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ChIP-seq of H3K27ac and H3K27me3 in the hippocampus of C57BL/6 mice after high methionine feeding for more than 8 weeks.

ABSTRACT: To explore whether high homocysteine status affects the enrichment of histone H3K27ac and H3K27me3 and thus affects the cognitive behavioral abilities of mice, we fed C57BL/6 mice with a high-methionine diet and a standard diet, then isolated the hippocampus for ChIP-seq studies of H3K27ac and H3K27me3. The sequencing data provided a new theoretical basis for the effects of high homocysteine on histone modification.

ORGANISM(S): Mus musculus

PROVIDER: GSE280827 | GEO | 2026/08/12

REPOSITORIES: GEO

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ChIP-seq of H3K27ac and H3K27me3 in the hippocampus of C57BL/6 mice after high methionine feeding for more than 8 weeks.

Project description:ChIP-seq of H3K27ac and H3K27me3 in the hippocampus of C57BL/6 mice after high methionine feeding for more than 8 weeks.

| PRJNA1180633 | ENA

RNA-seq of the cortex on C57BL/6 mice after high-methionine diet.

Project description:To investigate the genetic changes in the mouse cortex under high homocysteine conditions, we established normal and high methionine-fed mouse models.

2026-08-12 | GSE280828 | GEO

RNA-seq of hippocampal tissues from high-methionine diet-induced hyperhomocysteinemia mice with or without betaine treatment

Project description:To investigate the genetic changes in the mouse hippocampus under high homocysteine conditions, we established normal and high methionine-fed mouse models. Jianting, Li

2026-08-12 | GSE280829 | GEO

Transcriptomics on MDA-MB-231 cells adapted to methionine-free medium

Project description:Human cells can synthesize methionine from homocysteine and folate-coupled methyl groups via the B12-dependent enzyme methionine synthase (MTR). Yet, it has been known for decades that cancer cells fail to grow when methionine is replaced by homocysteine, a phenomenon known as methionine dependence. Here, we report single-cell RNA-sequencing data from MDA-MB-231 breast cancer cells adapted to grow without methionine in the presence of high levels of vitamin B12 for 21 days. Compared to parental cells (D0), the adapted “revertant” cells (D21) display gene expression signatures consistent with reduced invasion and metastasis.

2025-04-08 | GSE291735 | GEO

An Ezh2 and Ezh1 dual inhibitor, UNC1999, re-shapes the landscape of H3K27me3 versus H3K27ac in MLL-AF9-transformed murine leukemia

Project description:Ezh2 and EZH1 are histone H3 lysine 27 (H3K27)-specific methyltransferases. Their hyperactive mutations and overexpression were found in cancer including various hematological malignancies. UNC1999 is a highly selective inhibitor for both enzymes. It suppresses H3K27 tri- and di-methylation globally and inhibits growth of MLL-rearranged acute leukemia. Here we performed ChIP-Seq to profile how UNC1999 affects distribution of H3K27me3 and its antagonizing H3K27ac in MLL-AF9-immortalized leukemia cells. We also performed ChIP-seq of SUZ12, an essential common cofactor of EZH2 and EZH1 following compound treatments. We treated MLL-AF9 transformed murine leukemia cells with DMSO, UNC1999 or UNC2400 (an inactive analog compound of UNC1999). Cells were then collected and used for ChIP-Sequencing of Input, H3K27me3, SUZ12, and H3K27ac.

2014-10-30 | E-GEOD-62437 | biostudies-arrayexpress

Methionine stress induces ferroptosis in methionine dependent cancer cells

Project description:Dietary methionine restriction is associated with a reduction in tumor growth in preclinical studies and an increase in lifespan in animal models. The mechanism by which methionine restriction inhibits tumor growth while sparing normal cells is incompletely understood, except for the observation that normal cells can utilize methionine or homocysteine interchangeably (methionine independence) while most cancer cells are strictly dependent on methionine availability. Here, we compared a typical methionine dependent and a rare methionine independent melanoma cell line. We found that replacing methionine with homocysteine generally induced hypomethylation in gene promoters. We isolated nuclear proteins and submitted it for tandem mass tag (TMT) proteomics. This analysis revealed that several proteins involved in the mitochondrial integrated stress response (ISR) were upregulated in response to the replacement of methionine to homocysteine in both cell lines, but to a much greater degree in the methionine dependent cell line. Consistent with the ISR signature, a proteomic analysis of a subcellular fraction enriched for mitochondrial content revealed a strong enrichment for proteins involved in oxidative phosphorylation. Analysis of cellular bioenergetics confirmed that homocysteine induces a decrease in ATP production from oxidative phosphorylation and glycolysis, but to a similar extent in methionine dependent and methionine independent cells. The mitochondrial integrated stress response shared a signature with ferroptosis. Methionine dependent cells displayed a strong ferroptotic signature, which was decreased by half in methionine independent cells. Consistent with ferroptosis, malonaldehyde was increased in methionine independent cells grown in homocysteine, and viability could be rescued with the inhibitor ferrostatin. Therefore, we propose that methionine stress induces ferroptotic cell death in methionine dependent cancer cells.

2023-03-07 | MSV000091423 | MassIVE

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb.

Project description:The regulatory elements that direct tissue-specific gene expression in the developing mammalian embryo remain largely unknown. Although chromatin profiling has proven to be a powerful method for mapping regulatory sequences in cultured cells, chromatin states characteristic of active developmental enhancers have not been directly identified in embryonic tissues. Here we use whole transcriptome analysis coupled with genome-wide profiling of H3K27ac and H3K27me3 to map chromatin states and enhancers in mouse embryonic forelimb and hindlimb. We show that gene expression differences between forelimb and hindlimb, and between limb and other embryonic cell types, are correlated with tissue-specific H3K27ac signatures at promoters and distal sites. Using H3K27ac profiles, we identified 28,377 putative enhancers, many of which are likely to be limb-specific based on strong enrichment near genes highly expressed in the limb and comparisons with tissue-specific p300 sites and known enhancers. We describe a chromatin state signature associated with active developmental enhancers, defined by high levels of H3K27ac marking, nucleosome displacement, hypersensitivity to sonication, and strong depletion of H3K27me3. We also find that developmental enhancers exhibit components of this signature, including hypersensitivity, H3K27ac enrichment and H3K27me3 depletion, at lower levels in tissues in which they are not active. Our results establish histone modification profiling as a tool for developmental enhancer discovery, and suggest that enhancers maintain an open chromatin state in multiple embryonic tissues independent of their activity level. Examination of genome wide H3K27ac and H3K27me3 histone modifications and gene expression in early mouse embryonic limb tissue.

2012-03-16 | E-GEOD-30641 | biostudies-arrayexpress

TTC7A deficiency Impacts the H3K27ac and H3K27me3 histone marks

Project description:TTC7A deficiency Impacts the H3K27ac and H3K27me3 histone marks

| PRJEB22728 | ENA

Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modifications H3K27ac and H3K9me3 in liver tissues from high fat and regular chow diet mice.

Project description:Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modifications H3K27ac and H3K9me3 in liver tissues from high fat and regular chow diet mice.

2023-05-01 | GSE226171 | GEO

Epigenomic landscape during organ formation in human early embryos

Project description:Here we present the whole genome ChIP-Seq analyses of a wide variety of histone marks, H3K27ac, H3K4me1, H3K4me3, and H3K27me3 in the brain, heart, and liver, along with the RNA-seq data of these organs of early human embryos 12 weeks after gestation. In total, brain, heart, and liver of early human post-implantation embryos were used, and four histone modifications were detected, including H3K27ac, H3K4me1, H3K4me3 and H3K27me3. Also, the transcriptomes of these three organs were analyzed.

2016-07-05 | E-GEOD-63634 | biostudies-arrayexpress

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