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Series GSE89836 Query DataSets for GSE89836
Status Public on Sep 15, 2017
Title Genome-wide mapping of HIF binding sites by ChIP-seq in HUVEC cells exposed to hypoxia
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Cells adapt to environmental changes, including fluctuations in oxygen levels, through the induction of specific gene expression programs. To identify genes regulated by hypoxia at the transcriptional level, we pulse-labeled HUVEC cells with 4-thiouridine and sequenced nascent transcripts. Then, we searched genome-wide binding profiles from the ENCODE project for factors that correlated with changes in transcription and identified binding of several components of the Sin3A co-repressor complex, including SIN3A, SAP30 and HDAC1/2, proximal to genes repressed by hypoxia. SIN3A interference revealed that it participates in the downregulation of 75% of the hypoxia-repressed genes in endothelial cells. Unexpectedly, it also blunted the induction of 47% of the upregulated genes, suggesting a role for this corepressor in gene induction. In agreement, ChIP-seq experiments showed that SIN3A preferentially localizes to the promoter region of actively transcribed genes and that SIN3A signal was enriched in hypoxia-repressed genes, prior exposure to the stimulus. Importantly, SINA3 occupancy was not altered by hypoxia in spite of changes in H3K27ac signal. In summary, our results reveal a prominent role for SIN3A in the transcriptional response to hypoxia and suggest a model where modulation of the associated histone deacetylase activity, rather than its recruitment, determines the transcriptional output.
Overall design ChIP-Seq analysis of HIF1A, EPAS1, and ARNT binding in hypoxia in HUVEC cells compared with the preimmune control. The data is from a single biological replicate.
Contributor(s) Tiana M, del Peso L
Citation(s) 29059365
Submission date Nov 14, 2016
Last update date May 15, 2019
Contact name Luis del Peso
Phone +34 91 585 4440
Organization name Universidad Autonoma de Madrid
Department Biochemistry
Lab IIB-252
Street address Arzobispo Morcillo
City Madrid
State/province Madrid
ZIP/Postal code 28029
Country Spain
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (4)
GSM2390641 HIF1A_ChIPSeq
GSM2390642 EPAS1_ChIPSeq
This SubSeries is part of SuperSeries:
GSE89841 Transcriptional repression in hypoxia is mediated by the Sin3A histone deacetylase complex
BioProject PRJNA353504
SRA SRP093321

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE89836_RAW.tar 416.7 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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