Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns

Karol Szafranski^*¹ , Stefanie Schindler^*¹ , Stefan Taudien¹ , Michael Hiller² , Klaus Huse¹ , Niels Jahn¹ , Stefan Schreiber³ , Rolf Backofen² and Matthias Platzer¹

¹Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr., 07745 Jena, Germany

²Institute of Computer Science, Bioinformatics Group, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee, 79110 Freiburg, Germany

³Institute of Clinical Molecular Biology, Christian Albrechts University Kiel, Schittenhelmstr., 24105 Kiel, Germany

author email corresponding author email* Contributed equally

Genome Biology 2007, 8:R154doi:10.1186/gb-2007-8-8-r154


Published:	1 August 2007

Subject areas: Molecular biology, Genome studies, Genetics

Abstract

Background

Despite some degeneracy of sequence signals that govern splicing of eukaryotic pre-mRNAs, it is an accepted rule that U2-dependent introns exhibit the 3' terminal dinucleotide AG. Intrigued by anecdotal evidence for functional non-AG 3' splice sites, we carried out a human genome-wide screen.

Results

We identified TG dinucleotides functioning as alternative 3' splice sites in 36 human genes. The TG-derived splice variants were experimentally validated with a success rate of 92%. Interestingly, ratios of alternative splice variants are tissue-specific for several introns. TG splice sites and their flanking intron sequences are substantially conserved between orthologous vertebrate genes, even between human and frog, indicating functional relevance. Remarkably, TG splice sites are exclusively found as alternative 3' splice sites, never as the sole 3' splice site for an intron, and we observed a distance constraint for TG-AG splice site tandems.

Conclusion

Since TGs splice sites are exclusively found as alternative 3' splice sites, the U2 spliceosome apparently accomplishes perfect specificity for 3' AGs at an early splicing step, but may choose 3' TGs during later steps. Given the tiny fraction of TG 3' splice sites compared to the vast amount of non-viable TGs, cis-acting sequence signals must significantly contribute to splice site definition. Thus, we consider TG-AG 3' splice site tandems as promising subjects for studies on the mechanisms of 3' splice site selection.