DNA methylation reorganization of skeletal muscle-specific genes in response to gestational obesity

DNA methylation was measured in sixteen pregnant women [8-gestational obesity group; 8-control group] in umbilical cord using the Infinium Methylation EPIC Bead Chip microarray. Differentially methylated CpGs were identified with Beta Regression Models (false discovery rate (FDR)<0.05 and an Odds Ratio>1.5 or <0.67). DNA methylation interactions between CpGs of skeletal muscle-specific genes were studied using data from Pearson correlation matrices. In order to quantify the interactions within each network, the number of links was computed. The associations between methylation levels of skeletal muscle-specific genes in umbilical cord tissue and infant’s anthropometric and metabolic variables at birth and at age 6 were analyzed by Spearman’s correlation. Genomic DNA was extracted from the Wharton’s jelly and blood vessels using the Gentra PureGene tissue kit (Qiagen). Sodium bisulfite conversion of DNA was performed, and the chemically modified DNA was then used to analyze the methylation status of over 850,000 individual CpGs in umbilical cord tissue using the Infinium Methylation EPIC Bead Chip microarray (Illumina) at IIS La Fe (Valencia, Spain). DNA methylation data quality control and normalization were performed using the minify R-package (version 1.26.2).