ArticleProceedings of the National Academy of Sciences of the United States of America2017
Recurrent rewiring and emergence of RNA regulatory networks.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 43 citations in OpenAlex.
- Comprehensive mapping of the 5' and 3' untranslated regions ofRNA (New York, N.Y.) · 2026Article
- The release of sexual conflict after sex loss is associated with evolutionary changes in gene expression.Proceedings. Biological sciences · 2025Article
- Orthrus: a Pumilio-family gene involved in fruiting body and dark stipe development inFrontiers in fungal biology · 2025Article
- Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro.Nature communications · 2024Article
- Species-aware DNA language models capture regulatory elements and their evolution.Genome biology · 2024Article
- Understanding species-specific and conserved RNA-protein interactionsbioRxiv : the preprint server for biology · 2024Article
- Lessons on fruiting body morphogenesis from genomes and transcriptomes ofStudies in mycology · 2023Article
- The nexus between RNA-binding proteins and their effectors.Nature reviews. Genetics · 2023Review
- A comprehensive thermodynamic model for RNA binding by the Saccharomyces cerevisiae Pumilio protein PUF4.Nature communications · 2022Article
- PRD-2 mediates clock-regulated perinuclear localization of clock gene RNAs within the circadian cycle ofProceedings of the National Academy of Sciences of the United States of America · 2022Article
- How global RNA-binding proteins coordinate the behaviour of RNA regulons: An information approach.Computational and structural biotechnology journal · 2022Article
- Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast.RNA biology · 2021Article
- Functions of PUF Family RNA-Binding Proteins inJournal of microbiology and biotechnology · 2021Article
- PRD-2 directly regulateseLife · 2020Article
- Mitochondrial Biogenesis Is Positively Regulated by Casein Kinase I Hrr25 Through Phosphorylation of Puf3 inGenetics · 2020Article
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- A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins.Molecular cell · 2019Article
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- Article
- RNA-mediated gene regulation is less evolvable than transcriptional regulation.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
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7 authors at 2 institutions in 1 country.
Funding
Abstract
Alterations in regulatory networks contribute to evolutionary change. Transcriptional networks are reconfigured by changes in the binding specificity of transcription factors and their cognate sites. The evolution of RNA-protein regulatory networks is far less understood. The PUF (Pumilio and FBF) family of RNA regulatory proteins controls the translation, stability, and movements of hundreds of mRNAs in a single species. We probe the evolution of PUF-RNA networks by direct identification of the mRNAs bound to PUF proteins in budding and filamentous fungi and by computational analyses of orthologous RNAs from 62 fungal species. Our findings reveal that PUF proteins gain and lose mRNAs with related and emergent biological functions during evolution. We demonstrate at least two independent rewiring events for PUF3 orthologs, independent but convergent evolution of PUF4/5 binding specificity and the rewiring of the PUF4/5 regulons in different fungal lineages. These findings demonstrate plasticity in RNA regulatory networks and suggest ways in which their rewiring occurs.
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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.