We develop a thermodynamic model describing the binding of RNA binding proteins (RBP) to oligomers in vitro. We apply expectation-maximization to infer the specificity of RBPs, represented as position-specific weight matrices (PWMs), by maximizing the likelihood of RNA Bind'n Seq data from the ENCODE project. Analyzing these public data we find sequence motifs that can partly explain the data for more than half of the studied 111 RBPs, and for 48 of the proteins these motifs are consistent with the known specificity. Our code is publicly available, facilitating analysis of RBP binding data. Copyright: © 2024 Schlusser N and Zavolan M.
Niels Schlusser, Mihaela Zavolan. On the limits of inferring biophysical parameters of RBP-RNA interactions from in vitro RNA Bind'n Seq data. F1000Research. 2023;12:742
PMID: 39056095
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