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Updated: May 30, 2026
Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae
Published on: February 27, 2026
Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding
Sven Findeiss1, Jan Engelhardt, Sonja J Prohaska
1Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria. sven@tbi.univie.ac.at
Abstract:
Functional RNA elements can be embedded also within exonic sequences coding for functional proteins. While not uncommon in viruses, only a few examples of this type have been described in some detail for eukaryotic genomes. Here we use RNAz and RNAcode, two comparative genomics methods that measure signatures of stabilizing selection acting on RNA secondary structure and peptide sequence, resp., to survey the fruit fly genomes. We estimate that there might be on the order of 1000 loci that are subject to dual selection pressure. The used genome-wide screens also expose the limitations of the currently available methods.
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