ArticlePLoS genetics2014
Systematic analysis of the role of RNA-binding proteins in the regulation of RNA stability.
Article in PLoS genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 86 citations in OpenAlex.
- Flipper: An advanced framework for identifying differential RNA binding behavior with eCLIP data.bioRxiv : the preprint server for biology · 2026Article
- The patterns of alternative TSS usage explain the highly heterogeneous landscape of 5'UTR lengths in eukaryotes.NAR genomics and bioinformatics · 2025Article
- RNAtranslator: Modeling protein-conditional RNA design as sequence-to-sequence natural language translation.PLoS computational biology · 2025Article
- Dissecting RNA selectivity mediated by tandem RNA-binding domains.The Journal of biological chemistry · 2025Article
- Mapping the dynamics of epigenetic adaptation in S. pombe during heterochromatin misregulation.Developmental cell · 2024Article
- Long live the RNAs: The guardians of neuronal longevity?Molecular cell · 2024Article
- Cold-Inducible RNA Binding Protein Impedes Breast Tumor Growth in the PyMT Murine Model for Breast Cancer.Biomedicines · 2024Article
- RNA-Binding Protein-Mediated mRNA Deadenylation in Mammalian Cell Extracts.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Broad functional profiling of fission yeast proteins using phenomics and machine learning.eLife · 2023Article
- Surmounting Cancer Drug Resistance: New Perspective on RNA-Binding Proteins.Pharmaceuticals (Basel, Switzerland) · 2023Review
- Article
- Mitotic checkpoint gene expression is tuned by codon usage bias.The EMBO journal · 2022Article
- Genetic variants associated mRNA stability in lung.BMC genomics · 2022Article
- In heart failure reactivation of RNA-binding proteins is associated with the expression of 1,523 fetal-specific isoforms.PLoS computational biology · 2022Article
- The Fission Yeast Cell Integrity Pathway: A Functional Hub for Cell Survival upon Stress and Beyond.Journal of fungi (Basel, Switzerland) · 2021Review
- Effects of sequence motifs in the yeast 3' untranslated region determined from massively parallel assays of random sequences.Genome biology · 2021Article
- R-loops and regulatory changes in chronologically ageing fission yeast cells drive non-random patterns of genome rearrangements.PLoS genetics · 2021Article
- Predicting dynamic cellular protein-RNA interactions by deep learning using in vivo RNA structures.Cell research · 2021Article
- Anti-Inflammatory Effects of a Polyphenol, Catechin-7,4'-Pharmaceutics · 2021Article
- Ribosome profiling reveals ribosome stalling on tryptophan codons and ribosome queuing upon oxidative stress in fission yeast.Nucleic acids research · 2021Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
mRNA half-lives are transcript-specific and vary over a range of more than 100-fold in eukaryotic cells. mRNA stabilities can be regulated by sequence-specific RNA-binding proteins (RBPs), which bind to regulatory sequence elements and modulate the interaction of the mRNA with the cellular RNA degradation machinery. However, it is unclear if this kind of regulation is sufficient to explain the large range of mRNA stabilities. To address this question, we examined the transcriptome of 74 Schizosaccharomyces pombe strains carrying deletions in non-essential genes encoding predicted RBPs (86% of all such genes). We identified 25 strains that displayed changes in the levels of between 4 and 104 mRNAs. The putative targets of these RBPs formed biologically coherent groups, defining regulons involved in cell separation, ribosome biogenesis, meiotic progression, stress responses and mitochondrial function. Moreover, mRNAs in these groups were enriched in specific sequence motifs in their coding sequences and untranslated regions, suggesting that they are coregulated at the posttranscriptional level. We performed genome-wide RNA stability measurements for several RBP mutants, and confirmed that the altered mRNA levels were caused by changes in their stabilities. Although RBPs regulate the decay rates of multiple regulons, only 16% of all S. pombe mRNAs were affected in any of the 74 deletion strains. This suggests that other players or mechanisms are required to generate the observed range of RNA half-lives of a eukaryotic transcriptome.
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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.