ArticleNucleic acids research2011
Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers, 1 of them a synthesis that pooled it.
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Who cites it
49 citing papers in PubMed, 1 synthesis or guideline pooled it, 75 citations in OpenAlex.
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- 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
- Analysis of mRNA deadenylation by multi-protein complexes.Methods (San Diego, Calif.) · 2017Article
- [Effect of nucleolin silencing on differentiation of rat neural stem cells in vitro and the molecular mechanism].Nan fang yi ke da xue xue bao = Journal of Southern Medical University · 2017Article
- Comprehensive and quantitative mapping of RNA-protein interactions across a transcribed eukaryotic genome.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Structural basis for the dimerization of Nab2 generated by RNA binding provides insight into its contribution to both poly(A) tail length determination and transcript compaction in Saccharomyces cerevisiae.Nucleic acids research · 2017Article
- Nucleolin-Mediated RNA Localization Regulates Neuron Growth and Cycling Cell Size.Cell reports · 2016Article
- Translational Capacity of a Cell Is Determined during Transcription Elongation via the Ccr4-Not Complex.Cell reports · 2016Article
- Snf1-Dependent Transcription Confers Glucose-Induced Decay upon the mRNA Product.Molecular and cellular biology · 2016Article
- Gbp2 interacts with THO/TREX through a novel type of RRM domain.Nucleic acids research · 2016Article
- Integration of Posttranscriptional Gene Networks into Metabolic Adaptation and Biofilm Maturation in Candida albicans.PLoS genetics · 2015Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Post-transcriptional regulation of gene expression, including mRNA localization, translation and decay, is ubiquitous yet still largely unexplored. How is the post-transcriptional regulatory program of each mRNA encoded in its sequence? Hundreds of specific RNA-binding proteins (RBPs) appear to play roles in mediating the post-transcriptional regulatory program, akin to the roles of specific DNA-binding proteins in transcription. As a step toward decoding the regulatory programs encoded in each mRNA, we focused on specific mRNA-protein interactions. We computationally analyzed the sequences of Saccharomyces cerevisiae mRNAs bound in vivo by 29 specific RBPs, identifying eight novel candidate motifs and confirming or extending six earlier reported recognition elements. Biochemical selections for RNA sequences selectively recognized by 12 yeast RBPs yielded novel motifs bound by Pin4, Nsr1, Hrb1, Gbp2, Sgn1 and Mrn1, and recovered the known recognition elements for Puf3, She2, Vts1 and Whi3. Most of the RNA elements we uncovered were associated with coherent mRNA expression changes and were significantly conserved in related yeasts, supporting their functional importance and suggesting that the corresponding RNA-protein interactions are evolutionarily conserved.
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