Over 90% of all human genes give rise to multiple mRNA isoforms that arise from alternative splicing. Thus, alternative splicing vastly increases the protein coding capacity of genes. In addition, by generating unproductive, i.e. non-protein producing, mRNAs, alternative splicing can be used to achieve quantitative changes in gene expression. Because of this versatility, alternative splicing is heavily modulated in response to cellular stress such as hypoxia, thus enabling rapid adaptation.
Genome-wide analysis of splicing changes in endothelial cells showed that unproductive mRNA isoforms of the transcription factor MAX (MYC-associated factor X) are elevated, while wild type mRNA and protein are reduced in response to hypoxia (Fig. 1). Since MAX is the central part of the MYC/MAX/MXD network of transcription factors, this splicing event will significantly alter the transcriptional response to hypoxia.
In studying the hypoxia-inducible mRNA isoform E, we discovered a novel surveillance mechanism for the elimination of C-terminally truncated proteins. Intron retention leads to the production of an abundant mRNA coding for a C-terminally truncated protein isoform that contains the DNA-binding domain, but lacks the wild type-specific acidic and basic regions. Instead, this protein variant harbors specific amino acids at its C-terminus that cause highly efficient and constitutive protein decay. Decay is such efficient that it renders the protein undetectable even after very high ectopic expression of the respective cDNA. The encoded C-degron is also extremely efficient at promoting heterologous protein decay (Fig. 2). It is much more effective than the widely used PEST sequence. Future research will focus on identifying the degradation mechanism and residues that are important for efficient protein decay. In addition, we will evaluate the prevalence of this novel mRNA surveillance mechanism, which prevents the accumulation of non-functional C-terminally truncated proteins resulting from alternative splicing.