@Article{Hiller2007Sec,
  author =	 {Hiller, Michael and Zhang, Zhaiyi and Backofen, Rolf and 
                  Stamm, Stefan},
  title =	 {Pre-{mRNA} {Secondary} {Structures} {Influence} {Exon} 
                  {Recognition}},
  journal =	 {PLoS Genet},
  year =	 2007,
  volume =	 3,
  number =	 11,
  issn =         {1553-7404},
  issn =         {1553-7390},
  pages =	 {e204},
  user =	 {backofen},
  pmid =	 18020710,
  publists =	 {All and Michael Hiller and Rolf Backofen},
  doi = 	 {10.1371/journal.pgen.0030204},
  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.}
}