SLC15A4/PHT1 is a proton dependent peptide/histidine transporter abundantly expressed in brain and eye and, at low levels, in a variety of other tissues including liver, placenta, prostate, thymus and gastrointestinal tract. In vertebrates, SLC15A4 genes share an eight-exon/seven-intron organization and seem to undergo complex alternative splicing. As well as protein isoform diversity, alternative splicing can generate mRNAs carrying premature termination codons (PTCs) that are subject to the RNA surveillance pathway known as nonsense-mediated decay (NMD). We determined the alternative splicing patterns of vertebrate SLC15A4 genes and characterized the SLC15A4 splicing events that generate mRNAs that are targets of NMD.

To identify alternative splice forms, gene-EST/mRNA alignment methods and standard RT-PCR techniques were used. This analysis revealed that exon 3 of the mammalian and zebrafish SLC15A4 genes is alternatively spliced. Notably, we found that all the exon 3 alternative splicing events introduced a PTC that targeted the resulting mRNAs to the NMD pathway. Inhibition of NMD selectively stabilized PTC-containing SLC15A4 transcripts in human and rat cell lines, which provided evidence that these unproductive mRNAs are under the NMD control.

Our results demonstrate, for the first time, that conserved alternative splice forms of SLC15A4 genes are degraded by NMD and suggest that unproductive splicing is important for regulation of SLC15A4 expression.