Hypoxia-inducible factor (HIF)-3α is subject to extensive alternative splicing in human tissues and cancer cells and is regulated by HIF-1 but not HIF-2

The hypoxia-inducible transcription factors (HIFs) play a central role in the response of cells to hypoxia. HIFs are αβ dimers, the human α subunit having three isoforms. HIF-3α is unique among the HIF-α isoforms in that its gene is subject to extensive alternative splicing. Database analyses have predicted the generation of six HIF-3α splice variants that utilize three alternative transcription initiation sites. None of these variants is likely to act as an efficient transcription factor, but some of them have been reported to inhibit HIF-1 and HIF-2 functions. We analyzed here for the first time in detail whether these six variants are indeed generated in various human tissues and cell lines. We identified four novel variants, named here HIF-3α7 to HIF-3α10, whereas we obtained no evidence for the predicted HIF-3α3 and HIF-3α5. Distinct differences in the expression patterns of the variants were found between human tissues, the levels being particularly low in many cancer cell lines. Hypoxia upregulated transcription from all three alternative HIF-3α promoters. siRNA experiments showed that this induction is mediated specifically by HIF-1 and not by HIF-2. The tissue-specific differences in the expression patterns and levels of the HIF-3α variants can be expected to modulate the hypoxia response of various tissues and cell types to different extents during development and in pathological situations. A further level of regulation is brought about by the fact that the levels of the HIF-3α transcripts themselves are regulated by hypoxia and by changes in HIF-1 levels.