RNA structural patterns and splicing: molecular basis for an RNA-based enhancer.
Efficient splicing of the 325-nt yeast (Saccharomyces cerevisiae) rp51b intron requires the presence of two short interacting sequences located 200 nt apart. We used the powerful technique of randomization-selection to probe the overall structure of the intron and to investigate its role in pre-mRNA splicing. We identified a number of alternative RNA-RNA interactions in the intron that promote efficient splicing, and we showed that similar base pairings can also improve splicing efficiency in artificially designed introns. Only a very limited amount of structural information is necessary to create or maintain such a mechanism. Our results suggest that the base pairing contributes transiently to the spliceosome assembly process, most likely by complementing interactions between splicing factors. We propose that splicing enhancement by structure represents a general mechanism operating in large yeast introns that evolutionarily preceded the protein-based splicing enhancers of higher eukaryotes.
D001483:Base Sequence; D003001:Cloning, Molecular; D007438:Introns; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009690:Nucleic Acid Conformation; D012313:RNA / Q000378:metabolism; D012322:RNA Precursors / Q000737:chemistry / Q000378:metabolism; D012326:RNA Splicing; D012331:RNA, Fungal / Q000737:chemistry / Q000378:metabolism*; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism; D012269:Ribosomal Proteins / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D014170:Transformation, Genetic
D012322:RNA Precursors; D012331:RNA, Fungal; D012333:RNA, Messenger; C039919:RNA, recombinant; D012269:Ribosomal Proteins; C038698:ribosomal protein 51; D012313:RNA