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Chromatin capture defines AHCY as regulator of pluripotent stem cells proliferation

ABSTRACT: Chromatin capture defines AHCY as regulator of pluripotent stem cells proliferation

PROVIDER: PRJNA480266 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7500490.fastq.gz	Fastqsanger.gz
	SRR7500500.fastq.gz	Fastqsanger.gz
	SRR7500491.fastq.gz	Fastqsanger.gz
	SRR7500501.fastq.gz	Fastqsanger.gz
	SRR7500492.fastq.gz	Fastqsanger.gz

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Chromatin capture defines AHCY as regulator of pluripotent stem cells proliferation

Project description:Profiling of the proteome bound to the chromatin in a simple, direct and reliable manner might result key to uncover the role of unpredicted chromatin factors in physiology and disease. We have developed a biochemical strategy named iChrock to capture the chromatin in a single purification step that provides a global view of the cellular chromatome and enables the identification of chromatin-bound proteins de novo. Integrating iChrock with genomic and functional data, we have unveiled the unexpected chromatin function of Adenosylhomocysteinase (AHCY), a major one-carbon pathway metabolic enzyme, in gene activation. Our study reveals a new regulatory axis between the metabolic state of pluripotent cells, ribosomal protein production and cell division during early phase of embryo development, by favoring the metabolic flux of methylation reactions in a local milieu.

2019-03-19 | GSE116799 | GEO

Chromatin capture links the metabolic enzyme AHCY to stem cell proliferation

Project description:Profiling the chromatin-bound proteome (chromatome) in a simple, direct, and reliable manner might be key to uncovering the role of yet uncharacterized chromatin factors in physiology and disease. Here, we have design an experimental strategy to survey the chromatome of proliferating cells by using the DNA-mediated chromatin pull-down technology (Dm-ChP). Our approach provides a global view of cellular chromatome in normal physiological conditions and enables the identification of chromatin-bound proteins de novo. Integrating Dm-ChP with genomic and functional data, we have discovered an unexpected chromatin function for adenosylhomocysteinase (AHCY), a major one-carbon pathway metabolic enzyme, in gene activation. Our study reveals a new regulatory axis between the metabolic state of pluripotent cells, ribosomal protein production, and cell division during early phase of embryo development, in which the metabolic flux of methylation reactions is favored in a local milieu

2019-03-13 | PXD011670 | Pride

Next Generation Sequencing Facilitates Quantitative Analysis of WT AHCY E14.1 cell and T136A AHCY E14.1 cell

Project description:Purpose: To test the effect of AHCY O-GlcNAcylation on E14.1cell pluripotency and The goals of this study are to compare gene expression profiles of the WT AHCY rescue cells and the T136A AHCY rescue cells. Method:Total RNA was Trizol-extracted and purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. cDNA was synthesized using random hexamer primer and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair A-tailing and adapter added were implemented. The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated. Results:Significant alterations in gene expression levels were observed, with 1351 genes upregulated and 979 genes downregulated in the T136A AHCY rescue cells

2020-03-01 | GSE143756 | GEO

Analysis of the senescence transcriptome after knockdown of AHCY

Project description:IMR90 ER:RAS cells were infected with 2 different lentiviral pGIPZ shRNAs against AHCY or with an empty vector (EV). We treated IMR90 ER:RAS cells with 4OHT to induce RAS activation or with vehicle (DMSO) as a non-senescent control. RNA was collected 6 days after the start of the experiment once the senescence program has been fully implemented. Our previous experiments showed that knockdown of AHCY prevents senescence. By performing RNAseq, we have unveiled that AHCY knockdown prevents upregulation of a set of genes essential for the onset of senescence and its associated secretory phenotype.

2022-07-19 | GSE155904 | GEO

Chromatin capture links the metabolic enzyme AHCY to stem cell proliferation.

Project description:Profiling the chromatin-bound proteome (chromatome) in a simple, direct, and reliable manner might be key to uncovering the role of yet uncharacterized chromatin factors in physiology and disease. Here, we have designed an experimental strategy to survey the chromatome of proliferating cells by using the DNA-mediated chromatin pull-down (Dm-ChP) technology. Our approach provides a global view of cellular chromatome under normal physiological conditions and enables the identification of chromatin-bound proteins de novo. Integrating Dm-ChP with genomic and functional data, we have discovered an unexpected chromatin function for adenosylhomocysteinase, a major one-carbon pathway metabolic enzyme, in gene activation. Our study reveals a new regulatory axis between the metabolic state of pluripotent cells, ribosomal protein production, and cell division during the early phase of embryo development, in which the metabolic flux of methylation reactions is favored in a local milieu.

| S-EPMC6402848 | biostudies-literature

Transcriptome analysis of methionine restriction or CRISPR knockout of AHCY or MAT2A in Rael cells

Project description:RNAseq was used to identify host and viral transcriptome changes in methionine restricted Rael cells or Rael cells expressing control, AHCY or MAT2A sgRNAs.

2022-07-11 | GSE190937 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of WT AHCY E14.1 cell and T136A AHCY E14.1 cell

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of WT AHCY E14.1 cell and T136A AHCY E14.1 cell

| PRJNA601486 | ENA

Downregulation of Ahcy with and without blue light exposure significantly alters global gene expression in the Drosophila eye

Project description:One-carbon metabolism influences the response to oxidative stress through antioxidant biosynthesis and the transcriptional status of the cell via epigenetic mechanisms. One-carbon metabolism is responsible for the production of the universal methyl donor, S-adenosylmethionine (SAM), which generates the potent methyltransferase inhibitor, S-adenosylhomocysteine (SAH). The essential metabolic enzyme, S-adenosylhomocysteinase (AHCY), functions within one-carbon metabolism and is the sole enzyme to catabolize the metabolite S-adenosylhomocysteine (SAH). Under oxidative stress conditions, AHCY becomes oxidized at a critical residue for its activity correlating with increased SAH abundance in the Drosophila head. Here, we profiled the photoreceptor transcriptome at a single time point after 3-hour blue light exposure relative to untreated controls in the Drosophila eye. We used RNAi expressed in all cells of the eye under longGMR-Gal4 to knockdown Ahcy and examined photoreceptor cells enriched using nuclei-immunoenrichment. As a control, we expressed non-specific RNAi against mCherry.

2025-09-04 | GSE289458 | GEO

Regulation of the circadian clock by the metabolic enzyme AHCY

Project description:Mammalian circadian rhythms are based on coupled transcriptional-translational feedback loops driven by the transcription factors CLOCK and BMAL1. Chromatin remodeling mechanisms are essential for the proper timing and extent of circadian gene expression. We report that the S-adenosylhomocysteine (SAH) hydrolysing enzyme AHCY binds to CLOCK-BMAL1 at chromatin and drives circadian transcription by promoting cyclic H3K4 trimethylation and recruitment of BMAL1 to chromatin.

2020-02-01 | GSE125720 | GEO

Regulation of the circadian clock by the metabolic enzyme AHCY

2021-01-11 | GSE126851 | GEO