High resolution genome-wide mapping of HIF binding sites by ChIP-seq
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina Genome Analyzer II (Homo sapiens)
ORGANISM(S): Homo sapiens
SUBMITTER: David R Mole
PROVIDER: GSE28352 | GEO | 2011-04-05
SECONDARY ACCESSION(S): PRJNA139281
REPOSITORIES: GEO
Dataset's files
primary
| Action | DRS | |||
|---|---|---|---|---|
| GSE28352_RAW.tar | Raw | |||
| filelist.txt | Txt |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:We report ChIP-Seq analysis of HIF-1 alpha, HIF-2 alpha, and HIF-1 beta binding in MCF-7 breast cancer cells Sample analysis compared to pre-immune serum chromatin immunoprecipitation
2011-04-05 | E-GEOD-28352 | ArrayExpress
Project description:Hypoxia-inducible factor (HIF) regulates the major transcriptional cascade central to the response of all mammalian cells to alterations in oxygen tension. Expression arrays indicate that many hundreds of genes are regulated by this pathway, controlling diverse processes that in turn orchestrate both oxygen delivery and utilization. However, the extent to which HIF exerts direct versus indirect control over gene expression together with the factors dictating the range of HIF-regulated genes remains unclear. Using chromatin immunoprecipitation linked to high throughput sequencing, we identify HIF-binding sites across the genome, independently of gene architecture. Using gene set enrichment analysis, we demonstrate robust associations with the regulation of gene expression by HIF, indicating that these sites operate over long genomic intervals. Analysis of HIF-binding motifs demonstrates sequence preferences outside of the core RCGTG-binding motif but does not reveal any additional absolute sequence requirements. Across the entire genome, only a small proportion of these potential binding sites are bound by HIF, although occupancy of potential sites was enhanced approximately 20-fold at normoxic DNAse1 hypersensitivity sites (irrespective of distance from promoters), suggesting that epigenetic regulation of chromatin may have an important role in defining the response to hypoxia.
2011-01-01 | S-EPMC3374576 | BioStudies
Project description:Hypoxia Inducible Factor (HIF) regulates a cascade of transcriptional events in response to decreased oxygenation, acting from the cellular to the physiological level. This response is evolutionarily conserved, allowing the use of zebrafish (Danio rerio) as a model for studying the hypoxic response. Activation of the hypoxic response can be achieved in zebrafish by homozygous null mutation of the von Hippel-Lindau (vhl) tumour suppressor gene. Previous work from our lab has focused on the phenotypic characterisation of this mutant, establishing the links between vhl mutation, the hypoxic response and cancer. To further develop fish as a model for studying hypoxic signalling, we examine the transcriptional profile of the vhl mutant with respect to Hif-1?. As our approach uses embryos consisting of many cell types, it has the potential to uncover additional HIF regulated genes that have escaped detection in analogous mammalian cell culture studies.We performed high-density oligonucleotide microarray analysis of the gene expression changes in von Hippel-Lindau mutant zebrafish, which identified up-regulation of well-known hypoxia response genes and down-regulation of genes primarily involved in lipid processing. To identify the dependency of these transcriptional changes on HIF, we undertook Chromatin Immunoprecipitation linked next generation sequencing (ChIP-seq) for the transcription factor Hypoxia Inducible Factor 1? (HIF-1?). We identified HIF-1? binding sites across the genome, with binding sites showing enrichment for an RCGTG motif, showing conservation with the mammalian hypoxia response element.Transcriptome analysis of vhl mutant embryos detected activation of key hypoxia response genes seen in human cell models of hypoxia, but also suppression of many genes primarily involved in lipid processing. ChIP-seq analysis of Hif-1? binding sites unveiled an unprecedented number of loci, with a high proportion containing a canonical hypoxia response element. Whether these sites are functional remains unknown, nevertheless their frequent location near transcriptional start sites suggests functionality, and will allow for investigation into the potential hypoxic regulation of genes in their vicinity. We expect that our data will be an excellent starting point for analysis of both fish and mammalian gene regulation by HIF.
2015-01-01 | S-EPMC4642629 | BioStudies
Project description:Analysis of the binding sites of Hif-1α in both wild-type and von Hippel Lindau mutant zebrafish lines at 4dpf by ChIP linked next generation sequencing. The von Hippel Lindau mutant displays a systemic hypoxic response under normoxic conditions. Results show the extent of Hif-1α binding to the genome, and provide a basis for analysis of the transcriptional response to genetically induced hypoxia in zebrafish. Analysis of the DNA binding sites of Hif-1α in both wild-type and von Hippel Lindau mutant zebrafish lines at 4dpf. The von Hippel Lindau mutant displays a systemic hypoxic response under normoxic conditions. Results show the extent of Hif-1α binding to the genome, and provide a basis for analysis of the dependency of the transcriptional response on Hif-1α in conditions of genetically induced hypoxia in zebrafish.
2016-03-22 | E-GEOD-70727 | BioStudies
Project description:Kidney cancer accounts for more than 100,000 deaths per year world-wide. More than 80% are clear cell tumors (ccRCCs) and the majority are associated with loss of function of the von Hippel Lindau (pVHL) tumor suppressor resulting in upregulation of HIF-{alpha} subunits, and activation of HIF-dependent transcriptional pathways. Recent GWAS studies have discovered RCC-susceptibility loci both within EPAS1 (HIF-2{alpha}) and in an intergenic region of unknown function on 11q13.3. As part of an ongoing study to define the direct transcriptional targets of HIF-2 in renal cancer, we undertook a genome-wide analysis of HIF-2-binding sites in pVHL-defective 786-O cells (that lack functional HIF-1{alpha} due to a truncated transcript) using chromatin immunoprecipitation with antibodies directed against HIF-2{alpha} and its dimerization partner HIF-1{beta}, coupled to high-throughput sequencing (ChIP-seq). Amongst approximately 600 pangenomic HIF-2{beta} ChIP signals, we observed strong binding (ranked 12th by peak height) almost precisely coinciding with the RCC predisposition SNP rs7105934 on 11q13.3. We report binding of HIF-2{alpha} and HIF-1{beta} in 786-O clear cell renal carcinoma cells. 3 samples examined, HIF-2{alpha}, HIF-1{beta} and pre-immune control ChIP.
2012-02-01 | E-GEOD-34871 | ArrayExpress
Project description:Analysis of the binding sites of Hif-1α in both wild-type and von Hippel Lindau mutant zebrafish lines at 4dpf by ChIP linked next generation sequencing. The von Hippel Lindau mutant displays a systemic hypoxic response under normoxic conditions. Results show the extent of Hif-1α binding to the genome, and provide a basis for analysis of the transcriptional response to genetically induced hypoxia in zebrafish. Analysis of the DNA binding sites of Hif-1α in both wild-type and von Hippel Lindau mutant zebrafish lines at 4dpf. The von Hippel Lindau mutant displays a systemic hypoxic response under normoxic conditions. Results show the extent of Hif-1α binding to the genome, and provide a basis for analysis of the dependency of the transcriptional response on Hif-1α in conditions of genetically induced hypoxia in zebrafish.
2016-03-22 | E-GEOD-70727 | ArrayExpress
Project description:Constitutive functional HIF-2? was recently identified in cancer and stem cell lines under normoxia. In this study, BEAS-2B, a bronchial epithelial cell line, was shown to constitutively express active HIF-2? under normoxia and exhibit markers of pluripotency including Oct-4, Nanog, and sphere formation. Oct-4 expression was reduced after knockdown of HIF-2? under normoxia. Global enrichment analysis of HIF-2? demonstrated the diverse functions of HIF-2? under normoxia. Bioinformatics analysis of the enriched loci revealed an enhancer role of HIF-2? binding sites, involvement of HIF-2? interacting proteins, and enriched de novo motifs which suggest the diverse role of HIF-2? in pseudohypoxia. The low ratio of the discovered loci overlapping with those revealed in cancer cell lines 786-O (16.1%) and MCF-7 (15.9%) under hypoxia indicated a prevailing non-canonical mechanism. Hypoxia had positive, marginal or adverse effects on the enrichment of the selected loci in ChIP-PCR assays. Deletion of the N-terminal activation domain (N-TAD) of HIF-2? disrupted the reporting activity of two of the loci annotated to ELN and ANKRD31. Hypoxia incurring abundance variation of HIF-2? may misrepresent the N-TAD functions as canonical hypoxia inducible features via C-TAD activation. Elucidation of the pseudohypoxia functions of constitutive HIF-2? is useful for resolving its role in malignancy and pluripotency.
2016-01-01 | S-EPMC4931692 | BioStudies
Project description:Analysis of gene expression changes in the von Hippel Lindau when mutant compared to wild-type at 4dpf using a whole genome microarray expression profiling. The von Hippel Lindau mutant displays a systemic hypoxic response under normoxic conditions. We performed single-colour microarrays to identify the gene expression changes which underpin the hypoxic phenotype. We used 3 biological replicates from both mutant and control, followed by analysis using Limma to identify significant gene expression changes. This work, together with ChIP-seq data for the Hif-1α in von Hippel Lindau mutants, should allow for the Hif-1α dependency of these gene expression changes to be assessed. The changes in gene expression between von Hippel Lindau mutants and wild-type controls was measured at 4 days post fertilisation. For both wild-type and mutant, 3 biological replicates, each of 30 embryos were used.
2016-03-22 | E-GEOD-70885 | ArrayExpress
Project description:Purpose: We aimed to investigate in depth the regulation of microRNA expression by hypoxia in the breast cancer cell line MCF-7, establish the relationship between microRNA expression and HIF binding sites, pri-miRNA transcription and microRNA processing gene expression. Methods: microRNA sequencing data and gene expression microarray data were generated from MCF-7 cells submitted to an hypoxia timecourse (16h, 32h and 48h at 1% Oxygen). Data was integrated to 500 published high-stringency HIF binding sites identified in MCF-7 cells. Results: We identified 41 microRNAs significantly up- and 28 down- regulated, of which 38 mature and 20 star forms are reported in conjunction with hypoxia for the first time. HIF-1M-NM-1 and HIF-2M-NM-1 binding sites within 50kb distance of microRNA loci were found by integration of HIF ChIP-seq data, showing overall association between binding sites and up-regulation. Gene expression profiling analysis showed no full coordination between pri-miRNA and microRNA expression, pointing towards additional levels of regulation. Several transcripts playing a role in microRNA processing were found regulated by hypoxia, of which two were HIF dependent. Conclusions: The data support the hypothesis that microRNA expression under hypoxia is regulated at transcriptional and post-transcriptional level. HIF is involved at both levels, regulating the transcription of certain microRNAs and also the expression of key elements of the microRNA processing pathway. microRNA-seq profiles of MCF-7 exposed to hypoxia (1% Oxygen) for 16h (2 replicates), 32h (2 replicates) and 48h (2 replicates) and to normoxia (2 replicates) were generated using Illumina sequencing platform.
2014-02-13 | E-GEOD-47602 | BioStudies
Project description:Adaptation to hypoxia is mediated through a coordinated transcriptional response driven largely by Hypoxia-Inducible Factor 1 (HIF-1). The direct transcriptional targets of HIF-1 play important roles in facilitating both short-term and long-term adaptation to hypoxia. Alignment of the sequences encompassing all well-characterized HIF-1 binding sites has revealed a consensus core HRE motif of 5'-RCGTG-3' (R = A or G). Since the consensus HIF-1 binding motif is too promiscuous to accurately predict binding a priori, we used ChIP-chip to define HIF-1 chromatin binding on a genome-wide level. We integrated these results with gene expression profiling to interrogate mechanisms regulating hypoxia-induced gene expression, and to more comprehensively identify direct targets of HIF-1 transactivation. Overall design: HepG2 cells were cultured under normoxic (ambient) or hypoxic (0.5%O2, 4 h) conditions. HIF-1 ChIP was performed with a HIF-1 polyclonal Ab. Triplicate ChIPed DNA and inputs were amplified and hybridized onto the Affymetrix Gene-Chip Human Tiling 2.0R Array Set. The MAT algorithm was used to identify peaks of probe intensity (‘‘hits’’).
2009-06-02 | GSE16347 | GEO