Objective: To screen for abnormal methylation in CpG islands and CpG sites through whole genome of congenital microtia to identify their associated genes. To discuss the relationship between abnormal methylation level of genes and the etiology of congenital microtia.
Methods: Residual ear cartilage of 50 patients with microtia was collected with ear cartilage of 34 patients without ear malformations as control. Nimblegen CpG promoter array was chosen to screen the 28,226 CpG islands in the whole genome of both experimental and control groups. The genes with differential methylated CpG islands were selected. SpectroCHIP array was chosen to detect the methylation level of each CpG site in abnormal methyletion CpG islands of both experimental and control groups. The CpG sites with differential methylation level were selected.
Results: There were 36 CpG islands with differential methylated level in whole genome between experimental group and control group, among which 29 CpG islands were connected with 29 named genes. In the abnormal methylated CpG islands of COL18A1, MYH14, RBMY1A1 and ZIC3, 6 differentially methylated CpG sites were found with statistical significance. The methylation level of these 6 CpG sites in experimental group and control group were COL18A1_2_CpG_170.9783 +/- 0.0235 and 0.9526 +/- 0.0589; MYH14_CpG_170.9600 +/- 0.0414 and 0.9284 +/- 0.0655; RBMY1A1_1_CpG_3.40.9966 +/- 0.0055 and 0.9914 +/- 0.0069; RBMY1A1_1_CpG_130.9648 +/- 0.0118 and 0.9757 +/- 0.0127; ZIC3_3_CpG_150.0867 +/- 0.0212 and 0.0543 +/- 0.0399; ZIC3_2_CpG_270.3775 +/- 0.1816 and 0.472 3 +/- 0.0439.
Conclusions: The DNA methylation profile of the entire genome is initially established. The abnormal methylated CpG islands of COL18A1, MYH14, RBMY1A1 and ZIC3 might be related to the pathogenesis of microtia.