Genome-Wide Profiling of DNA Methylation Reveals a Class of Normally Methylated CpG Island Promoters

Department of Leukemia, The University of Texas at M. D. Anderson Cancer Center, Houston, Texas, USA.
PLoS Genetics (Impact Factor: 7.53). 11/2007; 3(10):2023-36. DOI: 10.1371/journal.pgen.0030181
Source: PubMed


The role of CpG island methylation in normal development and cell differentiation is of keen interest, but remains poorly understood. We performed comprehensive DNA methylation profiling of promoter regions in normal peripheral blood by methylated CpG island amplification in combination with microarrays. This technique allowed us to simultaneously determine the methylation status of 6,177 genes, 92% of which include dense CpG islands. Among these 5,549 autosomal genes with dense CpG island promoters, we have identified 4.0% genes that are nearly completely methylated in normal blood, providing another exception to the general rule that CpG island methylation in normal tissue is limited to X inactivation and imprinted genes. We examined seven genes in detail, including ANKRD30A, FLJ40201, INSL6, SOHLH2, FTMT, C12orf12, and DPPA5. Dense promoter CpG island methylation and gene silencing were found in normal tissues studied except testis and sperm. In both tissues, bisulfite cloning and sequencing identified cells carrying unmethylated alleles. Interestingly, hypomethylation of several genes was associated with gene activation in cancer. Furthermore, reactivation of silenced genes could be induced after treatment with a DNA demethylating agent or in a cell line lacking DNMT1 and/or DNMT3b. Sequence analysis identified five motifs significantly enriched in this class of genes, suggesting that cis-regulatory elements may facilitate preferential methylation at these promoter CpG islands. We have identified a group of non-X-linked bona fide promoter CpG islands that are densely methylated in normal somatic tissues, escape methylation in germline cells, and for which DNA methylation is a primary mechanism of tissue-specific gene silencing.

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Available from: Jiexin Zhang, Sep 17, 2014
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    • "CpG sites are not randomly distributed in the human genome; they are enriched in regions defined as CpG islands (CGI) and represent regions of at least 200 bp containing a proportion of guanine and cytosine greater than 50% and are observed at an expected CpG ratio greater than 0.6 [12]. CGIs, which are concentrated in the promoters of genes, are the first candidates to be investigated in gene expression-methylation studies [13,14]. In addition to CGIs, it has been shown that methylation on sequences up to 2 kb distant from CGI (shore islands) and sequences up to 2 kb distant from shore (shelve islands) can influence gene expression [15,16]. "
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    ABSTRACT: Background Chronic periodontitis represents a complex disease that is hard to control and is not completely understood. Evidence from past studies suggests that there is a key role for DNA methylation in the pathogenesis of periodontitis. However, all reports have applied technologies that investigate genes in a low throughput. In order to advance in the knowledge of the disease, we analyzed DNA methylation variations associated with gene transcription using a high-throughput assay. Infinium® HumanMethylation450 (Illumina) was performed on gingival samples from 12 periodontitis cases and 11 age-matched healthy individuals. Methylation data of 1,284 immune-related genes and 1,038 cell cycle-related genes from Gene Ontology (GO) and 575 genes from a dataset of stably expressed genes (genes with consistent expression in different physiological states and tissues) were extracted from a microarray dataset and analyzed using bioinformatics tools. DNA methylation variations ranging from −2,000 to +2,000 bp from the transcription start site (TSS) were analyzed, and the results were tested against a differential expression microarray dataset between healthy and periodontitis gingival tissues. Differences were evaluated using tests from the R Statistical Project. Results The comparison of probes between periodontitis and normal gingival tissues showed that the mean methylation scores and the frequency of methylated probes were significantly lower in genes related to the immune process. In the immune group, these parameters were negatively correlated with gene expression (Mann-Whitney test, p < 2.2e − 16). Conclusions Our results show that variations in DNA methylation between healthy and periodontitis cases are higher in genes related to the immune-inflammatory process. Thus, DNA methylation must be modulating chromatin regions and, consequently, modulating the mRNA transcription of immune-inflammatory genes related with periodontitis, impacting the prognosis of disease.
    Clinical Epigenetics 08/2014; 6(1):15. DOI:10.1186/1868-7083-6-15 · 4.54 Impact Factor
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    • "Results in Aberrant CGI Hypermethylation One puzzling observation was the finding that a specific subset of CGIs in HSCs actually showed increased DNA methylation levels after the ablation of Dnmt3a. Promoter CGI hypermethylation is a well-established cancer methylome phenotype (Figueroa et al., 2009; Shen et al., 2010, 2007), so this may be an important mechanism in the early stages of HSC transformation. "
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    ABSTRACT: Epigenetic regulation of hematopoietic stem cells (HSCs) ensures lifelong production of blood and bone marrow. Recently, we reported that loss of de novo DNA methyltransferase Dnmt3a results in HSC expansion and impaired differentiation. Here, we report conditional inactivation of Dnmt3b in HSCs either alone or combined with Dnmt3a deletion. Combined loss of Dnmt3a and Dnmt3b was synergistic, resulting in enhanced HSC self-renewal and a more severe block in differentiation than in Dnmt3a-null cells, whereas loss of Dnmt3b resulted in a mild phenotype. Although the predominant Dnmt3b isoform in adult HSCs is catalytically inactive, its residual activity in Dnmt3a-null HSCs can drive some differentiation and generates paradoxical hypermethylation of CpG islands. Dnmt3a/Dnmt3b-null HSCs displayed activated β-catenin signaling, partly accounting for the differentiation block. These data demonstrate distinct roles for Dnmt3b in HSC differentiation and provide insights into complementary de novo methylation patterns governing regulation of HSC fate decisions.
    Cell stem cell 08/2014; 15(3). DOI:10.1016/j.stem.2014.06.018 · 22.27 Impact Factor
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    • "tightly repressed by DNA methylation, preventing any deleterious effects that could occur if they were ectopically activated (Maatouk et al. 2006; Shen et al. 2007; Weber et al. 2007; Straussman et al. 2009; Borgel et al. 2010; Arand et al. 2012; Seisenberger et al. 2012; ). Thus, PGCs at this point display the transcription profiles, chromatin modifications, and DNA methylation levels and patterns characteristic of their somatic origin (Ohinata et al. 2005; Maatouk et al. 2006; Hajkova et al. 2010; Popp et al. 2010; Seisenberger et al. 2012). "
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    ABSTRACT: Methylation of DNA is an essential epigenetic control mechanism in mammals. During embryonic development, cells are directed toward their future lineages, and DNA methylation poses a fundamental epigenetic barrier that guides and restricts differentiation and prevents regression into an undifferentiated state. DNA methylation also plays an important role in sex chromosome dosage compensation, the repression of retrotransposons that threaten genome integrity, the maintenance of genome stability, and the coordinated expression of imprinted genes. However, DNA methylation marks must be globally removed to allow for sexual reproduction and the adoption of the specialized, hypomethylated epigenome of the primordial germ cell and the preimplantation embryo. Recent technological advances in genome-wide DNA methylation analysis and the functional description of novel enzymatic DNA demethylation pathways have provided significant insights into the molecular processes that prepare the mammalian embryo for normal development.
    Genes & development 04/2014; 28(8):812-28. DOI:10.1101/gad.234294.113 · 10.80 Impact Factor
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