ArticleNature communications2022
A comprehensive thermodynamic model for RNA binding by the Saccharomyces cerevisiae Pumilio protein PUF4.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 18 citations in OpenAlex.
- Decoding RNA-protein interactions using high-throughput methods.RNA biology · 2026Review
- Review
- Biochemical principles of miRNA targeting in flies.Nature communications · 2026Article
- Comprehensive mapping of the 5' and 3' untranslated regions ofRNA (New York, N.Y.) · 2026Article
- An A-T Hoogsteen Base Pair in a Naked DNA Hairpin Motif: A Protein-Recognized Conformation.Angewandte Chemie (International ed. in English) · 2025Article
- Systematic analysis of cotranscriptional RNA folding using transcription elongation complex display.Nature communications · 2025Article
- Thermodynamic modeling of RsmA - mRNA interactions capture novel direct binding across theFrontiers in molecular biosciences · 2025Article
- Puf4 -mediated oxidative stress virulence attenuation inFrontiers in cellular and infection microbiology · 2025Article
- High-throughput biochemistry in RNA sequence space: predicting structure and function.Nature reviews. Genetics · 2023Review
- Dissecting the energetic architecture within an RNA tertiary structural motif via high-throughput thermodynamic measurements.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
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Authors and funding
8 authors at 5 institutions in 1 country.
Funding
Abstract
Genomic methods have been valuable for identifying RNA-binding proteins (RBPs) and the genes, pathways, and processes they regulate. Nevertheless, standard motif descriptions cannot be used to predict all RNA targets or test quantitative models for cellular interactions and regulation. We present a complete thermodynamic model for RNA binding to the S. cerevisiae Pumilio protein PUF4 derived from direct binding data for 6180 RNAs measured using the RNA on a massively parallel array (RNA-MaP) platform. The PUF4 model is highly similar to that of the related RBPs, human PUM2 and PUM1, with one marked exception: a single favorable site of base flipping for PUF4, such that PUF4 preferentially binds to a non-contiguous series of residues. These results are foundational for developing and testing cellular models of RNA-RBP interactions and function, for engineering RBPs, for understanding the biophysical nature of RBP binding and the evolutionary landscape of RNAs and RBPs.
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