title: Pre-mRNA secondary structures influence exon recognition.
abstract: The secondary structure of a pre-mRNA influences a number of processing steps including alternative splicing. Since most splicing regulatory proteins bind to single-stranded RNA, the sequestration of RNA into double strands could prevent their binding. Here, we analyzed the secondary structure context of experimentally determined splicing enhancer and silencer motifs in their natural pre-mRNA context. We found that these splicing motifs are significantly more single-stranded than controls. These findings were validated by transfection experiments, where the effect of enhancer or silencer motifs on exon skipping was much more pronounced in single-stranded conformation. We also found that the structural context of predicted splicing motifs is under selection, suggesting a general importance of secondary structures on splicing and adding another level of evolutionary constraints on pre-mRNAs. Our results explain the action of mutations that affect splicing and indicate that the structural context of splicing motifs is part of the mRNA splicing code.
authors.affiliation: Bioinformatics Group, Albert-Ludwigs-University Freiburg, Freiburg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Hiller
authors.forename: Zhaiyi
authors.initials: Z
authors.lastname: Zhang
authors.forename: Rolf
authors.initials: R
authors.lastname: Backofen
authors.forename: Stefan
authors.initials: S
authors.lastname: Stamm
mesh_terms: D000818:Animals; D001483:Base Sequence; D002460:Cell Line; D030561:Databases, Nucleic Acid; D004742:Enhancer Elements, Genetic / Q000235:genetics; D005091:Exons / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012322:RNA Precursors / Q000737:chemistry*; D022821:RNA Splice Sites / Q000235:genetics; D012326:RNA Splicing / Q000235:genetics; D051381:Rats; D038621:Regulatory Sequences, Ribonucleic Acid / Q000235:genetics; D037941:Silencer Elements, Transcriptional / Q000235:genetics
chemical_list: D012322:RNA Precursors; D022821:RNA Splice Sites; D038621:Regulatory Sequences, Ribonucleic Acid