DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression

In multicellular organisms, cells, and tissues form as a result of differentiation of a single fertilized egg, and phenotypes are inherited over several cell generations without alteration in the DNA sequences. Epigenetic systems are recognized as memory systems for these inheritable gene functions and, in mammals, they comprise DNA methylation and histone modifications of chromatin. DNA methylation in tissue-dependent and differentially methylated regions (T-DMRs) is involved in expression of tissue-specific genes as well as expression of key transcription factors that constitute transcription networks governing tissue or cell specificity (Shen and Maniatis 1980; Cho et al. 2001; Imamura et al. 2001; Hattori et al. 2004b, 2007; Nishino et al. 2004). Abnormal methylation of T-DMRs has been implicated in the pathogenesis of certain diseases (Jones 2002; Ushijima 2005). DNA methylation occurs at the cytosine residue of CpG dinucleotides, which are unevenly distributed within the mammalian genome (Bird 1980). CpG islands (CGIs) have been identified as CpG-rich regions that are associated with ∼50% of the promoter regions in the mouse genome (Bird et al. 1985; Gardiner-Garden and Frommer 1987). Previous genome-wide DNA methylation analyses, focusing on CGIs, have indicated that every cell and tissue type has a unique DNA methylation profile, comprising at least hundreds of T-DMRs (Ohgane et al. 1998; Shiota et al. 2002; Strichman-Almashanu et al. 2002), and these data suggested that a methylation profile could be used to identify cell types (Shiota 2004). To identify genes with differentially methylated regions, several microarray technologies have been developed (Lieb et al. 2006), and microarray technology has been applied to identify aberrantly methylated regions in cancer cells and characterize cell lines such as human embryonic stem cells (Hatada et al. 2006; Keshet et al. 2006; Ordway et al. 2006; Rauch et al. 2006; Shen et al. 2006). However, the DNA methylation profiles obtained have not been directly related to gene function (Ching et al. 2005; Eckhardt et al. 2006; Khulan et al. 2006). The limited number of loci or regions available for genome-wide analysis of normal cells or tissues and the existence of method biases can affect the implementation of methylated profiles (for review, see Khulan et al. 2006). We developed a novel, low-bias method for genome-wide DNA methylation analysis, and examined the DNA methylation profile of the promoter regions in normal mouse liver by comparing them with those of cerebrum, kidney, and spleen. The results indicate that the resultant methylation profile was implicated in tissue-specific function.