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Evaluation of the impact of genetically suppression of DNA methyltransferase 1 (DNMT1) in aged vs young type 2 alveolar epithelial cells (AT2).

ABSTRACT: Evaluation of the impact of genetically suppression of DNA methyltransferase 1 (DNMT1) in aged vs young type 2 alveolar epithelial cells (AT2).

PROVIDER: PRJNA1161178 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30669000.fastq.gz	Fastqsanger.gz
	SRR30669001.fastq.gz	Fastqsanger.gz
	SRR30669002.fastq.gz	Fastqsanger.gz
	SRR30669003.fastq.gz	Fastqsanger.gz
	SRR30669004.fastq.gz	Fastqsanger.gz

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Evaluation of the impact of genetically suppression of DNA methyltransferase 1 (DNMT1) in aged vs young type 2 alveolar epithelial cells (AT2).

Project description:Using somatic genetic approaches, we aim for investigating the role of DNMT1 suppression in the regulation of transcriptom of young AT2 cells, in comparing with the effect of aging.

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Transcriptome of type 2 alveolar epithelial cells (AT2 cells) with DNMT1 inihibition in vivo

Project description:DNA methylation patterns alter with age. However, it remains largely unknown how suppression of DNA methyltransferase changes the DNA methylation in AT2 cells. Here we looked into the transcriptome of AT2 with in vivo treatment of DNMT1 inhibitor in young mice and inverstigated how that alters the transcriptome.

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Evaluation of the impact of genetically suppression of Nupr1 in aged vs young type 2 alveolar epithelial cells (AT2).

Project description:Our data demonstrated that Nupr1 has an age-specific function in the proliferation and differentiation of lung adenocarcinoma cells that are derived from AT2 cells. However, how Nupr1 impact AT2 cells in vivo has not been tested. Using somatic genetic approaches, we performed single-cell mRNA sequencing with primary AT2 cells with control or shRNAs targeting Nupr1.

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Inhibition of DNMT1 methyltransferase activity via glucose-regulated O-GlcNAcylation alters the epigenome

Project description:The DNA methyltransferase activity of DNMT1 is vital for genomic maintenance of DNA methylation. We report here that DNMT1 function is regulated by O-GlcNAcylation, a protein modification that is sensitive to glucose levels, and that elevated O-GlcNAcylation of DNMT1 from high glucose environment leads to alterations to the epigenome. Using mass spectrometry and complementary alanine mutation experiments, we identified S878 as the major residue that is O-GlcNAcylated on DNMT1. Functional studies further revealed that O-GlcNAcylation of DNMT1-S878 results in an inhibition of methyltransferase activity, resulting in a general loss of DNA methylation that is preferentially at partially methylated domains (PMDs). This loss of methylation corresponds with an increase in DNA damage and apoptosis. These results establish O-GlcNAcylation of DNMT1 as a mechanism through which the epigenome is regulated by glucose metabolism and implicates a role for glycosylation of DNMT1 in metabolic diseases characterized by hyperglycemia.

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Evaluation of the impact of genetically suppression of Nupr1 in aged vs young type 2 alveolar epithelial cells (AT2).

Project description:Evaluation of the impact of genetically suppression of Nupr1 in aged vs young type 2 alveolar epithelial cells (AT2).

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DNA methylome sequencing of aged vs young AT2 cells

Project description:EM-Seq of DNA derived from freshly sorted AT2 cells from aged (24-30 months old) and young (3-4 months old) C57BL6/J mice

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Transcriptome of type 2 alveolar epithelial cells (AT2 cells) with DNMT1 inihibition in vivo

Project description:Transcriptome of type 2 alveolar epithelial cells (AT2 cells) with DNMT1 inihibition in vivo

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Dnmt1 has de novo activity targeted to transposable elements

Project description:DNA methylation plays a critical role in development, particularly in repressing retrotransposons. The mammalian methylation landscape is dependent on the combined activities of the canonical maintenance enzyme Dnmt1 and the de novo Dnmts, 3a and 3b. Here we demonstrate that Dnmt1 displays de novo methylation activity in vitro and in vivo with specific retrotransposon targeting. We used whole-genome bisulfite and long-read Nanopore sequencing in genetically engineered methylation depleted embryonic stem cells to provide an in-depth assessment and quantification of this activity. Utilizing additional knockout lines and molecular characterization, we show that Dnmt1's de novo methylation activity depends on Uhrf1 and its genomic recruitment overlaps with targets that enrich for Trim28 and H3K9 trimethylation. Our data demonstrate that Dnmt1 can de novo add and maintain DNA methylation, especially at retrotransposons and that this mechanism may provide additional stability for long-term repression and epigenetic propagation throughout development.

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Critical Requirement of the DNA Methyltransferase, Dnmt1, for the Development and Function of Foxp3+ Regulatory T Cells

Project description:We investigated the role of DNMT1 in immune homeostasis by generating mice lacking DNMT1 in Foxp3+ T-regulatory (Treg) cells. These mice showed decreased peripheral Foxp3+ Tregs, complete loss of Foxp3+ Treg suppressive functions in vitro and in vivo, and died from autoimmunity by 3-4 weeks unless they received perinatal transfer of wild-type Tregs that prolonged their survival. Methylation of CpG-sites in the TSDR region of Foxp3 was unaffected by DNMT1 deletion, but microarray revealed more >500 proinflammatory and other genes were upregulated in DNMT1-/- Tregs. CD4-Cre-mediated DNMT1 deletion showed inability of conventional T cells to convert to Foxp3+ Treg under appropriate polarizing conditions. Hence, DNMT1 is absolutely necessary for maintenance of the gene program required for normal Treg development and function. RNA from three independent samples of magnetically separated CD4+CD25+ Treg of fl-DNMT1/Foxp3cre mice, compared to wild type (C57BL6) control

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Dual Targeting of G9a and DNMT1 for the Treatment of Experimental Cholangiocarcinoma

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