A novel genome-scale method for measuring RNA structure. RNA structure plays an important role in many biological processes. For genes that code for proteins, there is growing evidence that substantial regulation of their gene expression occurs post-transcriptionally. Much of this post-transcriptional regulation is thought to be mediated through secondary structure elements that are recognized by specific RNA binding proteins within the cell. The structures of RNA molecules are often important for their function and regulation, yet there are no experimental techniques for genome-scale measurement of RNA structure. Existing experimental methods for measuring RNA structure can only probe a single RNA structure per experiment and are typically limited in the length of the probed RNA. The outlined technology, termed parallel analysis of RNA structure (PARS), provides simultaneous in vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution.
The outlined invention introduces PARS, a combined computational and experimental method for measuring the secondary structure of thousands of RNA species in parallel. It is based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes. PARS was applied to profile the secondary structure of the messenger RNAs of the budding yeast Saccharomyces cerevisiae and obtain structural profiles for over 3,000 distinct transcripts.