Dataset Information

Metabolic control of imprinted gene expression in naive pluripotent cells

ABSTRACT: Naive pluripotent epiblast cells of the preimplantation embryo and their in vitro counterpart, naive murine embryonic stem (ES) cells , are characterised by global DNA hypomethylation. This is caused by elevated expression of TETs oxidases and by downregulation of DNA methyltransferases (DNMTs). However, the signal orchestrating such dynamic changes in vitro and in vivo are only partially understood. Here we report that Stat3 induces genomic hypomethylation via metabolic reconfiguration. In Stat3 -/- ES cells we observed reduced alpha-ketoglutarate (ɑKG) production from reductive glutaminolysis. This is accompanied by reduced levels of Tet2 and its product, hydroxy-methyl-cytosine, together with increased Dnmt3a/b expression and methyl-cytosine levels. Notably, genome methylation can be dynamically controlled by simply modulating αKG availability, mitochondrial activity or Stat3 activation. Stat3-/- ES cells show also general increased methylation at Imprinting Control Regions accompanied with differential expression of >60% of imprinted genes. Several of them, including Lin28a, Ndn and Peg10, are normally upregulated during differentiation, and displayed anticipated and enhanced expression in Stat3-/- cells, indicating faster differentiation kinetics. Single-cell transcriptome analysis of Stat3-/- embryos confirmed dysregulated expression of Dnmt3a/b, Tet2, imprinted genes and anticipated expression of differentiation markers. Our results reveal that Stat3 bridges the metabolic and epigenetic profiles of naive pluripotent cells and may be relevant under Stat3-dependent pathological conditions.

ORGANISM(S): Mus musculus

PROVIDER: GSE134450 | GEO | 2020/11/30

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Ten-eleven translocation (TET) proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytsosine (5fC), and 5-carboxylcytosine (5caC). 5fC/5caC can be excised and repaired by the base excision repair (BER) pathway, implicating 5mC oxidation in active DNA demethylation. Genome-wide DNA methylation is erased in the transition from metastable states to ground state of embryonic stem cells (ESCs) and in migrating primordial germ cells (PGCs), while some resistant regions become demethylated only in gonadal PGCs. Understanding the mechanisms underlying global hypomethylation in naïve ESCs and developing PGCs will be useful for realizing cellular pluripotency and totipotency. In this study, we found that PRDM14, the PR-domain-containing transcriptional regulator, accelerates the TET-BER cycle, resulting in the promotion of active DNA demethylation in ESCs. Induction of PRDM14 expression rapidly removed the 5mC associated with transient elevation of 5hmC at pluripotency-associated genes, germline-specific genes, and imprinted loci but not across the entire genome, which resemble second wave of DNA demethylation in gonadal PGCs. PRDM14 physically interacts with TET1/TET2 and enhances the recruitment of TET1/TET2 at target loci. Knockdown of Tet1/Tet2 impaired transcriptional regulation and DNA demethylation by PRDM14. The repression of the BER pathway by administration of pharmacological inhibitors against APE1 and PARP1 and the knockdown of thymine DNA glycosylase (TDG) also impaired DNA demethylation by PRDM14. Furthermore, DNA demethylation induced by PRDM14 normally takes place in the presence of aphidicolin, which is an inhibitor of G1/S progression. Together, our analysis provides mechanistic insight into DNA demethylation in naive pluripotent stem cells and developing PGCs. To investigate the function of TET1/TET2 in transcriptional regulation by PRDM14 in ESCs, we exploited microarray analysis using total mRNA derived from Scramble, Scramble + PRDM14, Tet1/Tet2 KD, Tet1/Tet2 KD + PRDM14 mouse ESC.

Project description:Deleterious somatic mutations in DNMT3A or TET2 are associated with clonal expansion of haematopoietic cells and higher risk of cardiovascular disease (CVD). In mice, most studies have indicated an over-activation of the inflammatory program in myeloid cells with reduced DNMT3A or TET2 expression. However, the effect of loss of function of DNMT3A and TET2 in human myeloid cells remains poorly understood. Here, we investigated the roles of DNMT3A and TET2 in normal human monocyte- derived macrophages (mDM), in mDM isolated from individuals with DNMT3A or TET2 mutations and in macrophages isolated from human atherosclerotic plaques. Using a combination of transcriptomic, epigenetic, and imaging assays, we provide evidence that, in addition to distinct roles in regulation of macrophage gene expression, DNMT3A and TET2 share a common role in maintaining mitochondrial DNA integrity by regulating the expression of Transcription Factor A, Mitochondria ( TFAM ). This shared function is dependent on interactions of DNMT3A and TET2 with RBPJ and ZNF143 at regulatory elements in the TFAM gene. Experimental reduction of DNMT3A or TET2 expression in normal human mDMs results in downregulation of TFAM, release of mtDNA into the cytoplasm and consequent activation of a type I interferon response mediated by cGAS. Single-cell RNA-seq analysis of mDMs from individuals with heterozygous loss-of-function mutations in DNMT3A and TET2 revealed a similar transcriptional signature. In addition, single-cell RNA-seq analysis of normal mDM and macrophages residing in human atherosclerotic plaques revealed higher expression of type I IFN signature genes specifically in cells with lower DNMT3A or TET2 expression. The production of IFN as a component of the type I IFN response induces activation of interferon-stimulated genes in neighbouring cells, representing a mechanism by which partial loss of function of DNMT3A or TET2 in a small fraction of cells could exert pathogenic effects in the artery wall. These findings suggest that targeting the type I IFN pathway may have therapeutic value in reducing risk of cardiovascular disease in patients with DNMT3A or TET2 mutations.

Dataset Information

Metabolic control of imprinted gene expression in naive pluripotent cells

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets