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RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates
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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6116022/ https://www.ncbi.nlm.nih.gov/pubmed/30071678 http://dx.doi.org/10.3390/genes9080392 |
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author | Thiel, Bernhard C. Ochsenreiter, Roman Gadekar, Veerendra P. Tanzer, Andrea Hofacker, Ivo L. |
author_facet | Thiel, Bernhard C. Ochsenreiter, Roman Gadekar, Veerendra P. Tanzer, Andrea Hofacker, Ivo L. |
author_sort | Thiel, Bernhard C. |
collection | PubMed |
description | 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). |
format | Online Article Text |
id | pubmed-6116022 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-61160222018-08-31 RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates Thiel, Bernhard C. Ochsenreiter, Roman Gadekar, Veerendra P. Tanzer, Andrea Hofacker, Ivo L. Genes (Basel) Article 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). MDPI 2018-08-01 /pmc/articles/PMC6116022/ /pubmed/30071678 http://dx.doi.org/10.3390/genes9080392 Text en © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Thiel, Bernhard C. Ochsenreiter, Roman Gadekar, Veerendra P. Tanzer, Andrea Hofacker, Ivo L. RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates |
title | RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates |
title_full | RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates |
title_fullStr | RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates |
title_full_unstemmed | RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates |
title_short | RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates |
title_sort | rna structure elements conserved between mouse and 59 other vertebrates |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6116022/ https://www.ncbi.nlm.nih.gov/pubmed/30071678 http://dx.doi.org/10.3390/genes9080392 |
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