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Genome-wide Measurement of RNA Secondary Structure in Yeast

Michael Kertesz1*, Yue Wan2*, Elad Mazor1, John L. Rinn3, Robert C. Nutter4, Howard Y. Chang2†, Eran Segal1,5†

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. Here, we describe a novel strategy termed Parallel Analysis of RNA Structure (PARS), which is based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes, thus providing simultaneous in-vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution. We apply PARS to profile the secondary structure of the mRNAs of the budding yeast S. cerevisiae and obtain structural profiles for over 3000 distinct transcripts. Analysis of these profiles reveals several RNA structural properties of yeast transcripts, including the existence of more secondary structure over coding regions compared to untranslated regions, a three-nucleotide periodicity of secondary structure across coding regions, and a relationship between the efficiency with which an mRNA is translated and the lack of structure over its translation start site. PARS is readily applicable to other organisms and to profiling RNA structure in diverse conditions, thus enabling studies of the dynamics of secondary structure at a genomic scale.

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1 Dept. of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel.
2 Howard Hughes Medical Institute, Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
3 The Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
4 Life Technologies, Foster City, CA 94404, USA
5 Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel.
* These authors contributed equally to this work.
Correspondence should be addressed to H.C. or E.S. .