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Methylome profiling of GADD45 deficient mouse embryonic stem cells

ABSTRACT: In order to study the physiological impact of GADD45 proteins on DNA methylation, we compared the methylation levels of Gadd45a,b,g triple knockout (TKO) and wild-type (Control) mouse embryonic stem cells (mESC) via whole genome bisulfite sequencing (WGBS).

ORGANISM(S): Mus musculus

PROVIDER: GSE127712 | GEO | 2019/05/31

REPOSITORIES: GEO

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Gene expression changes in GADD45 deficient 2-cell mouse embryos

Project description:To study the role of GADD45 proteins in early mouse development, RNA-seq expression profiling was performed with Gadd45a/Gadd45b double knockout (DKO) and wild-type (WT) mouse embryos at 2-cell stage (2C).

2019-05-31 | GSE127719 | GEO

Role of GADD45 proteins in embryonic stem cells and their derivatives

Project description:We generated Gadd45a,b,g triple-knockout mouse embryonic stem cells and performed RNA-seq expression profiling under six different conditions of cell culture and in vitro differentiation.

2019-05-31 | GSE84401 | GEO

Neuronal activity, TGFβ signaling and unpredictable chronic stress affect transcription of Gadd45 family members in vitro and in vivo [Affymetrix]

Project description:Neuronal activity is altered in several neurological and psychiatric diseases. Upon depolarization not only neurotransmitters are released but also cytokines and other activators of signaling cascades. Unraveling their complex implication in transcriptional control in receiving cells will contribute to understand specific central nervous system (CNS) pathologies and will be of therapeutical interest. In this study we depolarized mature hippocampal neurons in vitro using KCl and revealed increased release not only of Brain-derived neurotrophic factor (BDNF), but also of Transforming growth factor beta (TGFB). Neuronal activity together with BDNF and TGFB controls transcription of DNA modifying enzymes specifically members of the DNA-damage-inducible (Gadd) family, Gadd45a, Gadd45b, and Gadd45g. MeDIP followed by massive parallel sequencing and transcriptome analyses revealed less DNA methylation upon KCl treatment. Thereby, psychiatric disorder-related genes, namely Tshz1, Foxn3, Jarid2, Per1, Map3k5, and Arc are transcriptionally activated and demethylated upon neuronal activation. To analyze whether misexpression of Gadd45 family members can be associated with psychiatric diseases, we applied unpredictable chronic mild stress (UCMS) as established model for depression to mice.UCMS lead to a reduced expression of Gadd45 family members. Taken together, our data demonstrate that Gadd45 family members are new putative targets for UCMS treatments.

2017-12-31 | GSE90508 | GEO

Neuronal activity, TGFβ signaling and unpredictable chronic stress affect transcription of Gadd45 family members in vitro and in vivo [MeDIP-Seq]

2017-12-31 | GSE90509 | GEO

Loss of Tet proteins impairs mouse embryonic stem cells differentiation toward cardiomyocytes progenitors

Project description:DNA methylation mediated epigenetic regulation plays a critical role in regulating cardiomyocytes (CM) differentiation. Tet protein mediated DNA methylation oxidation have been reported to play an important role in regulating embryonic stem cell (ESC) differentiation toward different lineages. In our study, we utilized CRISPR/Cas9 based genome editing method to generated Tet single, double and triple deficient mouse ESC (mESC) expressing emGFP under NKX2.5 promoter and differentiated these cells toward CM progenitors. By modulating emGFP population as cardiac progenitor cells, we found that deletion of Tet1 and Tet2 significantly impairs mESC differentiation toward CM progenitors. Further single-cell RNA-seq analysis in differentiated control and Tet-triple knockout (TKO) mESC reveals that Tet deletion resulted in accumulation of mesoderm progenitors and impairs CM differentiation. Overexpression the catalytic domain of Tet1 could rescue the development defects in Tet-TKO mESC and restore NKX2.5 gene expression. In addition, loci-specific dCas9-Tet1CD mediated epigenome editing at Hand1 loci confirmed its directly transcriptional regulation during CM differentiation. Overall, out studies suggested that Tet protein mediated epigenomic remodeling is a genome-wide event and is essential to maintain proper transcription network during mESC differentiation toward CM progenitors.

2023-02-08 | GSE168061 | GEO

Characterization of the DNA methylome in embryonic retina, retinal progenitors, and RGCs

Project description:We investigated the dynamics of DNA methylation during differentiation of retinal progenitor cells (RPCs) into retinal neurons using the whole-genome bisulfite sequencing (WGBS) approach

2019-07-23 | GSE126474 | GEO

Genome-wide sequencing and comparative profiling of cattle sperm DNA methylome

Project description:Using whole-genome bisulfite sequencing (WGBS), we profiled the DNA methylome of cattle sperms through comparison with three bovine somatic tissues (mammary grand, brain and blood). Large differences between cattle sperms and somatic tissues were observed in the methylation patterns.

2018-03-08 | GSE106538 | GEO

Methylome profiling of GADD45 deficient mouse embryonic stem cells

Project description:Methylome profiling of GADD45 deficient mouse embryonic stem cells

| PRJNA525089 | ENA

BLUEPRINT methylome of the HapMap cell line GM18507 (Coriell cell line NA18507)

Project description:Whole genome bisulfite sequencing (WGBS) of the NA18507 (Yoruba) lymphoblastoid cell line high resolution methylome of one cell type

2016-02-25 | E-GEOD-66285 | biostudies-arrayexpress

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

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