ArticleScientific reports2015
Integrated multi-omics analyses reveal the pleiotropic nature of the control of gene expression by Puf3p.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 58 citations in OpenAlex.
- Puf3 contributes to changes in mRNA solubility, translation elongation dynamics at rare arginine codons and loss of protein homeostasis in cells lacking Not4.RNA (New York, N.Y.) · 2026Article
- Beyond RNA-binding domains: determinants of protein-RNA binding.RNA (New York, N.Y.) · 2024Article
- PUF3 RNA binding protein ofHeliyon · 2024Article
- Interaction of the La-related protein Slf1 with colliding ribosomes maintains translation of oxidative-stress responsive mRNAs.Nucleic acids research · 2023Article
- Not4-dependent targeting of MMF1 mRNA to mitochondria limits its expression via ribosome pausing, Egd1 ubiquitination, Caf130, no-go-decay and autophagy.Nucleic acids research · 2023Article
- Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish.Life science alliance · 2023Article
- A non-canonical Puf3p-binding sequence regulates CAT5/COQ7 mRNA under both fermentable and respiratory conditions in budding yeast.PloS one · 2023Article
- A comprehensive thermodynamic model for RNA binding by the Saccharomyces cerevisiae Pumilio protein PUF4.Nature communications · 2022Article
- Integrated multi-omics reveals common properties underlying stress granule and P-body formation.RNA biology · 2021Article
- Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast.RNA biology · 2021Article
- Article
- mRNA Targeting, Transport and Local Translation in Eukaryotic Cells: From the Classical View to a Diversity of New Concepts.Molecular biology · 2021Article
- Mitochondrial Biogenesis Is Positively Regulated by Casein Kinase I Hrr25 Through Phosphorylation of Puf3 inGenetics · 2020Article
- Ribosome pausing, a dangerous necessity for co-translational events.Nucleic acids research · 2020Review
- Review
- A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins.Molecular cell · 2019Article
- Novel insights into global translational regulation through Pumilio family RNA-binding protein Puf3p revealed by ribosomal profiling.Current genetics · 2019Article
- Article
- Translational regulation in response to stress in Saccharomyces cerevisiae.Yeast (Chichester, England) · 2019Review
- An Integrated, High-Throughput Strategy for Multiomic Systems Level Analysis.Journal of proteome research · 2018Article
Corrections and comments
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
Abstract
The PUF family of RNA-binding proteins regulate gene expression post-transcriptionally. Saccharomyces cerevisiae Puf3p is characterised as binding nuclear-encoded mRNAs specifying mitochondrial proteins. Extensive studies of its regulation of COX17 demonstrate its role in mRNA decay. Using integrated genome-wide approaches we define an expanded set of Puf3p target mRNAs and quantitatively assessed the global impact of loss of PUF3 on gene expression using mRNA and polysome profiling and quantitative proteomics. In agreement with prior studies, our sequencing of affinity-purified Puf3-TAP associated mRNAs (RIP-seq) identified mRNAs encoding mitochondrially-targeted proteins. Additionally, we also found 720 new mRNA targets that predominantly encode proteins that enter the nucleus. Comparing transcript levels in wild-type and puf3∆ cells revealed that only a small fraction of mRNA levels alter, suggesting Puf3p determines mRNA stability for only a limited subset of its target mRNAs. Finally, proteomic and translatomic studies suggest that loss of Puf3p has widespread, but modest, impact on mRNA translation. Taken together our integrated multi-omics data point to multiple classes of Puf3p targets, which display coherent post-transcriptional regulatory properties and suggest Puf3p plays a broad, but nuanced, role in the fine-tuning of gene expression.
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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.