GSE129491
HIF-3a2 overexpression ChIP-seq in Hep3B cells and 1 % hypoxia
Hypoxia-inducible factor (HIF), an aß dimer, is the master regulator of oxygen homeostasis. HIF induces the expression of several hundred genes under hypoxic conditions. Three HIF isoforms differing in the oxygen-sensitive a subunit exist in vertebrates. While HIF-1 and HIF-2 are known transcription activators, HIF-3 has been considered as a negative regulator of the hypoxia response pathway by formation of inactive dimers between the HIF-3a and HIF-1a or HIF-2a subunit. However, the human HIF3A mRNA is subject to complex alternative splicing, which leads to production of both long and short HIF-3a variants. It has been shown recently that the long HIF-3a variants can form aß dimers that possess transcriptional activation capacity, while the short splice variant inhibits hypoxia-inducible gene expression. Chromatin immunoprecipitation analyses of HIF-3a2 overexpression in Hep3B cells show that HIF-3a2 binding associates with canonical hypoxia response elements (5'-RCGTG-3') in the promoter regions of the erythropoietin (EPO) gene among others. Luciferase reporter assays show that the identified HIF-3a2 chromatin-binding regions are sufficient to promote transcription by HIF-3a2 and HIF-1. Furthermore, HIF-3a2 overexpression and knock-down studies by siRNA targeting the HIF3A gene show that EPO mRNA and protein levels are upregulated and downregulated, respectively. Taken together, the results show that HIF-3a2 is a transcription activator that is directly involved in erythropoietin signaling. Overall design: 1.6 million Hep3B cells transfected with the V5-tagged HIF-3a2 and wildtype HIF-ß overexpression plasmids. ChIP was performed with V5 antibody. Samples were prepared in triplicate and pooled for ChIP. HIF-3a2-associated enrichment is compared to input DNA.