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Chromosome wide analysis of parental allele specific chromatin and DNA methylation in mouse

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE26947 | GEO | 2011/03/31

SECONDARY ACCESSION(S): PRJNA136949

REPOSITORIES: GEO

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Chromosome-wide analysis of parental allele-specific chromatin and DNA methylation.

Project description:To reveal the extent of domain-wide epigenetic features at imprinted gene clusters, we performed a high-resolution allele-specific chromatin analysis of over 100 megabases along the maternally or paternally duplicated distal chromosome 7 (Chr7) and Chr15 in mouse embryo fibroblasts (MEFs). We found that reciprocal allele-specific features are limited to imprinted genes and their differentially methylated regions (DMRs), whereas broad local enrichment of H3K27me3 (BLOC) is a domain-wide feature at imprinted clusters. We uncovered novel allele-specific features of BLOCs. A maternally biased BLOC was found along the H19-Igf2 domain. A paternal allele-specific gap was found along Kcnq1ot1, interrupting a biallelic BLOC in the Kcnq1-Cdkn1c domain. We report novel allele-specific chromatin marks at the Peg13 and Slc38a4 DMRs, Cdkn1c upstream region, and Inpp5f_v2 DMR and paternal allele-specific CTCF binding at the Peg13 DMR. Additionally, we derived an imprinted gene predictor algorithm based on our allele-specific chromatin mapping data. The binary predictor H3K9ac and CTCF or H3K4me3 in one allele and H3K9me3 in the reciprocal allele, using a sliding-window approach, recognized with precision the parental allele specificity of known imprinted genes, H19, Igf2, Igf2as, Cdkn1c, Kcnq1ot1, and Inpp5f_v2 on Chr7 and Peg13 and Slc38a4 on Chr15. Chromatin features, therefore, can unequivocally identify genes with imprinted expression.

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Chromosome wide analysis of parental allele specific chromatin and DNA methylation

Project description:Imprinted genes are monoallelically expressed according to parental inheritance. The maternally and paternally expressed alleles are distinguished epigenetically by DNA methylation and histone modifications. RNA was extracted from MatDup.dist7 and PatDup.dist7 MEFs for hybridization to Affymetrix microarrays Comparsion of gene expression in MatDup.dist7 and PatDup.dist7 MEFs

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Chromosome wide analysis of parental allele specific chromatin and DNA methylation

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Chromosome wide analysis of parental allele specific chromatin and DNA methylation in mouse

Project description:This SuperSeries is composed of the following subset Series: GSE26720: Chromosome wide analysis of parental allele specific chromatin and DNA methylation GSE26891: Chromosome wide analysis of parental allele specific chromatin and DNA methylation along mouse distal chr7 GSE26892: Chromosome wide analysis of parental allele specific chromatin and DNA methylation along the central part of mouse chr7 GSE26893: Chromosome wide analysis of parental allele specific chromatin and DNA methylation along mouse distal chr15 Refer to individual Series

2011-03-31 | E-GEOD-26947 | biostudies-arrayexpress

Chromosome wide analysis of parental allele specific chromatin and DNA methylation along mouse distal chr15

Project description:Imprinted genes are monoallelically expressed according to parental inheritance. The maternally and paternally inherited alleles are distinguished epigenetically by DNA methylation and histone modifications. Chromosome-wide Chromatin immunoprecipitation (ChIP) and MIRA analysis of MatDup.dist7 and PatDup.dist7 MEFs provided a panoramic map of reciprocal allele-specific histone modifications and DNA methylation at imprinted genes along distal chromosome 7 and 15. ChIP-chip and MIRA-chip was done to map histone modifications and DNA methylation along distal chr15 in the maternal allele and paternal allele in Patdup.dist7=MatDup.dist15 and Patdup.dist7=MatDupdis15 MEFs, respectively, using Nimblegen tiling arrays for chr15.

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Chromosome wide analysis of parental allele specific chromatin and DNA methylation along mouse distal chr7

Project description:Imprinted genes are monoallelically expressed according to parental inheritance. The maternally and paternally inherited alleles are distinguished epigenetically by DNA methylation and histone modifications. Chromosome-wide Chromatin immunoprecipitation (ChIP) and MIRA analysis of MatDup.dist7 and PatDup.dist7 MEFs provided a panoramic map of reciprocal allele-specific histone modifications and DNA methylation at imprinted genes along distal chromosome 7 and 15. ChIP-chip and MIRA-chip was done to map histone modifications and DNA methylation along distal chr7 in the maternal allele and paternal allele in Matdup.dist7 and Patdup.dist7 MEFs, respectively, using Nimblegen tiling arrays for distal chr7.

2011-03-31 | E-GEOD-26891 | biostudies-arrayexpress

Chromosome wide analysis of parental allele specific chromatin and DNA methylation along mouse distal chr15

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Chromosome wide analysis of parental allele specific chromatin and DNA methylation along the central part of mouse chr7

Project description:Imprinted genes are monoallelically expressed according to parental inheritance. The maternally and paternally inherited alleles are distinguished epigenetically by DNA methylation and histone modifications. Chromosome-wide Chromatin immunoprecipitation (ChIP) and MIRA analysis of MatDup.dist7 and PatDup.dist7 MEFs provided a panoramic map of reciprocal allele-specific histone modifications and DNA methylation at imprinted genes along distal chromosome 7 and 15. ChIP-chip and MIRA-chip was done to map histone modifications and DNA methylation along central chr7 in the maternal allele and paternal allele in Matdup.dist7 and Patdup.dist7 MEFs, respectively, using Nimblegen tiling arrays for central chr7.

2011-03-31 | E-GEOD-26892 | biostudies-arrayexpress

Chromosome wide analysis of parental allele specific chromatin and DNA methylation along the central part of mouse chr7

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