Identification of Splicing Silencers and Enhancers in Sense Alus: a Role for Pseudoacceptors in Splice Site Repression

Abstract

Auxiliary splicing signals in introns play an important role in splice site selection, but these elements are poorly understood. We show that a subset of serine/arginine (SR)-rich proteins activate a cryptic 3′ splice site in a sense Alu repeat located in intron 4 of the human LST1 gene. Utilization of this cryptic splice site is controlled by juxtaposed Alu-derived splicing silencers and enhancers between closely linked short tandem repeats TNFd and TNFe. Systematic mutagenesis of these elements showed that AG dinucleotides that were not preceded by purine residues were critical for repressing exon inclusion of a chimeric splicing reporter. Since the splice acceptor-like sequences are present in excess in exonic splicing silencers, these signals may contribute to inhibition of a large number of pseudosites in primate genomes.

SUPPLEMENTAL MATERIAL

Supplemental material for this article may be found at http://mcb.asm.org/.

ACKNOWLEDGMENTS

This study was supported by grants from the European Commission and the Wellcome Trust, the Karolinska Institute, and the University of Southampton School of Medicine.

We thank C. W. J. Smith, University of Cambridge; G. Screaton, University of Oxford; J. Cáceres, Medical Research Council Human Genetics Unit, Edinburgh; J. Královičová, University of Southampton; M. Boutros, DKFZ; S. Marsh and N. Mayor, Anthony Nolan Research Institute, London; and A. Krainer, Cold Spring Harbor Laboratory, for reagents and/or helpful discussions.