NOVEL MODELS FOR RNA SPLICING THAT INVOLVE A SMALL NUCLEAR-RNA

Nucleotide sequences of mammalian small nuclear (sn)RNA were analyzed with a computer program for complementarity with sequences around a splice junction of various eukaryotic mRNA precursors (pre-mRNA). A region in U2 RNA or some other snRNA can form base pairs with both exons surrounding an intron of certain pre-mRNA and, thereby, can align the 2 junctions leading to correct splicing of the pre-mRNA. A snRNA such as U2 can be involved in splicing certain pre-mRNA by pairing with exons, called an exon model for splicing, as compared with the model involving U1 RNA presented by Lerner et al. A secondary structure model of U1 RNA was constructed and the capacity of base pairing with pre-mRNA was studied on the basis of both primary and secondary structures of U1 RNA. An alternative model for splicing is presented that involves U1 RNA, which assumes base pairing of noncontiguous regions of U1 RNA with an intron of a pre-mRNA. Pairing of an snRNA with exons could explain correct matching of the 2 junctions that bound one and the same intron, which is not explained by pairing with consensus sequences at the ends of an intron as proposed by Lerner et al. Pairing of an intron with U1 RNA and pairing of the surrounding exons with another snRNA such as U2 RNA could take place at the same time to insure specificity of splicing.