Summary: MOLECULAR AND CELLULAR BIOLOGY, May 2008, p. 35133525 Vol. 28, No. 10
0270-7306/08/$08.00 0 doi:10.1128/MCB.02279-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.
Multifactorial Interplay Controls the Splicing Profile of Alu-Derived Exons
Oren Ram, Schraga Schwartz, and Gil Ast*
Department of Human Genetics and Molecular Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
Received 24 December 2007/Returned for modification 14 January 2008/Accepted 28 February 2008
Exonization of Alu elements creates primate-specific genomic diversity. Here we combine bioinformatic and
experimental methodologies to reconstruct the molecular changes leading to exon selection. Our analyses revealed
an intricate network involved in Alu exonization. A typical Alu element contains multiple sites with the potential to
serve as 5 splice sites (5 ss). First, we demonstrated the role of 5 ss strength in controlling exonization events.
Second, we found that a cryptic 5 ss enhances the selection of a more upstream site and demonstrate that this is
mediated by binding of U1 snRNA to the cryptic splice site, challenging the traditional role attributed to U1 snRNA
of binding the 5 ss only. Third, we used a simple algorithm to identify specific sequences that determine splice site
selection within specific Alu exons. Finally, by inserting identical exons within different sequences, we demonstrated
the importance of flanking genomic sequences in determining whether an Alu exon will undergo exonization.
Overall, our results demonstrate the complex interplay between at least four interacting layers that affect Alu
exonization. These results shed light on the mechanism through which Alu elements enrich the primate transcrip-
tome and allow a better understanding of the exonization process in general.
An average human mRNA precursor is 28,000 nucleotides