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

• Published in: RNA (Cambridge) 2001-01, Vol.7 (1), p.133-142, Article S1355838201001844
• Main Authors: DU, HANSEN, ROSBASH, MICHAEL
• Format: Article
• Language: English
• Subjects: 5' Untranslated Regions - chemistry; Base Pairing; Base Sequence; Binding Sites; Cross-Linking Reagents; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Ribonuclease H; Ribonucleoprotein, U1 Small Nuclear - chemistry; Ribonucleoprotein, U1 Small Nuclear - metabolism; RNA Precursors - chemistry; RNA Precursors - metabolism; RNA, Fungal - chemistry; RNA, Fungal - metabolism; RNA, Small Nuclear - chemistry; RNA, Small Nuclear - metabolism; Saccharomyces cerevisiae - genetics; snRNP U1 protein; Trioxsalen - analogs & derivatives
• ISSN: 1355-8382; 1469-9001
• DOI: 10.1017/S1355838201001844

Base pairing between the 5′ end of U1 snRNA and the conserved 5′ splice site of pre-mRNA is important for commitment complex formation in vitro. However, the biochemical mechanisms by which pre-mRNA is initially recognized by the splicing machinery is not well understood. To evaluate the role of this base pairing interaction, we truncated U1 snRNA to eliminate the RNA–RNA interaction and surprisingly found that U1 snRNP can still form a nearly normal RNA–protein complex and maintain sequence specificity. We propose that some feature of U1 snRNP, perhaps one or more protein factors, is more important than the base pairing for initial 5′ splice site recognition. In addition, at least five sets of interactions contribute to complex formation or stability. Only one of these is base pairing between the 5′ splice site and the 5′ end of U1 snRNA, without which the U1 snRNP–pre-mRNA complex is less stable and has a somewhat altered conformation.