In the last decade it has been recognized that the expression level of a gene is not solely determined by its transcription rate, but in contrast every step on the RNA level is tightly regulated, starting with pre-mRNA processing in the nucleus and ending with degradation of the mature mRNA in the cytoplasm. These processes contribute to the observation that, on a genome-wide scale, protein levels are often only modestly correlated with the transcript levels. Such posttranscriptional gene regulation is often exploited in cellular stress response and recognized as the causative agent in several human diseases.

In addition to the well studied transcriptional response, hypoxia vastly modulates mRNA stability and translation efficiency. Until now several miRNAs and RNA-binding proteins implicated in this posttranscriptional regulation have been identified. What is less well understood, but seems to be an important factor for hypoxia adaptation, is the regulation of pre-mRNA splicing. On average human genes contain 6 to 7 intronic sequences, which have to be removed before the mature mRNA is exported to the cytoplasm. Genome-wide studies show that > 90% of all human genes are alternatively spliced, thereby dramatically increasing the genomic complexity. Alternatively spliced mRNAs either code for variant protein isoforms, e.g. with different cellular localization and additional sometimes even opposing functions, or target the mRNA for degradation via the nonsense-mediated decay (NMD) pathway.

We are interested in hypoxia-dependent alternative splicing in endothelial cells. Therefore, we compared genome-wide splicing patterns of endothelial cells incubated for 48 hours under normoxic or hypoxic (1% oxygen) conditions. We identified nine alternative splicing events in genes until now not related to hypoxia adaptation. One event occurs in the transcription factor MAX (MYC-associated factor X). Here, hypoxia induces retention of the last intronic sequence. This results in several mRNAs that either code for truncated protein isoforms or NMD targets.