Yeast U1 snRNP-pre-mRNA complex formation without U1snRNA-pre-mRNA base pairing

Base pairing between the 5' end of U1 snRNA and the conserved 5' splice sit e of pre-mRNA is important for commitment complex formation in vitro. Howev er, the biochemical mechanisms by which pre-mRNA is initially recognized by the splicing machinery is not well understood. To evaluate the role of thi s base pairing interaction, we truncated U1 snRNA to eliminate the RNA-RNA interaction and surprisingly found that U1 snRNP can still form a nearly no rmal RNA-protein complex and maintain sequence specificity. We propose that some feature of Ut snRNP, perhaps one or more protein factors, is more imp ortant than the base pairing for initial 5' splice site recognition. In add ition, at least five sets of interactions contribute to complex formation o r stability. Only one of these is base pairing between the 5' splice site a nd the 5' end of U1 snRNA, without which the U1 snRNP-pre-mRNA complex is l ess stable and has a somewhat altered conformation.