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Methylation status in human sperm

ABSTRACT: Genomic imprinting describes the expression of a subset of mammalian genes from one parental chromosome. The parent-of-origin specific expression of imprinted genes relies on DNA methylation of CpG-dinucleotides at differentially methylated regions (DMRs) during gametogenesis. We identified the paternally methylated DMR at human chromosome 2 near the imprinted ZDBF2 gene using a methylated-DNA immunoprecipitation-on-chip (meDIP-on-chip) method applied to DNA from sperm.

ORGANISM(S): Homo sapiens

PROVIDER: GSE18178 | GEO | 2010/05/05

SECONDARY ACCESSION(S): PRJNA129045

REPOSITORIES: GEO

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Methylation status in human sperm

Project description:Genomic imprinting describes the expression of a subset of mammalian genes from one parental chromosome. The parent-of-origin specific expression of imprinted genes relies on DNA methylation of CpG-dinucleotides at differentially methylated regions (DMRs) during gametogenesis. We identified the paternally methylated DMR at human chromosome 2 near the imprinted ZDBF2 gene using a methylated-DNA immunoprecipitation-on-chip (meDIP-on-chip) method applied to DNA from sperm. To analyze whether or not the GPR1-ZDBF2 DMR is conserved in human genome, methylation analysis of human sperm sample was performed using MeDIP and genome tiling array.

2010-05-05 | E-GEOD-18178 | biostudies-arrayexpress

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2010-05-05 | GSE18126 | GEO

Methylation screening of reciprocal genome-wide UPDs identifies novel human specific imprinted genes

Project description:Utilizing reciprocal genome-wide uniparental disomy samples presenting with Beckwith-Wiedemann and Silver-Russell syndrome-like phenotypes, we have analyzed ~0.1% of CpG dinucleotides present in the human genome for imprinted differentially methylated regions (DMRs) using the Illumina Infinium HumanMethylation27 BeadChip microarray. This approach identified 15 imprinted DMRs associated with previously characterized imprinted domains, and confirmed the maternal methylation of the RB1 DMR. In addition, we discovered two novel DMRs: a maternally methylated region overlapping the FAM50B promoter CpG island, which results in paternal expression of this retrotransposon, and a paternally methylated region located between maternally expressed ZNF597 and NAT15 genes.

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Project description:A tripartite paternally methylated region within the Gpr1-Zdbf2 imprinted domain on mouse chromosome 1 identified by meDIP-on-chip

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A Novel Approach Identifies New Differentially Methylated Regions (DMRs) Associated with Imprinted Genes

Project description:Imprinted genes are critical for normal human growth and neurodevelopment. We developed a strategy to identify new DNA differentially methylated regions (DMRs), a hallmark of imprinted genes. Using genome-wide methylation profiling, candidate DMRs were selected by identifying CpGs with putative allelic differential methylation in normal biparental tissues. In parallel, we looked for parent of origin-specific DNA methylation patterns in paternally derived human androgenetic complete hydatidiform mole (AnCHM), and maternally derived mature cystic ovarian teratoma (MCT). Using this approach, we found known DMRs associated with imprinted genomic regions as well as new DMRs for known imprinted genes, NAP1L5 and ZNF597. Most importantly, novel candidate imprinted genes were identified. The paternally methylated DMR for one candidate, AXL, a receptor tyrosine kinase, was validated by methylation analyses in humans. Further validation in mouse embryos showed that Axl was expressed preferentially from the maternal allele in a DNA methylation–dependent manner. We have analyzed 3 androgenetic complete hydatidiform mole (AnCHM), 16 white blood cell (WBC), 1 mature cystic ovarian teratoma (MCT), 5 placenta, and 1 lymphoblastoid cell line paternal UPD4 sample

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Zfp57 inactivation illustrates the relationship between DNA methylation and imprinted gene expression in mouse neural precursor cells

Project description:ZFP57 interacts with the germline-derived differentially methylated regions (DMRs) of imprinted genes, and is required to maintain DMR methylation in mouse embryonic stem cells (ESCs). Although DNA methylation has a key role in maintaining genomic imprinting, several imprinted genes are controlled by different mechanisms, and a comprehensive study of the relationship between DMR methylation and imprinted gene expression is lacking. To address this issue, we differentiated wild-type and Zfp57 -/- hybrid mouse ESCs into neural precursor cells (NPCs) and evaluated allelic expression of imprinted genes. In Zfp57-mutant NPCs, we observed loss of allelic bias of all the 35 genes that were imprinted in wild-type cells, demonstrating that Zfp57-dependent methylation is required to globally maintain gene expression imprinting. Analysis of bulk expression showed that most of the genes expressed from the non-methylated chromosome were up-regulated, and most of those expressed from the methylated chromosome were down-regulated in mutant cells, but also that several other imprinted genes acquiring biallelic expression were not significantly affected, suggesting the existence of compensatory mechanisms that control their RNA level. Since neuronal differentiation was impaired in Zfp57-mutant cells, this study also indicates that deregulation of imprinted genes and/or other ZFP57-target non-imprinted genes is incompatible with proper neurogenesis.

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