Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Thiel, Bernhard C., Ochsenreiter, Roman, Gadekar, Veerendra P., Tanzer, Andrea, Hofacker, Ivo L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2018
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
_version_ 1783351515955593216
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
work_keys_str_mv AT thielbernhardc rnastructureelementsconservedbetweenmouseand59othervertebrates
AT ochsenreiterroman rnastructureelementsconservedbetweenmouseand59othervertebrates
AT gadekarveerendrap rnastructureelementsconservedbetweenmouseand59othervertebrates
AT tanzerandrea rnastructureelementsconservedbetweenmouseand59othervertebrates
AT hofackerivol rnastructureelementsconservedbetweenmouseand59othervertebrates