Sequence, Structure and Context Preferences of Human RNA Binding Proteins

Production of functional cellular RNAs requires multiple processing steps principally mediated by RNA binding proteins (RBPs). Here we present the affinity landscape of 78 human RNA binding proteins using an unbiased assay that determines the sequence, structure, and context preferences of RBPs from...

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Bibliographic Details
Published inbioRxiv
Main Authors Dominguez, Daniel, Freese, Peter, Alexis, Maria S, Su, Amanda, Hochman, Myles, Palden, Tsultrim, Bazile, Cassandra, Lambert, Nicole J, Van Nostrand, Eric L, Pratt, Gabriel A, Yeo, Gene W, Graveley, Brenton, Burge, Christopher B
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 12.10.2017
Subjects
Nucleotide sequence
Protein structure
Proteins
RNA processing
RNA-binding protein
Secondary structure
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Summary:Production of functional cellular RNAs requires multiple processing steps principally mediated by RNA binding proteins (RBPs). Here we present the affinity landscape of 78 human RNA binding proteins using an unbiased assay that determines the sequence, structure, and context preferences of RBPs from a diverse RNA pool. The importance of RBP specificities in regulation of RNA processing is shown through integrative analysis with in vivo binding and loss of function studies. While we find that many proteins bind similar short sequence elements, specificities across factors diverge when additional features such as secondary structure, bipartite motifs and nucleotide context are considered. These data present a more comprehensive view of how RBPs bind their targets, a central requirement for understanding RNA processing mechanisms and outcomes.
DOI:10.1101/201996