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Hypoxia-inducible factors (HIF) are heterodimeric transcription factors that allow cells to adapt and survive during hypoxia. Regulation of  HIF1A  and  HIF2A  mRNA is well characterized, whereas  HIF3A  mRNA regulation and function are less clear. Using RNA-Seq analysis of primary human umbilical vein endothelial cells, we found two isoforms of  HIF3A  were expressed,  HIF3A2  and  HIF3A3 . Comparing  HIF3A  expression profiles to  HIF1A  mRNA during 48 hours of hypoxia revealed that  HIF1A  message peaked at 4 hours, whereas  HIF3A  expression increased while  HIF1A  was decreasing. Given that  HIF1A  mRNA is regulated by miR-429, we tested miR-429 effects on both  HIF3A  isoforms and found that they too were regulated by miR-429. Analysis of a HIF-3 target, DNA-damage-inducible transcript 4, a key survival gene, indicated that  DDIT4  mRNA is induced by HIF-3 and negatively regulated by miR-429 through miR-429’s actions on  HIF3A  message. This provides a compelling model for how hypoxia-induced miR-429 regulates the switch between HIF-1 adaptive responses to HIF-3 survival responses by rapidly decreasing  HIF1A  levels while simultaneously slowing the progression of  HIF3A  expression until the miR-429 levels drop below normoxic levels. Since HIF-1 drives  HIF3A  and miR-429 expression, this establishes a regulatory network in which miR-429 plays a pivotal role.

miR-429 regulates the transition between Hypoxia-Inducible Factor (HIF)1A and HIF3A expression in human endothelial cells