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MESC histone modifications under normoxia and hypoxia

ABSTRACT: mESC histone modifications under normoxia and hypoxia

PROVIDER: PRJNA1251635 | ENA |

REPOSITORIES: ENA

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mESC histone modifications under normoxia and hypoxia

Project description:The physiological behavior of mouse embryonic stem cells (mESCs) is intricately regulated by microenvironmental oxygen levels, with normoxia (21% O₂) and hypoxia (1-5% O₂) exhibiting distinct impacts on self-renewal, differentiation, and metabolic adaptation. However, the epigenetic mechanisms underlying oxygen-dependent gene expression remain poorly characterized. This study investigates the dynamic alterations of histone modifications associated with transcriptional regulation—specifically, the active promoter mark H3K4me3 (trimethylation of histone H3 lysine 4) and the enhancer mark H3K27ac (acetylation of histone H3 lysine 27)—in mESCs under normoxic versus hypoxic conditions. Utilizing chromatin immunoprecipitation followed by sequencing (ChIP-seq), we systematically mapped genome-wide occupancy patterns of H3K4me3 and H3K27ac, identifying oxygen-sensitive epigenetic landscapes that correlate with differential gene activity. Comparative analysis revealed hypoxia-induced redistribution of these marks at loci linked to pluripotency maintenance, hypoxia-responsive pathways (e.g., HIF-1α targets), and metabolic reprogramming. These findings highlight the role of oxygen tension in reshaping the epigenetic architecture of mESCs, providing insights into how microenvironmental cues fine-tune stem cell functionality through histone modification dynamics. This work advances our understanding of epigenetic plasticity in stem cells and may inform strategies for optimizing in vitro culture conditions or manipulating cell fate under physiological or pathological oxygen gradients.

2025-07-23 | GSE294812 | GEO

Normoxia and Hypoxia transcriptomics

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Renal Cell Carcinoma (Renca) Extracellular Vesicles under Hypoxia and Normoxia

Project description:Extracellular vesicles (EVs) represent a diverse group of small membrane-encapsulated particles and provide a universal molecular cell-cell communication system. Hypoxia is a typical condition in solid tumors, and cancer-derived EVs support growth and invasion of tissues by tumor cells. EVs were purified from cell culture medium by ultracentrifugation followed by size exclusion chromatography with Exo-spin™ columns (Cell Guidance Systems Ltd). We performed proteomic analysis of five hypoxia/normoxia pairs of EV samples; each of these replicates for either hypoxia or normoxia was analyzed in duplicates. Obtained data were compared with proteomics analysis of corresponding cell culture media supernatants (SN) after EV removal with 100 000 g ultracentrifugation. We found that exposure of tumor cells to hypoxia (1% oxygen) induced EV secretion, altered EV sizes, and led to notable changes in the EV protein cargo in comparison to normoxia.

2022-02-16 | PXD023546 | Pride

Aspergillus fumigatus transcriptome under normoxia and hypoxia conditions

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2013-03-31 | E-GEOD-30579 | biostudies-arrayexpress

Transcription profiling of Lymphatic endothelial cells were grown under normoxia, hypoxia (1% 0xygen) and conditioned media from NSLCN growth under normoxia or hypoxia

Project description:Lymphatic endothelial cells were grown under normoxia, hypoxia (1% 0xygen) and conditioned medio from NSLCN growth under normoxia or hypoxia. Gene expression was measured and comparition between samples performed Experiment Overall Design: RNA from different donnors where extracted, pooled to avoid interindividual differences and labelled. Microarrays hybridized and analyzed

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Transcriptomic profiling of wild-type and Bmal1-/- myoblasts under normoxia or actue hypoxia conditions

Project description:Purpose: The goal of this study is to investigate the role of interplay between circadian clock and oxygen-sensing pathways in determining myogenic progenitor cell fate. Methods: Total RNAs were extracted from wild-type and Bmal1-/- myoblasts following exposure to normoxia (21% O2) or hypoxia (1% O2) for 6 hours, and subjected to RNA-sequencing. Results: There were significantly up-regulated (443 in normoxia versus 477 in hypoxia) and down-regulated (745 in normoxia versus 796 in hypoxia) genes in Bmal1-/- cells compared to wild-type, with a large degree of overlap between hypoxia and normoxia, although the fold change of differential gene expression was generally greater under hypoxia versus normoxia. Conclusion: Loss of Bmal1 in myoblasts leads to a premature differentiation-prone transcriptome, which was exaggerated following exposure to hypoxia.

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Mycobacterium tuberculosis normoxia hypoxia reactivation with ActivX-desthiobiotin FP probe

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2016-10-10 | MSV000080238 | MassIVE

Dictyostelium discoideum whole cell proteome from AX3 (WT) vegetative cells under hypoxia or normoxia 5h incubation time

Project description:Dictyostelium discoideum whole cell proteome from WT (AX3) vegetative cells under hypoxia were analyzed at 0h (before any treatment) and 5h after hypoxia or normoxia treatment. The experiment consists of 6 Biological Replicates, with 3 Technical Replicates each, by comparing AX3 at 0h against AX3 at 5h under hypoxia or normoxia incubations.

2025-11-04 | PXD061993 | Pride

RNA-seq of ITPR3 and RELB knockout in SW480 under normoxia and hypoxia

Project description:Here we compare the transcriptional profiles of SW480 cells with ITPR3 or RELB knockout with control cells under normoxia and hypoxia.

2022-09-20 | GSE197576 | GEO

Proteomic analysis of CAF secretome under hypoxia vs normoxia conditions

Project description:This study investigated the differences in secreted proteins from cancer-associated fibroblasts (CAF) cultured under hypoxic and normoxic conditions. Culture supernatants from three CAF cell lines cultured under hypoxia and three CAF cell lines cultured under normoxia were analyzed by shotgun proteomics using LC-MS/MS to identify and quantify differentially expressed proteins.

2025-10-31 | PXD070130 | JPOST Repository

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