Genomics

Dataset Information

4

Chromatin IP for H3 K27me3 modified histone tails in the liver of control mice, Phenobarbital exposed mice and a resulting Ctnnb1 mutated PB liver tumour [ChIP-seq]


ABSTRACT: Through the analysis of mouse liver tumours promoted by distinct routes (DEN exposure alone, DEN exposure plus non-genotoxic insult with phenobarbital and non-alcoholic fatty liver disease); we report that the cancer associated hyper-methylated CGI events in mice are also predicated by silent promoters that are enriched for both the DNA modification 5-hydroxymethylcytosine (5hmC) and the histone modification H3K27me3 in normal liver. During cancer progression these CGIs undergo hypo-hydroxymethylation, prior to subsequent hyper-methylation; whilst retaining H3K27me3. A similar loss of promoter-core 5hmC is observed in Tet1 deficient mouse livers indicating that reduced Tet1 binding at CGIs may be responsible for the epigenetic dysregulation observed during hepatocarcinogenesis. Consistent with this reduced Tet1 protein levels are observed in mouse liver tumour lesions. As in human, DNA methylation changes at CGIs do not appear to be direct drivers of hepatocellular carcinoma progression in mice. Instead dynamic changes in H3K27me3 promoter deposition are strongly associated with tumour-specific activation and repression of transcription. Our data suggests that loss of promoter associated 5hmC in diverse liver tumours licences DNA methylation reprogramming at silent CGIs during cancer progression. We carry out Chromatin immunoprecipitation (ChIP) prior to sequencing on Illumina Hiseq 2500 to report on the genome-wide H3K27me3 patterns in normal mouse liver, 12 week Phenobarbital exposed mouse livers and 35 week pehonbarbital exposed liver tumours.

ORGANISM(S): Mus musculus  

SUBMITTER: Richard R Meehan   John Paterson Thomson  John P Thomson 

PROVIDER: E-GEOD-77728 | ArrayExpress | 2016-05-17

SECONDARY ACCESSION(S): SRP069818GSE77728PRJNA311320

REPOSITORIES: GEO, ArrayExpress, ENA

Dataset's files

Source:
Action DRS
E-GEOD-77728.idf.txt Idf
E-GEOD-77728.processed.1.zip Processed
E-GEOD-77728.processed.2.zip Processed
E-GEOD-77728.processed.3.zip Processed
E-GEOD-77728.sdrf.txt Txt
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