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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression changes in mouse embryonic fibroblasts (MEF cells) deficient for Ing1 and Gadd45a

ABSTRACT: ING1b and GADD45a are nuclear proteins involved in the regulation of cell growth, apoptosis and DNA repair. We found that ING1b and GADD45a physically and functionally interact in the epigenetic regulation of specific target genes. In order to study this interaction further, we analysed the transcriptional changes in MEF cells from single and double Ing1/Gadd45 knockout mice via microarray profiling. Mouse embryonic fibroblasts (MEF cells) were isolated from embryonic day E15.5 male embryos, either wild-type (WT) or knockout for Ing1 (Ing1-/-), Gadd45a (Gadd45a-/-) or Ing1/Gadd45a (double knockout, DKO), and cultured for 3 passages. Samples were then collected in duplicates per MEF line for expression array profiling.

ORGANISM(S): Mus musculus

SUBMITTER: Emil Karaulanov

PROVIDER: E-GEOD-43318 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Ing1 functions in DNA demethylation by directing Gadd45a to H3K4me3.

Schäfer Andrea A Karaulanov Emil E Stapf Ulrike U Döderlein Gabi G Niehrs Christof C

Genes & development 20130201 3

Active DNA demethylation regulates epigenetic gene activation in numerous processes, but how the target site specificity of DNA demethylation is determined and what factors are involved are still poorly understood. Here we show that the tumor suppressor inhibitor of growth protein 1 (Ing1) is required for targeting active DNA demethylation. Ing1 functions by recruiting the regulator of DNA demethylation growth arrest and DNA damage protein 45a (Gadd45a) to histone H3 trimethylated at Lys 4 (H3K4 ...[more]

PMID: 23388825

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Gene expression changes in mouse embryonic fibroblasts (MEF cells) deficient for Ing1 and Gadd45a

2013-02-04 | GSE43318 | GEO

Gene expression changes in white adipose tissue from Ing1- and Gadd45a- single- or double-knockout mice

Project description:ING1b and GADD45a are nuclear proteins involved in the regulation of cell growth, apoptosis and DNA repair. We previously found that ING1b is essential to target GADD45a-mediated active DNA-demethylation via TET1 to specific loci. Hence, GADD45a and ING1 play a crucial role in epigenetic gene regulation. In order to study the physiological role of ING1-GADD45a on gene expression regulation, we compared the expression profiles of white adipose tissue (WAT) from wildtype, Ing1-/-, Gadd45-/- and double-knockout (DKO) mice.

2018-06-11 | GSE99605 | GEO

Gene expression changes in Ing1- and Gadd45a- single- or double-knockout mouse embryonic fibroblasts during adipogenesis

Project description:ING1b and GADD45a are nuclear proteins involved in the regulation of cell growth, apoptosis and DNA repair. We previously found that ING1b is required to target GADD45a-mediated active DNA-demethylation via TET1 to specific loci. In order to study the impact of ING1-GADD45a on MEF-to-adipocyte differentiation, we compared the gene expression profile of wildtype mouse embryonic fibroblasts (MEFs) with Ing1- and Gadd45a- single- or double-knockout (DKO) MEFs at day 6 of adipogenic differentiation via RNA-sequencing.

2018-06-11 | GSE99604 | GEO

Gadd45a and Ing1 interaction in epigenetic gene regulation

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-02-04 | E-GEOD-43319 | biostudies-arrayexpress

Gene expression changes in Ing1- and Gadd45a- single- or double-knockout mouse embryonic fibroblasts

Project description:ING1b and GADD45a are nuclear proteins involved in the regulation of cell growth, apoptosis and DNA repair. We previously found that ING1b is required to target GADD45a-mediated active DNA-demethylation via TET1 to specific loci. In order to study the impact of ING1-GADD45a on gene expression, we compared the expression profile of wildtype mouse embryonic fibroblasts (MEFs) with Ing1- and Gadd45a- single- or double-knockout (DKO) MEFs.

2018-06-11 | GSE115187 | GEO

Whole genome bisulfite sequencing of Ing1/Gadd45a double knockout and wildtype mouse embryonic fibroblasts

Project description:ING1b and GADD45a are nuclear proteins involved in the regulation of cell growth, apoptosis and DNA repair. We previously found that ING1b is essential to target GADD45a-mediated active DNA-demethylation via TET1 to specific loci. In order to study the physiological impact of ING1-GADD45a on DNA methylation in base-resolution genome-wide, we compared the methylation levels of wildtype mouse embryonic fibroblasts (MEFs) with Ing1/Gadd45a double-knockout MEFs via whole genome bisulfite sequencing.

2018-06-11 | GSE99601 | GEO

NG Capture-C analysis of GADD45a-bound adipogenic super-enhancers

Project description:ING1b and GADD45a are nuclear proteins involved in the regulation of cell growth, apoptosis and DNA repair. We previously found that ING1b is essential to target GADD45a-mediated active DNA-demethylation via TET1 to specific loci. In order to study the physical interaction of distant GADD45a and ING1 bound regions, we performed multiplexed NG Capture-C chromatin conformation capture assay in wildtype and knockout mouse embryonic fibroblasts.

2018-06-11 | GSE99606 | GEO

Gene expression changes in HEK293T cells upon overexpression of ING1b and GADD45a

Project description:ING1b and GADD45a are nuclear proteins involved in the regulation of cell growth, apoptosis and DNA repair. We found that ING1b and GADD45a physically and functionally interact in the epigenetic regulation of specific target genes. In order to characterise the functional ING1b-GADD45a interaction, we performed a gain-of-function experiment in HEK293T cells by individual and combinatorial plasmid transfections and then analysed the transcriptional response via expression microarray profiling. HEK293T cells were transiently transfected with expression plasmids encoding human GADD45a and/or human ING1b (full-length or without its PHD-domain) and harvested 48h post-transfection for Illumina microarray profiling. Two independently transfected replicate samples of each condition were analysed. Empty vector (control) transfections served as reference samples.

2013-02-04 | E-GEOD-43317 | biostudies-arrayexpress

Gadd45a promotes DNA demethylation through TDG

Project description:Growth arrest and DNA-damage-inducible protein 45 (Gadd45) family members have been implicated in DNA demethylation in vertebrates. However, it remained unclear how they contribute to the demethylation process. Here, we demonstrate that Gadd45a promotes active DNA demethylation through thymine DNA glycosylase (TDG) which has recently been shown to excise 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) generated in Ten-eleven-translocation (Tet) -initiated oxidative demethylation. The connection of Gadd45a with oxidative demethylation is evidenced by the enhanced activation of a methylated reporter gene in HEK293T cells expressing Gadd45a in combination with catalytically active TDG and Tet. Gadd45a interacts with TDG physically and increases the removal of 5fC and 5caC from genomic and transfected plasmid DNA by TDG. Knockout of both Gadd45a and Gadd45b from mouse ES cells leads to hypermethylation of specific genomic loci most of which are also targets of TDG and show 5fC enrichment in TDG-deficient cells. These observations indicate that the demethylation effect of Gadd45a is mediated by TDG activity. This finding thus unites Gadd45a with the recently defined Tet-initiated demethylation pathway. The dataset includes RRBS anlysis of 2 WT ES cell samples and 2 Gadd45a/b DKO ES cell samples.

2015-05-07 | E-GEOD-62496 | biostudies-arrayexpress

GADD45a ChIP-Seq in mouse embryonic fibroblasts

Project description:GADD45a is a nuclear protein involved in the regulation of cell growth, apoptosis and DNA repair. We previously found that GADD45a physically and functionally interacts with TET1 to mediate active DNA demethylation and is recruited by ING1 to its target sites. In this study, we identified GADD45a bound genomic loci in mouse embryonic fibroblasts (MEFs) via ChIP-Sequencing.

2018-06-11 | GSE99602 | GEO

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