Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Utility of HM450 BeadArray on Mouse Samples

ABSTRACT: Illumina Infinium Human Methylation (HM) BeadChips are a widely used platform for measuring genome-scale DNA methylation, particularly in relation to epigenetic GWAS (EWAS) studies. The methylation profile of human samples can be assessed accurately and reproducibly using the HM27 BeadChip (27,578 CpG sites) or its successor, the HM450 BeadChip (485,577 CpG sites). To date no mouse equivalent has been developed greatly hindering the application of this methodology to the wide range of valuable murine models of disease and development in existence. We found 1,308 and 13,715 probes from HM27 and HM450 BeadChip uniquely matched the reference mouse genome (mm9) respectively. We demonstrate reproducible measurements of DNA methylation at these probes in a range of mouse tissue samples and in a murine cell line model of acute myeloid leukaemia. In the absence of a mouse counterpart, the Infinium HumanMethylation BeadChip arrays have utility in carrying out methylation profiling in non-human species. GPL13534: 12 samples analysed in total. Two array replicates, two bisulfite conversion replicates and two biological replicates of mouse samples. 1 Human sample analysed in parallel. GPL8490: 3 samples

ORGANISM(S): Mus musculus

SUBMITTER: Nicholas Wong

PROVIDER: E-GEOD-43226 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Exploring the utility of human DNA methylation arrays for profiling mouse genomic DNA.

Wong Nicholas C NC Ng Jane J Hall Nathan E NE Lunke Sebastian S Salmanidis Marika M Brumatti Gabriela G Ekert Paul G PG Craig Jeffrey M JM Saffery Richard R

Genomics 20130429 1

Illumina Infinium Human Methylation (HM) BeadChips are widely used for measuring genome-scale DNA methylation, particularly in relation to epigenome-wide association studies (EWAS) studies. The methylation profile of human samples can be assessed accurately and reproducibly using the HM27 BeadChip (27,578 CpG sites) or its successor, the HM450 BeadChip (482,421 CpG sites). To date no mouse equivalent has been developed, greatly hindering the application of this methodology to the wide range of v ...[more]

PMID: 23639479

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Project description:Cancer is characterised by DNA hypermethylation and gene silencing of CpG island-associated promoters, including tumour suppressor genes The methyl-CpG-binding domain (MBD) family of proteins bind to methylated DNA and can aid in the meditation of gene silencing by interaction with histone deacetylases and histone methyltransferases. However the mechanisms responsible for eliciting CpG island hypermethylation in cancer, and the potential role that MBD may proteins play in modulation of the methylome remain unclear. Our previous work demonstrated that MBD2 preferentially binds to the hypermethylated GSTP1 promoter CpG island in prostate cancer cells. Here, we use functional genetic approaches to investigate if MBD2 plays an active role in promoting DNA methylation. First, we show that loss of MBD2 results in inhibition of both maintenance and spread of de novo methylation of a transfected construct containing the GSTP1 promoter CpG island in prostate cancer cells and Mbd2-/- mouse fibroblasts. De novo methylation was rescued by transient expression of Mbd2 in Mbd2-/- cells. Second, we show that MBD2 depletion triggers significant hypomethylation genome-wide in prostate cancer cells with concomitant loss of MBD2 binding at promoter and enhancer regulatory regions. Finally, CpG islands and shores that become hypomethylated after MBD2 depletion in LNCaP cancer cells show significant hypermethylation in clinical prostate cancer, highlighting a potential active role of MBD2 in promoting cancer specific hypermethylation. Importantly, co-immunoprecipiation of MBD2 reveals that MBD2 associates with DNA methyltransferase (DNMT) enzymes 1 and 3A. Together our results demonstrate that MBD2 plays a critical role in â??rewritingâ?? the cancer methylome at specific regulatory regions. LNCaP prostate cancer cell line clones with reduced MBD2 expression were establised by using shRNA to MBD2 and scrambled control clones were established with scrambled control shRNA. To interrogate methylation changes induced by MBD2 knock-down we profiled three stably transfected scrambled control clones and three MBD2 knockdown clones on Illumina HumanMethylation450K arrays. Differential methylation analysis was carried out to identified CpG sites hypo-/hyper-methylated as a result of MBD2 knockdown.

Dataset Information

Utility of HM450 BeadArray on Mouse Samples

Publications

Exploring the utility of human DNA methylation arrays for profiling mouse genomic DNA.

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