Identification of DNA methylation differences correlated with transcriptional divergence between humans and chimpanzees in chromosomes 21 and 22

While some studies have reported gene expression differences between humans and chimpanzees, the mechanisms underlying such changes remain poorly understood. To address this issue, we examined, by MeDIP-chip, DNA methylation patterns of peripheral blood cells from age- and sex- matched human and chimpanzee individuals. Our analysis identified some differentially methylated regions between the two species and suggests that changes in DNA methylation pattern are involved in the diversification of transcriptome during evolution. Pooled genomic DNA of peripheral blood cells from four human or chimpanzee females were immunoprecipitated by anti-methylcytosine antibody (MeDIP) or fragmented (control), then subjected to Affymetrix microarray analysis. Both the MeDIP and control data were obtained from three technical replicates. The information about the human and chimpanzee individuals we used are as follows: Human 1: female 27yo Human 2: female 33yo Human 3: female 35yo Human 4: female 42yo Chimp 1: female 27yo Chimp 2: female 30yo Chimp 3: female 31yo Chimp 4: female 40yo