Lack of correlation between DNA methylation of promoter regions and allelic imbalance in expression of non-imprinted genes in lymphoblastoid cell lines

¹Aabida Saferali, ²Sanny Moussette, ³Eef Harmsen, ³Donna Sinnett, ³Bing Ge, ³David Serre, ^1,3Tomi Pastinen, ^1,2Anna Naumova
¹Department of Human Genetics, McGill University Montreal H3A 1B1, Canada, ²Department of Obstetrics and Gynecology, McGill University Health Centre Montreal H3A 1A1, Canada, ³McGill University and Genome Quebec Innovation Centre, Montreal H3A 1A4, Canada

The goal of the Gene Regulators in Disease (GRID) project is elucidation of the regulatory mechanisms that lead to allelic imbalance (AI) in gene expression. One of the mechanisms that can lead to allele-specific differences in gene expression levels is DNA methylation. To understand its role in regulatory variation in humans, we investigated the role of DNA methylation in the genesis of AI. Among 32 genes with AI and evidence of regulatory cis-elements, we selected 5 genes: catalase (CAT); follicular lymphoma variant translocation 1 (FVT1); peptidylprolyl isomerase D (PPID); RAB7 family-like 1 (RAB7L1); and vitamin D receptor (VDR), that satisfied the following criteria: 1) contained CG-islands spanning the promoter region and the first exon, 2) showed no allelic differences in promoter activities in in vitro assays; 3) homozygotes had similar levels of expression. We developed sodium bisulfite sequencing assays and established DNA methylation patterns of promoter regions of these genes in human lymophoblastoid cell lines. The gene BTN3A2 was used as a negative control. As a positive control, DNA methylation of three imprinting control regions, the intragenic differentially methylated region (IG DMR) in chromosome 14q32, the paternally expressed gene1/mesoderm specific transcript (PEG1/MEST DMR), and the H19 DMR was characterized. Our results show that regulatory variation is not associated with allele-specific DNA methylation of promoters of the six genes with AI. We also found abnormal methylation of the IG DMR that may reflect the influence of long-term cell culture on epigenetic profiles. Conclusion: Allele-specific DNA methylation is not the most common mechanism underlying AI that is found in lymphoblastoid cell lines.