Identification of methylated genes in BALB/c mice liver using monoclonal antibody combined with the high-throughput cDNA microarray approach

We have employed a microarray-based genome-wide methylation detection method to analyse methylation in internal coding regions of genes in a sequence-independent manner in liver tissue of BALB/c mouse. Using mouse 7.4k cDNA microarray, methylation status of genes spotted on the array was analysed. We detected methylation in coding and its proximal regions of 1415 genes, 70% of which contained CpG islands. Gene ontology analyses of these 1415 genes revealed that they were mainly involved in nucleic acid metabolism and signal transduction processes. Molecular function analysis revealed that these genes were mainly transcription factors, DNA repair proteins, chromatin remodelling enzymes and receptor molecules. The set of methylated genes also contained 11 imprinted genes and 9 genes known to be hyper-methylated in liver cancers. Our analysis has led to the identification of methylation in many new regions. The analysis thus provides a methylation landscape in normal mouse liver. The platform can be used to analyse epigenetic alterations during oncogenesis, ageing, in response to environmental stimuli, etc.