@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},
doi = {10.1371/journal.pgen.0030204},
volume = {3},
user = {backofen},
publists = {All and Michael Hiller and Rolf Backofen},
pmid = {18020710},
pages = {e204},
number = {11},
issn = {1553-7404},
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.}
}