ArticleMolecular cell2012
Genome-wide measurement of RNA folding energies.
Article in Molecular cell, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers.
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Who cites it
117 citing papers in PubMed.
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- Unveiling RNA structure-mediated regulations of RNA stability in wheat.Nature communications · 2024Article
- Identification of RNA structures and their roles in RNA functions.Nature reviews. Molecular cell biology · 2024Review
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- Single-molecule quantitation of RNA-binding protein occupancy and stoichiometry defines a role for Yra1 (Aly/REF) in nuclear mRNP organization.Cell reports · 2023Article
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- Rock, scissors, paper: How RNA structure informs function.The Plant cell · 2023Article
- Identification of exceptionally potent adenosine deaminases RNA editors from high body temperature organisms.PLoS genetics · 2023Article
- Genome-wide sequencing identifies a thermal-tolerance related synonymous mutation in the mussel, Mytilisepta virgata.Communications biology · 2023Article
- Response and regulatory mechanisms of heat resistance in pathogenic fungi.Applied microbiology and biotechnology · 2022Review
- Getting to the bottom of lncRNA mechanism: structure-function relationships.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Review
- Small and intermediate size structural RNAs in the unicellular parasiteMicrobial genomics · 2022Article
- E2F4 may be a core transcription factor in the lncRNA-TF regulatory network in cervical cancer.Journal of clinical laboratory analysis · 2022Article
- mSRFR: a machine learning model using microalgal signature features for ncRNA classification.BioData mining · 2022Article
- An ultra low-input method for global RNA structure probing uncovers Regnase-1-mediated regulation in macrophages.Fundamental research · 2022Article
57 more citing papers are in PubMed but not listed here.
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10 authors.
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Abstract
RNA structural transitions are important in the function and regulation of RNAs. Here, we reveal a layer of transcriptome organization in the form of RNA folding energies. By probing yeast RNA structures at different temperatures, we obtained relative melting temperatures (Tm) for RNA structures in over 4000 transcripts. Specific signatures of RNA Tm demarcated the polarity of mRNA open reading frames and highlighted numerous candidate regulatory RNA motifs in 3' untranslated regions. RNA Tm distinguished noncoding versus coding RNAs and identified mRNAs with distinct cellular functions. We identified thousands of putative RNA thermometers, and their presence is predictive of the pattern of RNA decay in vivo during heat shock. The exosome complex recognizes unpaired bases during heat shock to degrade these RNAs, coupling intrinsic structural stabilities to gene regulation. Thus, genome-wide structural dynamics of RNA can parse functional elements of the transcriptome and reveal diverse biological insights.
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