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Genes 2018, 9(8), 392; https://doi.org/10.3390/genes9080392

RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates

1
Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstraße 17, 1090 Wien, Austria
2
Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Währingerstraße 29, 1090 Wien, Austria
*
Authors to whom correspondence should be addressed.
Received: 15 May 2018 / Revised: 25 July 2018 / Accepted: 27 July 2018 / Published: 1 August 2018
(This article belongs to the Special Issue Computational Analysis of RNA Structure and Function)
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Abstract

In this work, we present a computational screen conducted for functional RNA structures, resulting in over 100,000 conserved RNA structure elements found in alignments of mouse (mm10) against 59 other vertebrates. We explicitly included masked repeat regions to explore the potential of transposable elements and low-complexity regions to give rise to regulatory RNA elements. In our analysis pipeline, we implemented a four-step procedure: (i) we screened genome-wide alignments for potential structure elements using RNAz-2, (ii) realigned and refined candidate loci with LocARNA-P, (iii) scored candidates again with RNAz-2 in structure alignment mode, and (iv) searched for additional homologous loci in mouse genome that were not covered by genome alignments. The 3’-untranslated regions (3’-UTRs) of protein-coding genes and small noncoding RNAs are enriched for structures, while coding sequences are depleted. Repeat-associated loci make up about 95% of the homologous loci identified and are, as expected, predominantly found in intronic and intergenic regions. Nevertheless, we report the structure elements enriched in specific genome elements, such as 3’-UTRs and long noncoding RNAs (lncRNAs). We provide full access to our results via a custom UCSC genome browser trackhub freely available on our website (http://rna.tbi.univie.ac.at/trackhubs/#RNAz). View Full-Text
Keywords: RNA secondary structure; conserved RNA structure elements; RNAz; structural alignment; RNA regulation RNA secondary structure; conserved RNA structure elements; RNAz; structural alignment; RNA regulation
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Thiel, B.C.; Ochsenreiter, R.; Gadekar, V.P.; Tanzer, A.; Hofacker, I.L. RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates. Genes 2018, 9, 392.

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