ArticleGenome biology2013
Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed, 105 citations in OpenAlex.
- Bridging sequence-structure motifs and genetic variants for genome-wide dynamic RNA-protein interaction profiling.Nature communications · 2026Article
- Iterative SCRaMbLE for engineering synthetic genome modules and chromosomes.Nature communications · 2025Article
- GCLiPP: global crosslinking and protein purification method for constructing high-resolution occupancy maps for RNA binding proteins.Genome biology · 2023Article
- Dynamic characterization and interpretation for protein-RNA interactions across diverse cellular conditions using HDRNet.Nature communications · 2023Article
- Genome-wide probing of eukaryotic nascent RNA structure elucidates cotranscriptional folding and its antimutagenic effect.Nature communications · 2023Article
- Interaction of the La-related protein Slf1 with colliding ribosomes maintains translation of oxidative-stress responsive mRNAs.Nucleic acids research · 2023Article
- A non-canonical Puf3p-binding sequence regulates CAT5/COQ7 mRNA under both fermentable and respiratory conditions in budding yeast.PloS one · 2023Article
- Managing the Steady State Chromatin Landscape by Nucleosome Dynamics.Annual review of biochemistry · 2022Review
- The Translational Regulation in mTOR Pathway.Biomolecules · 2022Review
- Compartmentalization and metabolic regulation of glycolysis.Journal of cell science · 2021Review
- Subcellular Localization of Fad1p inLife (Basel, Switzerland) · 2021Article
- Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast.RNA biology · 2021Article
- Analysis of RNA-protein networks with RNP-MaP defines functional hubs on RNA.Nature biotechnology · 2021Article
- A 4-Base-Pair Core-Enclosing Helix in Telomerase RNA Is Essential for Activity and for Binding to the Telomerase Reverse Transcriptase Catalytic Protein Subunit.Molecular and cellular biology · 2020Article
- Article
- Mitochondrial Biogenesis Is Positively Regulated by Casein Kinase I Hrr25 Through Phosphorylation of Puf3 inGenetics · 2020Article
- Article
- Probing In Vivo Structure of Individual mRNA 3' Isoforms Using Dimethyl Sulfate.Current protocols in molecular biology · 2019Article
- Beyond CLIP: advances and opportunities to measure RBP-RNA and RNA-RNA interactions.Nucleic acids research · 2019Review
- The Inescapable Effects of Ribosomes on In-Cell NMR Spectroscopy and the Implications for Regulation of Biological Activity.International journal of molecular sciences · 2019Review
3 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundProtein-RNA interactions are integral components of nearly every aspect of biology, including regulation of gene expression, assembly of cellular architectures, and pathogenesis of human diseases. However, studies in the past few decades have only uncovered a small fraction of the vast landscape of the protein-RNA interactome in any organism, and even less is known about the dynamics of protein-RNA interactions under changing developmental and environmental conditions.
resultsHere, we describe the gPAR-CLIP (global photoactivatable-ribonucleoside-enhanced crosslinking and immunopurification) approach for capturing regions of the untranslated, polyadenylated transcriptome bound by RNA-binding proteins (RBPs) in budding yeast. We report over 13,000 RBP crosslinking sites in untranslated regions (UTRs) covering 72% of protein-coding transcripts encoded in the genome, confirming 3' UTRs as major sites for RBP interaction. Comparative genomic analyses reveal that RBP crosslinking sites are highly conserved, and RNA folding predictions indicate that secondary structural elements are constrained by protein binding and may serve as generalizable modes of RNA recognition. Finally, 38% of 3' UTR crosslinking sites show changes in RBP occupancy upon glucose or nitrogen deprivation, with major impacts on metabolic pathways as well as mitochondrial and ribosomal gene expression.
conclusionsOur study offers an unprecedented view of the pervasiveness and dynamics of protein-RNA interactions in vivo.
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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.