Genome-wide probing of nascent RNA structure in eukaryotes reveals dynamics of cotranscriptional folding and its anticorrelation with spontaneous mutation rate of DNA

The transcriptional intermediates of RNA fold into secondary structures with multiple regulatory roles, yet details of such cotranscriptional folding of nascent RNA is largely unresolved in eukaryotes. In this study, we developed a novel assay named eSPET-seq (the Structural Probing of Elongating Transcripts in eukaryotes) and experimentally assessed the in vivo pairing status of all four nucleotides near the transcription site in Saccharomyces cerevisiae. We presented a novel experimental evaluation of cotranscriptional folding in eukaryotes, and demonstrated the genome-wide generality and magnitude of the antimutator effect of nascent RNA folding.