Exon definition may facilitate splice site selection in RNAs with multiple exons

Interactions at the 3′ end of the intron initiate spliceosome assembly and splice site selection in vertebrate pre-mRNAs. Multiple factors, including U1 small nuclear ribonucleoproteins (snRNPs), are involved in initial recognition at the 3′ end of the intron. Experiments were designed to test the possibility that U1 snRNP interaction at the 3′ end of the intron during early assembly functions to recognize and define the downstream exon and its resident 5′ splice site. Splicing precursor RNAs constructed to have elongated second exons lacking 5′ splice sites were deficient in spliceosome assembly and splicing activity in vitro. Similar substrates including a 5′ splice site at the end of exon 2 assembled and spliced normally as long as the second exon was less than 300 nucleotides long. U2 snRNPs were required for protection of the 5′ splice site terminating exon 2, suggesting direct communication during early assembly between factors binding the 3′ and 5′ splice sites bordering an exon. We suggest that exons are recognized and defined as units during early assembly by binding of factors to the 3′ end of the intron, followed by a search for a downstream 5′ splice site. In this view, only in the presence of both a 3′ and a 5′ splice site in the correct orientation and within 300 nucleotides of one another will stable exon complexes be formed. Concerted recognition of exons may help explain the 300-nucleotide-length maximum of vertebrate internal exons, the mechanism whereby the splicing machinery ignores cryptic sites within introns, the mechanism whereby exon skipping is normally avoided, and the phenotypes of 5′ splice site mutations that inhibit splicing of neighboring introns.