Initial recognition of U12-dependent introns requires both U11/5' splice-site and U12/branchpoint interactions

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Abstract
We have investigated the formation of prespliceosomal complex A in HeLa nuclear extracts on a splicing substrate containing an AT-AC (U12-type) intron from the P120 gene. Using an RNase H protection assay and specific blocking oligonucleotides, we find that recognition of the 5′ splice-site (5′ss) and branchpoint sequence (BPS) elements by U11 and U12 snRNPs, respectively, displays strong cooperativity, requiring both sites in the pre-mRNA substrate for efficient complex formation. Deletion analysis indicates that beside the 5′ss and BPS, no additional elements in the pre-mRNA are necessary for A-complex formation, although 5′ exon sequences provide stimulation. Cross-linking studies with pre-mRNAs containing the 5′ss or BPS alone indicate that recognition of the BPS by the U12 snRNP is stimulated at least 20- to 30-fold by the binding of the U11 snRNP to the 5′ss in the same pre-mRNA molecule, whereas recognition of the 5′ss by U11 is stimulated approximately fivefold by the U12/BPS interaction. These results argue that intron recognition in the U12-dependent splicing pathway is carried out by a single U11/U12 di-snRNP complex, suggesting greater rigidity in the intron recognition process than in the major spliceosome.