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RRBS profiling and Transcriptome profiling of Stat3 wild-type, Stat3 knock-out, Dnmt3a/b wild-type and Dnmt3a/b knock-out mouse embryonic stem cells (mES cells)

ABSTRACT: RRBS profiling and Transcriptome profiling of Stat3 wild-type, Stat3 knock-out, Dnmt3a/b wild-type and Dnmt3a/b knock-out mouse embryonic stem cells (mES cells)

PROVIDER: PRJNA553145 | ENA |

REPOSITORIES: ENA

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RRBS profiling and Transcriptome profiling of Stat3 wild-type, Stat3 knock-out, Dnmt3a/b wild-type and Dnmt3a/b knock-out mouse embryonic stem cells (mES cells)

Project description:Naive pluripotent epiblast cells of the preimplantation murine embryo and their in vitro counterpart, embryonic stem (ES) cells, have the capacity to give rise to all cells of the adult. Such developmental plasticity is associated with global genome hypomethylation. It is unclear whether genome methylation is dynamically regulated only via differential expression of DNA methyltransferases (DNMTs) and Ten-eleven Translocation (TET) enzymes, which oxidase methylated DNA. Here we show that LIF/Stat3 signalling induces genomic hypomethylation via metabolic reconfiguration. In Stat3-/- ES cells we observed decreased alpha-ketoglutarate (ɑKG) production from reductive Glutamine metabolism, leading to decreased TET activity, increased Dnmt3a/b expression and to a global increase in DNA methylation. Notably, genome methylation is dynamically controlled by simply modulating αKG availability, mitochondrial activity or Stat3 activation in mitochondria, indicating an effective crosstalk between metabolism and the epigenome. Stat3-/- ES cells also show increased methylation at Imprinting Control Regions accompanied with differential expression of >50% of imprinted genes. Single-cell transcriptome analysis of Stat3-/- embryos confirmed dysregulated expression of Dnmt3a/b, Tet2, and imprinted genes in vivo. Our results reveal that the LIF/Stat3 signal bridges the metabolic and epigenetic profiles of naive pluripotent cells, ultimately controlling genome methylation and imprinted gene expression. Several imprinted genes regulate cell proliferation and are often misregulated in tumours. Moreover, a wide range of cancers display Stat3-overactivation, raising the possibility that the molecular module we described here is exploited under pathological conditions.

2020-11-27 | GSE133926 | GEO

Microarray of wild type, Shp2 knock-out, Pten knock-out and double knock-out erythroblasts

Project description:the gene expression profiling results provide important information for the genes regulated by crosstalk between Shp2 and Pten mediated signal pathways Total RNA was extracted from CD71mid Ter119high erythroblasts isolated from the bone marrow of wide type, Shp2 knock-out, Pten knock-out and double knock-out mice

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Expression data from hippocampus of Phf8 knock out and wild type mice

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Gene expression in wild type and mENT1 knock out mice

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Expression data from Adam17 knock out mice and wild type

Project description:Adam17, a shedding protease, is strongly upregtulated during inflammation and cancer. Here we investigate the genome wide effects of Adam17 knock out on the transcriptome.

2010-06-18 | GSE21691 | GEO

In vitro maturation of intestinal organoids differentiated from wild type and STAT3 knock out human embryonic stem cells

Project description:In vitro maturation of intestinal organoids differentiated from wild type and STAT3 knock out human embryonic stem cells

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Gene expression of E. coli MG1655 wild type and rpoS knock-out strains

Project description:The role of rpoS gene in the formation of Escherichia coli biofilms were investigated. The gene expression was compared among E. coli MG1655 wild type strain and rpoS knock-out strain in the biofilms, the planktonic exponential phase, and the planktonic stationary phase. The analysis revealed that the wild type bilfilms (WBF) showed similar pattern of gene expression with the WT planktonic stationary phase (WS), whereas the rpoS knock-out biofilms (MBF) showed similar pattern of gene expression with the wild type planktonic exponential phase (WE). Genes involved in the energy metabolism and the flagella synthesis showed higher expression in the rpoS knock-out biofilms (MBF), but not in the wild type biofilms (WBF). Moreover, genes involved in the stress responses showed higher expression in the wild type biofilms (WBF), but not in the rpoS knock-out biofilms (MBF). Keywords: cell type comparison (biofilms vs planktonic cells, wild type vs rpoS knock-out strains)

2008-05-23 | GSE7885 | GEO

Expression data from Adam10 knock out mice and wild type

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In vitro maturation of intestinal organoids differentiated from wild type and STAT3 knock out human embryonic stem cells

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Transcriptional profiling of an HtrA proteases knock-out compared to wild type

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