the IKZF3-GSDMA region in human epithelial cells.
abstract: Chromosomal region 17q12-q21 is associated with asthma and harbors regulatory polymorphisms that influence expression levels of all five protein-coding genes in the region: IKAROS family zinc finger 3 (Aiolos) (IKZF3), zona pellucida binding protein 2 (ZPBP2), ORMDL sphingolipid biosynthesis regulator 3 (ORMDL3), and gasdermins A and B (GSDMA, GSDMB). Furthermore, DNA methylation in this region has been implicated as a potential modifier of the genetic risk of asthma development. To further characterize the effect of DNA methylation, we examined the impact of treatment with DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (5-aza-dC) that causes DNA demethylation, on expression and promoter methylation of the five 17q12-q21 genes in the human airway epithelium cell line NuLi-1, embryonic kidney epithelium cell line 293T and human adenocarcinoma cell line MCF-7. 5-aza-dC treatment led to upregulation of expression of GSDMA in all three cell lines. ZPBP2 was upregulated in NuLi-1, but remained repressed in 293T and MCF-7 cells, whereas ORMDL3 was upregulated in 293T and MCF-7 cells, but not NuLi-1. Upregulation of ZPBP2 and GSDMA was accompanied by a decrease in promoter methylation. Moreover, 5-aza-dC treatment modified allelic expression of ZPBP2 and ORMDL3 suggesting that different alleles may respond differently to treatment. We also identified a polymorphic CTCF-binding site in intron 1 of ORMDL3 carrying a CG SNP rs4065275 and determined its methylation level. The site's methylation was unaffected by 5-aza-dC treatment in NuLi-1 cells. We conclude that modest changes (8-13%) in promoter methylation levels of ZPBP2 and GSDMA may cause substantial changes in RNA levels and that allelic expression of ZPBP2 and ORMDL3 is mediated by DNA methylation.
authors.affiliation: The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.
authors.forename: Sanny
authors.initials: S
authors.lastname: Moussette
authors.affiliation: Department of Human Genetics, McGill University Montreal, Quebec, Canada.
authors.forename: Abeer
authors.initials: A
authors.lastname: Al Tuwaijri
authors.affiliation: The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.
authors.forename: Hamid-Reza
authors.initials: HR
authors.lastname: Kohan-Ghadr
authors.affiliation: The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.
authors.forename: Samar
authors.initials: S
authors.lastname: Elzein
authors.affiliation: The Meakins-Christie Laboratories at the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.
authors.forename: Raquel
authors.initials: R
authors.lastname: Farias
authors.affiliation: The Meakins-Christie Laboratories at the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.
authors.forename: Julie
authors.initials: J
authors.lastname: Bérubé
authors.affiliation: Department of Human Genetics, McGill University Montreal, Quebec, Canada.
authors.forename: Bianca
authors.initials: B
authors.lastname: Ho
authors.affiliation: Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Quebec, Canada.
authors.forename: Catherine
authors.initials: C
authors.lastname: Laprise
authors.affiliation: The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.|Department of Pediatrics and Experimental Medicine, McGill University, Montreal, Quebec, Canada.
authors.forename: Cynthia G
authors.initials: CG
authors.lastname: Goodyer
authors.affiliation: The Meakins-Christie Laboratories at the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.
authors.forename: Simon
authors.initials: S
authors.lastname: Rousseau
authors.affiliation: The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.|Department of Human Genetics, McGill University Montreal, Quebec, Canada.|Department of Obstetrics and Gynecology, McGill University, Montreal, Quebec, Canada.
authors.forename: Anna K
authors.identifier: http://orcid.org/0000-0001-8481-5765
authors.initials: AK
authors.lastname: Naumova
mesh_terms: D000483:Alleles; D020816:Amino Acid Motifs; D001374:Azacitidine / Q000737:chemistry; D001665:Binding Sites; D002460:Cell Line; D019175:DNA Methylation; D004527:Egg Proteins / Q000235:genetics; D004847:Epithelial Cells / Q000378:metabolism*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D005838:Genotype; D057809:HEK293 Cells; D006801:Humans; D051740:Ikaros Transcription Factor / Q000235:genetics*; D061986:MCF-7 Cells; D008565:Membrane Proteins / Q000235:genetics; D009363:Neoplasm Proteins / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D015854:Up-Regulation; D000094524:Gasdermins
chemical_list: D001374:Azacitidine; D004527:Egg Proteins; D051740:Ikaros Transcription Factor; D008565:Membrane Proteins; D009363:Neoplasm Proteins; C485887:GSDMA protein, human; D000094524:Gasdermins; C527978:GSDMB protein, human; C106285:IKZF3 protein, human; C479482:ZPBP2 protein, human