Minimal Conditions for Exonization of Intronic Sequences: 5’ Splice Site Formation in Alu Exons

Rotem Sorek,1,2,5; Galit Lev-Maor,1,5; Mika Reznik,1,5; Tal Dagan,3; Frida Belinky,3;

Dan Graur,4; and Gil Ast1

1Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel; 2Compugen, Tel Aviv, Israel; 3Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel; 4Department of Biology and Biochemistry, University of Houston, Houston, Texas. Molecular Cell, Vol. 14, 1–20, April 23, 2004

Abstract

Alu exonization, which is an evolutionary pathway that creates primate-specific transcriptomic diversity, is a powerful tool for studying alternative-splicing regulation. Through bioinformatic analyses combined with experimental methodology, we identified the mutational changes needed to create functional 5_ splice sites in Alu. We revealed a complex mechanism by which the sequence composition of the 5_ splice site and its base pairing with the small nuclear RNA U1 govern alternative splicing. We show that in Alu-derived GC introns the strength of the base pairing between U1 snRNA and the 5_ splice site controls the skipping/inclusion ratio of alternative splicing. Based on these findings, we identified 7810 Alus within the human genome that are prone to exonization. Mutations in these Alus may cause genetic disorders or contribute to human-specific protein diversity.