Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids |
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| Authors: | Findeiss Sven Engelhardt Jan Prohaska Sonja J Stadler Peter F |
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| Institution: | aDepartment of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria;bInterdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany;cComputational EvoDevo Group, Department of Computer Science, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany;dBioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany;eMax Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D-04103 Leipzig, Germany;fFraunhofer Institut für Zelltherapie und Immunologie – IZI, Perlickstraße 1, D-04103 Leipzig, Germany;gCenter For Non-Coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark;hSanta Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA |
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| 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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| Keywords: | Dual RNAs RNA secondary structures Coding sequence RNAz RNAcode |
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