title: Genome-wide measurement of RNA folding energies.
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.
authors.affiliation: Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Yue
authors.initials: Y
authors.lastname: Wan
authors.forename: Kun
authors.initials: K
authors.lastname: Qu
authors.forename: Zhengqing
authors.initials: Z
authors.lastname: Ouyang
authors.forename: Michael
authors.initials: M
authors.lastname: Kertesz
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.forename: Robert
authors.initials: R
authors.lastname: Tibshirani
authors.forename: Debora L
authors.initials: DL
authors.lastname: Makino
authors.forename: Robert C
authors.initials: RC
authors.lastname: Nutter
authors.forename: Eran
authors.initials: E
authors.lastname: Segal
authors.forename: Howard Y
authors.initials: HY
authors.lastname: Chang
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D019295:Computational Biology; D004734:Energy Metabolism; D063326:Exosome Multienzyme Ribonuclease Complex / Q000737:chemistry* / Q000235:genetics; D020869:Gene Expression Profiling; D016678:Genome; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs / Q000235:genetics; D012313:RNA / Q000737:chemistry / Q000235:genetics; D059370:RNA Folding; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D013696:Temperature
chemical_list: D020413:3' Untranslated Regions; D012313:RNA; D063326:Exosome Multienzyme Ribonuclease Complex