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• W2146940435 abstract "While many RNA-binding proteins (RBPs) bind RNA in a sequence-specific manner, their sequence preferences alone do not distinguish known target RNAs from other potential targets that are coexpressed and contain the same sequence motifs. Recently, the mRNA targets of dozens of RNA-binding proteins have been identified, facilitating a systematic study of the features of target transcripts. Using these data, we demonstrate that calculating the predicted structural accessibility of a putative RBP binding site allows one to significantly improve the accuracy of predicting in vivo binding for the majority of sequence-specific RBPs. In our new in silico approach, accessibility is predicted based solely on the mRNA sequence without consideration of the locations of bound trans -factors; as such, our results suggest a greater than previously anticipated role for intrinsic mRNA secondary structure in determining RBP binding target preference. Target site accessibility aids in predicting target transcripts and the binding sites for RBPs with a range of RNA-binding domains and subcellular functions. Based on this work, we introduce a new motif-finding algorithm that identifies accessible sequence-specific RBP motifs from in vivo binding data." @default.
• W2146940435 created "2016-06-24" @default.
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• W2146940435 date "2010-04-23" @default.
• W2146940435 modified "2023-10-14" @default.
• W2146940435 title "Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure" @default.
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• W2146940435 doi "https://doi.org/10.1261/rna.2017210" @default.
• W2146940435 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2874161" @default.
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