ArticleProceedings of the National Academy of Sciences of the United States of America2015
Target selection by natural and redesigned PUF proteins.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 35 citations in OpenAlex.
- Engineering a xylose fermenting yeast for lignocellulosic ethanol production.Nature chemical biology · 2025Article
- PUF partner interactions at a conserved interface shape the RNA-binding landscape and cell fate in Caenorhabditis elegans.Developmental cell · 2024Article
- Fusarium oxysporum f. sp.mBio · 2023Article
- Genetic and Chemical Controls of Sperm Fate and Spermatocyte Dedifferentiation via PUF-8 and MPK-1 inCells · 2023Article
- A non-canonical Puf3p-binding sequence regulates CAT5/COQ7 mRNA under both fermentable and respiratory conditions in budding yeast.PloS one · 2023Article
- TOR complex 2 is a master regulator of plasma membrane homeostasis.The Biochemical journal · 2022Article
- Expanding the binding specificity for RNA recognition by a PUF domain.Nature communications · 2021Article
- Phosphorylation of mRNA-Binding Proteins Puf1 and Puf2 by TORC2-Activated Protein Kinase Ypk1 Alleviates Their Repressive Effects.Membranes · 2021Article
- Functions of PUF Family RNA-Binding Proteins inJournal of microbiology and biotechnology · 2021Article
- easyCLIP analysis of RNA-protein interactions incorporating absolute quantification.Nature communications · 2021Article
- Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity.Nucleic acids research · 2019Article
- A Sir2-regulated locus control region in the recombination enhancer of Saccharomyces cerevisiae specifies chromosome III structure.PLoS genetics · 2019Article
- Functional and molecular characterization of the conserved Arabidopsis PUMILIO protein, APUM9.Plant molecular biology · 2019Article
- Methods to study RNA-protein interactions.Nature methods · 2019Review
- Purification of cross-linked RNA-protein complexes by phenol-toluol extraction.Nature communications · 2019Article
- Article
- Toward Identifying Subnetworks from FBF Binding Landscapes inG3 (Bethesda, Md.) · 2019Article
- The PUF Protein Family: Overview on PUF RNA Targets, Biological Functions, and Post Transcriptional Regulation.International journal of molecular sciences · 2018Review
- Translational co-regulation of a ligand and inhibitor by a conserved RNA element.Nucleic acids research · 2018Article
- High-resolution mapping ofProceedings of the National Academy of Sciences of the United States of America · 2017Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Pumilio/fem-3 mRNA binding factor (PUF) proteins bind RNA with sequence specificity and modularity, and have become exemplary scaffolds in the reengineering of new RNA specificities. Here, we report the in vivo RNA binding sites of wild-type (WT) and reengineered forms of the PUF protein Saccharomyces cerevisiae Puf2p across the transcriptome. Puf2p defines an ancient protein family present throughout fungi, with divergent and distinctive PUF RNA binding domains, RNA-recognition motifs (RRMs), and prion regions. We identify sites in RNA bound to Puf2p in vivo by using two forms of UV cross-linking followed by immunopurification. The protein specifically binds more than 1,000 mRNAs, which contain multiple iterations of UAAU-binding elements. Regions outside the PUF domain, including the RRM, enhance discrimination among targets. Compensatory mutants reveal that one Puf2p molecule binds one UAAU sequence, and align the protein with the RNA site. Based on this architecture, we redesign Puf2p to bind UAAG and identify the targets of this reengineered PUF in vivo. The mutant protein finds its target site in 1,800 RNAs and yields a novel RNA network with a dramatic redistribution of binding elements. The mutant protein exhibits even greater RNA specificity than wild type. The redesigned protein decreases the abundance of RNAs in its redesigned network. These results suggest that reengineering using the PUF scaffold redirects and can even enhance specificity in vivo.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.