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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Methylation profiling of mouse liver by D-REAM

ABSTRACT: Genome-wide DNA methylation profiling of mouse liver analyzed by D-REAM

ORGANISM(S): Mus musculus

SUBMITTER: Shinya Sato

PROVIDER: E-TABM-887 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Enrichment of short interspersed transposable elements to embryonic stem cell-specific hypomethylated gene regions.

Muramoto Hiroki H Yagi Shintaro S Hirabayashi Keiji K Sato Shinya S Ohgane Jun J Tanaka Satoshi S Shiota Kunio K

Genes to cells : devoted to molecular & cellular mechanisms 20100613 8

Embryonic stem cells (ESCs) have a distinctive epigenome, which includes their genome-wide DNA methylation modification status, as represented by the ESC-specific hypomethylation of tissue-dependent and differentially methylated regions (T-DMRs) of Pou5f1 and Nanog. Here, we conducted a genome-wide investigation of sequence characteristics associated with T-DMRs that were differentially methylated between ESCs and somatic cells, by focusing on transposable elements including short interspersed e ...[more]

PMID: 20629982

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Methylation profiling of mouse pluripotent stem cells by D-REAM

Project description:Genome-wide DNA methylation profiling of embryonic stem cells, embryonic germ cells, induced pluripotent stem cells, and their progenitors (MEF, hepatocytes) analyzed by D-REAM

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DNA methylation profiling of murine neural progenitor cells

Project description:Tissue and their component cells have unique DNA methylation profiles comprising DNA methylation patterns of tissue-dependent and differentially methylated regions (T-DMRs). T-DMRs are found throughout the genome and influence tissue-specific gene expression. DNA methylation profile of T-DMRs underlies the network of tissue- and developmental stage-specific transcription factors and their targets. The adult brain consists of various kinds of cells that sequentially appear as neurons, astrocytes, and oligodendrocytes from late gestation through the neonatal period. Distinctive neural progenitor cells (NPCs) that exhibit different differentiation poteintials to neurons to glial cells are generated during mid-to-late gestation. To explore DNA methylation profiles of mouse NPCs, we compared neurospheres derived from telencephalons at embryonic day 11.5 (E11.5NSph) and 14.5 (E14.5NSph) by T-DMR profiling with restriction tag-mediated amplification (D-REAM) combined with Affymetrix GeneChip Mouse Promoter 1.0R Array. We used HpyCH4IV, a methylation-sensitive restriction enzyme that recognizes ACGT residues. Because these are uniformly distributed across the genome, it enables less biased analysis. By comparing D-REAM data between E11.5NSph and E14.5NSph, we identified genes with T-DMRs including those involved in neural develpment and/or associated with neurological disorders in humans. The present study elucidates the underlying dynamics of the DNA methylation profile of T-DMRs during neural development, including insights into developmental stage-specific hypomethylation of T-DMRs around TSSs.

2012-12-01 | E-MTAB-1150 | biostudies-arrayexpress

DNA methylation profile of mTEC

Project description:DNA methylation profiling by D-REAM

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Mapping of EZH2-WT and EZH2-mTP5 binding sites to human promoter regions

Project description:To gain genome wide information on the association of EZH2 with promoter regions in HeLa cells, DamID experiments and subsequent analysis by promoter arrays (Affymetrix GeneChip Human Promoter 1.0R ) were performed. The DamID method uses fusions of the bacterial Dam DNA methylase and the protein of interest, to direct the enzymatic activity to the proteinM-bM-^@M-^Ys genomic binding sites, where the DNA is methylated. Methylated DNA is then extracted, enriched and further analysed by microarray. EZH2 is the enzymatic subunit of the Polycomb Repressive Complex 2, which deposits the H3K27me3 mark on chromatin. This mark is associated with low gene expression, either in polycomb repressed regions or, in combination with methylation of H3K4, at poised promoters. An EZH2-T416A mutant (EZH2-mTP5) fails to bind to NIPP1, a factor implied in the regulation of PRC2 binding to a subset of target regions. To obtain a genome wide picture of differential binding of EZH2-WT and the EZH2-mTP5 mutant to promoter regions, the mutant was subjected to DamID/microanalysis as well. DamID of EZH2-WT (2 replicates) and EZH2-mTP5(T416A)(2 replicates) vs. control (Dam without fused protein)(4 samples)

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2019-10-31 | E-MTAB-7885 | biostudies-arrayexpress

Dot1 and Histone H3K79 Methylation in Natural Heterochromatic and HML-HMR Silencing

Project description:ChIP-on-Chip of Sir proteins in WT and dot1 deletion strains

2011-02-09 | E-MEXP-3108 | biostudies-arrayexpress

ChIP-chip by array of H2BK123ub, H3K4me3, H3K36me3, H3K79me3, and H3K79me2 using Affymetrix tiling arrays.

Project description:Genome-wide mapping of H2BK123ub, H3K4me3, H3K36me3, H3K79me3, and H3K79me2 using Affymetrix tiling arrays.

2011-12-08 | E-MEXP-3217 | biostudies-arrayexpress

Chromatin immunoprecipitation in dot1 deletion and G1 or G2 arrested yeast cells to identify methylation patterns

Project description:To define the molecular regulators required for differential pattern of H3K79 methylation by Dot1, we performed a GPS screen and discovered that the components of the cell cycle-regulated SBF complex were required for normal levels of H3K79 di- but not trimethylation. Genome-wide mapping revealed that H3K79 di- and trimethylation to present a mutually exclusive pattern on chromatin with M/G1 cell-cycle-regulated genes significantly enriched for H3K79 dimethylation. Since H3K79 trimethylation requires prior monoubiquitination of H2B, we performed genome-wide profiling of H2BK123 monoubiquitination and showed that H2BK123 monoubiquitination is excluded from cell cycle regulated genes and sites containing H3K79me2 but not from H3K79me3 containing regions. A genome-wide screen for factors responsible for the establishment/removal of H3K79 dimethylation resulted in the identification of several genes including NRM1 and WHI3, which both impact the transcription by the SBF, and MBF complexes, further linking the regulation of H3K79's methylation status to the cell cycle.

2009-10-19 | E-MEXP-2273 | biostudies-arrayexpress

Eaf7 identifies a native protein trimer linked to RNA polymerase-coupled nucleosome recycling

Project description:The NuA4 histone acetyltransferase (HAT) complex is required for gene specific regulation, cell cycle progression, and DNA repair. Dissection of the 13-subunit complex reveals that the Eaf7 subunit bridges Eaf5 with Eaf3, a H3K36me3-binding chromodomain protein, and this Eaf5/7/3 trimer is anchored to NuA4 through Eaf5. This subcomplex represents a functional module as deletions of these genes create similar phenotypes and a large portion of the trimer exists in a native form outside the NuA4 complex. Gene-specific and genome-wide location analyses indicate that the Eaf5/7/3 trimer correlates with transcription activity and is enriched over the coding region. In agreement with a role in transcription elongation, the Eaf5/7/3 trimer interacts with phosphorylated RNA polymerase II and helps its progression. In addition, loss of Eaf5/7/3 partially suppresses intragenic cryptic transcription arising in set2 mutant cells, suggesting a role in nucleosome destabilization. Such a function is supported by genetic interactions with the FACT histone chaperone. On the other hand, loss of the trimer leads to an increase of replication-independent histone exchange over the coding region of transcribed genes. Taken together, these results lead to a model where Eaf5/7/3 associates with elongating polymerase and is involved in the disassembly of nucleosomes in front of the polymerase, but also in their recycling in its wake.

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