Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Methyl-CpG-binding domain (MBD) sequencing of 15 primary stage 4S neuroblastoma tumors

ABSTRACT: The DNA methylome of 15 primary stage 4S neuroblastoma tumors is profiled by enrichment with a methyl-CpG-binding domain (MBD) and massively parallel sequencing DNA of 15 primary stage 4S tumors is sheared (fragments of Â± 200 bp), followed by MBD-based (MethylCap kit of Diagenode) enrichement, library preparation and multiplexing. Both input DNA and captured DNA were sequenced paired-end on Illumina Hiseq2000

ORGANISM(S): Homo sapiens

SUBMITTER: Anneleen Decock

PROVIDER: E-GEOD-69268 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma.

Decock Anneleen A Ongenaert Maté M Cannoodt Robrecht R Verniers Kimberly K De Wilde Bram B Laureys Geneviève G Van Roy Nadine N Berbegall Ana P AP Bienertova-Vasku Julie J Bown Nick N Clément Nathalie N Combaret Valérie V Haber Michelle M Hoyoux Claire C Murray Jayne J Noguera Rosa R Pierron Gaelle G Schleiermacher Gudrun G Schulte Johannes H JH Stallings Ray L RL Tweddle Deborah A DA De Preter Katleen K Speleman Frank F Vandesompele Jo J

Oncotarget 20160101 2

Accurate assessment of neuroblastoma outcome prediction remains challenging. Therefore, this study aims at establishing novel prognostic tumor DNA methylation biomarkers. In total, 396 low- and high-risk primary tumors were analyzed, of which 87 were profiled using methyl-CpG-binding domain (MBD) sequencing for differential methylation analysis between prognostic patient groups. Subsequently, methylation-specific PCR (MSP) assays were developed for 78 top-ranking differentially methylated region ...[more]

PMID: 26646589

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Project description:Epigenetic modification plays important roles in plant and animal development. DNA methylation can impact the transposable element (TE) silencing, gene imprinting and regulate gene expression.Through a genome-wide analysis, DNA methylation peaks were respectively characterized and mapped in maize embryo and endosperm genome. Distinct methylation level across maize embryo and endosperm was observed. The maize embryo genome contained more DNA methylation peaks than endosperm. However, the endosperm chloroplast genome contained more DNA methylation peaks to compare with the embryo chloroplast genome. DNA methylation regions were characterized and mapped in genome. More CG island (CGI) shore are methylated than CGI in maize suggested that DNA methylation level is not positively correlated with CpG density. The DNA methylation occurred more frequently in the promoter sequence and transcriptional termination region (TTR) than other regions of the genes. The result showed that 99% TEs we characterized are methylated in maize embryo, but some (34.8%) of them are not methylated in endosperm. Maize embryo and endosperm exhibit distinct pattern/level of methylation. The most differentially methylated two regions between embryo and endosperm are High CpG content promoters (HCPs) and high CpG content TTRs (HCTTRs). DNA methylation peaks distinction of mitochondria and chloroplast DNA were less than the nucleus DNA. Our results indicated that DNA methylation is associated with the gene silencing or gene activation in maize endosperm and embryo. Many genes involved in embryogenesis and seed development were found differentially methylated in embryo and endosperm. We found 17 endosperm-specific expressed imprinting genes were hypomethylated in endosperm and were hypermethylated in embryo. The expression of a maize DEMETER -like (DME-like) gene and MBD101 gene (MBD4 homolog) which direct bulk genome DNA demethylation were higher in endosperm than in embryo. These two genes may be associated with the distinct methylation level across maize embryo and endosperm.The methylomes of maize embryo and endosperm was obtained by MeDIP-seq method. The global mapping of maize embryo and endosperm methylation in this study broadened our knowledge of DNA methylation patterns in maize genome, and provided useful information for future studies on maize seed development and regulation of metabolic pathways in different seed tissues. Examination of DNA methylated modifications in 2 maize tissues.

Dataset Information

Methyl-CpG-binding domain (MBD) sequencing of 15 primary stage 4S neuroblastoma tumors

Publications

Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma.

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