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Genome-wide binding sites of Hypoxia inducible factor 1(HI1) in renal epithelial cells.

ABSTRACT: Genome-wide binding sites of Hypoxia inducible factor 1(HI1) in renal epithelial cells.

PROVIDER: PRJNA871273 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21141206.fastq.gz	Fastqsanger.gz
	SRR21141207.fastq.gz	Fastqsanger.gz

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Genome-wide binding sites of Hypoxia inducible factor 1(HI1) in renal epithelial cells.

Project description:We report the high-throughput profiling of HIF1 in human kidney-2 cells (HK-2) under normoxia and 1% 24 hours hypoxia. By obtaining over two billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of HK-2 under normoxia and hypoxia. We found that HIF1 binds to both transcriptional starting sites and enhancer regions. This study provides novel insights into the epigenetic regulation of HIF1 in renal epithelial cells.

2022-08-26 | GSE211665 | GEO

Renal Cell Carcinoma: Hypoxia and Endocytosis

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Renal Cell Carcinoma: Hypoxia and Endocytosis

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Genome-wide maps of HIF1a binding sites in ccRCC cell line under hypoxia condition

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Project description:We report the high-throughput profilings of HIF1 and histone modifications in human umbilical vein endothelial cells (HUVEC). By obtaining over two billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of HUVEC under normoxia and hypoxia. We find that HIF1binds to not only to transcriptional starting sites but also enhancer regions and that HIF1 binding sites were overlapped with lysine 4 trimethylatio, monomethylation and lysine 27 acetylation . Finally, we show that chromatin state can change under hypoxia by using chromatin conformational capture assay. This study provides novel insights into the interaction between HIF1 and KDM3A and also the epigenetic regulation of HIF1.

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Hypoxia-inducible factor 2α attenuates renal ischemia-reperfusion injury by suppressing CD36-mediated lipid accumulation in dendritic cells

Project description:Hypoxia is a hallmark of renal ischemia reperfusion injury (IRI) and serves as an essential regulator of innate immune responses during this process, although the mechanisms of this regulation remain unclear. Here, we show that dendritic cell (DC)-specific genetic ablation of hypoxia-inducible factor (HIF) 2α, a transcription factor induced by oxygen shortage, leads to hyperactivation of natural killer T cells (NKTs), ultimately exacerbating renal IRI in mice. HIF-2α deficiency in DCs triggers IFN-γ and IL-4 production in NKTs, along with upregulation of type I interferon (IFN) and chemokine responses critical for NKT activation. Mechanistically, loss of HIF-2α in DCs promotes their expression of CD36, a scavenger receptor for lipid uptake, resulting in increased lipid accumulation. Furthermore, HIF-2α binds directly to a reverse hypoxia-responsive element (rHRE) in the CD36 promoter, supporting its transcriptional regulation of CD36. Importantly, CD36 blockade by sulfo-N-succinimidyl oleate (SSO), reduces NKT activation and abolishes the exacerbation of renal IRI in mice with DC-specific HIF-2α knockout. Taken together, our study reveals a previously unrecognized role of a HIF-2α-CD36 regulatory axis in rewiring DC lipid metabolism under IRI-associated hypoxia, and suggests a potential therapeutic target to resolve long-standing obstacles in clinical treatment of this severe complication.

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Genome-wide binding sites of Hypoxia inducible factor 1 (HIF1) and histone modifications

2012-07-12 | E-GEOD-39089 | biostudies-arrayexpress

Hypoxia-inducible PRMT2 addiction in cancers

Project description:Hypoxia-inducible PRMT2 addiction in cancers

| PRJNA986065 | ENA

DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumour immunotolerance [WGBS]

Project description:Background: Hypoxia is pervasive in cancer and other diseases. Cells sense and adapt to hypoxia by activating hypoxia-inducible transcription factors (HIFs), but it is still an outstanding question why cell types differ in their transcriptional response to hypoxia. Results: Here, we report that HIFs fail to bind CpG dinucleotides that are methylated in their consensus binding sequence, both in in vitro biochemical binding assays and in vivo studies of differentially methylated isogenic cell lines. Based on in silico structural modelling, we show that 5-methylcytosine indeed causes steric hindrance in the HIF binding pocket. A model wherein cell-type-specific methylation landscapes, as laid-down by the differential expression and binding of other transcription factors under normoxia control cell-type-specific hypoxia responses is observed. We also discover ectopic HIF binding sites in repeat regions which are normally methylated. Genetic and pharmacological DNA demethylation, but also cancer-associated DNA hypomethylation, expose these binding sites, inducing HIF-dependent expression of cryptic transcripts. In line with such cryptic transcripts being more prone to cause double-stranded RNA and viral mimicry, we observe low DNA methylation and high cryptic transcript expression in tumours with high immune checkpoint expression, but not in tumours with low immune checkpoint expression, where they would compromise tumour immunotolerance. In a low-immunogenic tumour model, DNA demethylation upregulates cryptic transcript expression in a HIF-dependent manner, causing immune activation and reducing tumour growth. Conclusions: Our data elucidate the mechanism underlying cell-type specific responses to hypoxia, and suggest DNA methylation and hypoxia to underlie tumour immunotolerance.

2020-06-18 | GSE85355 | GEO

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