Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3

Abstract

CpG islands are present in one-half of all human and mouse genes and typically overlap with promoters or exons. We developed a method for high-resolution analysis of the methylation status of CpG islands genome-wide, using arrays of BAC clones and the methylation-sensitive restriction enzyme NotI. Here we demonstrate the accuracy and specificity of the method. By computationally mapping all NotI sites, methylation events can be defined with single-nucleotide precision throughout the genome. We also demonstrate the unique expandability of the array method using a different methylation-sensitive restriction enzyme, BssHII. We identified and validated new CpG island loci that are methylated in a tissue-specific manner in normal human tissues. The methylation status of the CpG islands is associated with gene expression for several genes, including SHANK3, which encodes a structural protein in neuronal postsynaptic densities. Defects in SHANK3 seem to underlie human 22q13 deletion syndrome. Furthermore, these patterns for SHANK3 are conserved in mice and rats.

Identification of DNA hypermethylation of SOX9 in association with bladder cancer progression using CpG microarrays

“…CpG island arrays represent a high-throughput technology for the discovery of CpG island loci frequently hypermethylated during disease progression (Yan et al, 2000;Ching et al, 2005). Gene profiling analyses of cancer cells after exposure to demethylating agents may also uncover critical genes susceptible to be epigenetically silenced (Liang et al, 2002).…”

Dynamic and reversibility of heterochromatic gene silencing in human disease

“…One of these genome wide approaches known as Restriction Landmark Genome Scanning (RLGS) has enabled to identify in six mice tissues a large number of differentially methylated regions (TDMs) which exhibit a tissue-specific expression pattern that is consistent with methylation status and a role in tissue differentiation [50]. Furthermore, Ching et al [51], by using BAC microarray have identified CpG island loci that are methylated in a tissue-specific manner in normal human tissues, including SHANK3 whose differential methylation in different tissues was also evolutionary conserved.…”

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

“…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).…”