GSE39680
Genome-wide measurement of RNA folding energies
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 non-coding versus coding RNAs, 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. Overall design: RNA structure probing at 5 different temperatures (23°C , 30°C , 37°C , 55°C and 75°C) using RNase V1 on polyA-selected log phase S288C yeast RNAs was followed by library construction using a modified SOLiD small RNA cloning kit and deep sequencing on the SOLiD platform. We performed 2 biological replicates for each temperature.