A Genome-Wide Screen for Normally Methylated Human CpG Islands That Can Identify Novel Imprinted Genes

Abstract

DNA methylation is a covalent modification of the nucleotide cytosine that is stably inherited at the dinucleotide CpG by somatic cells, and 70% of CpG dinucleotides in the genome are methylated. The exception to this pattern of methylation are CpG islands, CpG-rich sequences that are protected from methylation, and generally are thought to be methylated only on the inactive X-chromosome and in tumors, as well as differentially methylated regions (DMRs) in the vicinity of imprinted genes. To identify chromosomal regions that might harbor imprinted genes, we devised a strategy for isolating a library of normally methylated CpG islands. Most of the methylated CpG islands represented high copy number dispersed repeats. However, 62 unique clones in the library were characterized, all of which were methylated and GC-rich, with a GC content >50%. Of these, 43 clones also showed a CpG obs /CpG exp >0.6, of which 30 were studied in detail. These unique methylated CpG islands mapped to 23 chromosomal regions, and 12 were differentially methylated regions in uniparental tissues of germline origin, i.e., hydatidiform moles (paternal origin) and complete ovarian teratomas (maternal origin), even though many apparently were methylated in somatic tissues. We term these sequences gDMRs, for germline differentially methylated regions. At least two gDMRs mapped near imprinted genes, HYMA1 and a novel homolog of Elongin A and Elongin A2, which we term Elongin A3. Surprisingly, 18 of the methylated CpG islands were methylated in germline tissues of both parental origins, representing a previously uncharacterized class of normally methylated CpG islands in the genome, and which we term similarly methylated regions (SMRs). These SMRs, in contrast to the gDMRs, were significantly associated with telomeric band locations (P = .0008), suggesting a potential role for SMRs in chromosome organization. At least 10 of the methylated CpG islands were on average 85% conserved between mouse and human. These sequences will provide a valuable resource in the search for novel imprinted genes, for defining the molecular substrates of the normal methylome, and for identifying novel targets for mammalian chromatin formation.

Promoter methylation negatively correlated with mRNA expression but not tissue differential expression after heat stress

“…In our study, the methylation level of chicken HSP70 promoter CpG island was detected using the MassARRAY system, and it revealed hypomethylation of this region in the control, 3-, and 6-h treatment groups in various tissues. The low level of methylation agreed with current data showing that in normal somatic cells, CpG islands are unmethylated or hypomethylated (Strichman-Almashanu et al, 2002;Song et al, 2005). The results of DNA methylation analysis indicated that regardless of tissue type, the chicken HSP70 promoter showed a similar methylation incident, meaning that the tissue-dependent expression of chicken HSP70 was not associated with the DNA methylation pattern, but interestingly, the methylation level may be negatively associated with mRNA expression because the methylation level of the control and 6-h treatment groups was slightly higher than that of the 3-h treatment group (except in liver tissue), whereas mRNA expression was higher in the 3-h treatment group, and correlation analysis showed that the methylation level was negatively associated with the mRNA level of HSP70 in leg muscle (P = 0.0124).…”

Genome imprinting regulated by the mouse Polycomb group protein Eed

“…There are more than 60 identified autosomal imprinted genes, about half of which are paternally repressed and half maternally repressed. Most imprinted genes that have been examined contain at least one DMR located in the 5′ promoter region or in the body of the gene itself 3 . Recently, several proteins (DNA methyltransferases, CpG methyl binding proteins, chromatin insulators) have been identified as trans-acting factors involved in the epigenetic regulation of these loci 4 .…”

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

“…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;GardinerGarden 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).…”