Unknown,Transcriptomics,Genomics,Proteomics

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CpG island-specific demethylation pathway in ES cells

ABSTRACT: Following erasure in the early animal embryo, a new bimodal DNA methylation pattern is regenerated at the time of implantation in each individual through a wave of generalized de novo modification with CpG islands specifically left unmethylated. In this paper, we ask whether CpG islands are M-bM-^@M-^\protectedM-bM-^@M-^] from de novo methylation or, alternatively, acquire their unmodified state through M-bM-^@M-^\demethylation.M-bM-^@M-^] Using a genetic approach, we demonstrate that ES cells indeed have the ability to specifically demethylate CpG islands through pathways involving hydroxymethylation (Tet1), deamination (Aid), glycosylation (Mbd4) and excision repair (Gadd45a) genes. Surprisingly, this demethylation system is not actually necessary for generating the overall bimodal methylation pattern in ES cells. This general activity does, however, appear to be involved both in somatic cell reprogramming, as well as the normal methylation reprogramming that takes place in the early embryo. CpG-methylated genomic DNA was enriched using a methyl-DNA immunoprecipitation (mDIP) assay. DNA from the input and bound (enriched) DNA for each sample were labeled and hybridized on the array to define the methylation state of each region.

ORGANISM(S): Mus musculus

SUBMITTER: Ofra sabag

PROVIDER: E-GEOD-48923 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Using glutathione peroxidase, Gpx1 and Gpx2, double knockout (Gpx1/2-KO) mice as a model of inflammatory bowel disease predisposing to intestinal cancer, we analyzed genome-wide DNA methylation and chromatin changingM-bM-^@M-^Ys in the mouse ileum during chronic inflammation, aging and cancer. We found that inflammation leads to aberrant DNA methylation in Polycomb target genes, with 70% of the ~250 genes methylated in the inflamed tissue being PcG targets in embryonic stem cells and 58% of the methylated genes being marked by H3K27 trimethylation in the ileum of adult wildtype mice. Acquisition of DNA methylation at CpG islands in the ileum of Gpx-1/2-KO mice frequently correlated with loss of H3K27 trimethylation at the same loci. Inflammation-associated DNA methylation occurs preferentially in tissue-specific silent genes and, importantly, is much more frequently represented in tumors than is age-dependent DNA methylation. 60% of aberrant methylation found in tumors is also present in the inflamed tissue. In summary, inflammation creates a signature of aberrant DNA methylation, which is observed later in the malignant tissue and is directed by the PcG complex. In our study we used mice Gpx1/2-ko with B6 and B6.129 genetic background which are characterized by different level of inflammation in ileum and different tumor susceptibility. DNA methylation was analyzed by using MIRA-assisted Microarrays approach. Changing of the DNA methylation in intestinal epithelium during inflammation and tumorgenesis in Gpx1/2-KO mice were compared to healthy control mice with matching age. Aged dependent DNA methylation was study by comparing DNA methylation between 28-days-old healthy control mice with 8-month-old mice. To detect DKO-specific DNA methylation, we compared the changing DNA methylation in liver from Gpx1/2-KO mice with liver from control mice at age 28 days and 8 month. Association of the inflammation dependent DNA methylation with Polycomb targets and loss of H3K27me3 were verified by ChIp-on-ChIp experiments using H3K27me3 antibodies.

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CpG island-specific demethylation pathway in ES cells

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