Knock-down of all HIF3A splice variants under 1 % hypoxia by siRNA targeting a shared region in Hep3B cells

The human HIF3A gene undergoes extensive alternative splicing resulting in seven known isoforms. The short splice variant, HIF-3alpha4, is an inhibitor of the hypoxia response driven by HIF-1 and HIF-2. The role of the long isoforms remains unclear. We used cDNA microarray to study the overall impact of HIF3A knock-down by transfecting Hep3B cells with siRNA targeting a region shared by all splice variants under 1 % hypoxia. Hep3B cells were transfected twice either with control siRNA or siRNA targeting human HIF3A. The cells were first incubated 24 h in normoxia and then 24 h in 1 % hypoxia after the second transfection.