Uncovering RNA Editing Sites in Long Non-Coding RNAs

RNA editing is an important co/post-transcriptional molecular process able to modify RNAs by nucleotide insertions/deletions or substitutions. In human, the most common RNA editing event involves the deamination of adenosine (A) into inosine (I) through the adenosine deaminase acting on RNA proteins...

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Detalles Bibliográficos
Autores: Picardi, Ernesto, D´Erchia, Anna Maria, Gallo, Angela, Montalvo Correa, Antonio, Pesole, Graziano
Tipo de recurso: artículo
Fecha de publicación:2014
País:España
Institución:Universidad de Cantabria (UC)
Repositorio:UCrea Repositorio Abierto de la Universidad de Cantabria
Idioma:inglés
OAI Identifier:oai:repositorio.unican.es:10902/5922
Acceso en línea:http://hdl.handle.net/10902/5922
Access Level:acceso abierto
Palabra clave:A-to-I editing
RNA editing
RNA-Seq
lncRNA
Long non-coding RNA
ncRNA
Transcriptome
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spelling Uncovering RNA Editing Sites in Long Non-Coding RNAsPicardi, ErnestoD´Erchia, Anna MariaGallo, AngelaMontalvo Correa, AntonioPesole, GrazianoA-to-I editingRNA editingRNA-SeqlncRNALong non-coding RNAncRNATranscriptomeRNA editing is an important co/post-transcriptional molecular process able to modify RNAs by nucleotide insertions/deletions or substitutions. In human, the most common RNA editing event involves the deamination of adenosine (A) into inosine (I) through the adenosine deaminase acting on RNA proteins. Although A-to-I editing can occur in both coding and non-coding RNAs, recent findings, based on RNA-seq experiments, have clearly demonstrated that a large fraction of RNA editing events alter non-coding RNAs sequences including untranslated regions of mRNAs, introns, long non-coding RNAs (lncRNAs), and low molecular weight RNAs (tRNA, miRNAs, and others). An accurate detection of A-to-I events occurring in non-coding RNAs is of utmost importance to clarify yet unknown functional roles of RNA editing in the context of gene expression regulation and maintenance of cell homeostasis. In the last few years, massive transcriptome sequencing has been employed to identify putative RNA editing changes at genome scale. Despite several efforts, the computational prediction of A-to-I sites in complete eukaryotic genomes is yet a challenging task. We have recently developed a software package, called REDItools, in order to simplify the detection of RNA editing events from deep sequencing data. In the present work, we show the potential of our tools in recovering A-to-I candidates from RNA-Seq experiments as well as guidelines to improve the RNA editing detection in non-coding RNAs, with specific attention to the lncRNAs.FrontiersUniversidad de Cantabria20142014-12-05journal articlehttp://purl.org/coar/resource_type/c_6501NAhttp://purl.org/coar/version/c_be7fb7dd8ff6fe43info:eu-repo/semantics/articlehttp://hdl.handle.net/10902/5922Frontiers in Bioengineering and Biotechnology. 2014 Dec 5;2:64reponame:UCrea Repositorio Abierto de la Universidad de Cantabriainstname:Universidad de Cantabria (UC)Inglésengopen accesshttp://purl.org/coar/access_right/c_abf2Atribución 3.0 Españahttp://creativecommons.org/licenses/by/3.0/es/info:eu-repo/semantics/openAccessoai:repositorio.unican.es:10902/59222026-06-02T12:39:31Z
dc.title.none.fl_str_mv Uncovering RNA Editing Sites in Long Non-Coding RNAs
title Uncovering RNA Editing Sites in Long Non-Coding RNAs
spellingShingle Uncovering RNA Editing Sites in Long Non-Coding RNAs
Picardi, Ernesto
A-to-I editing
RNA editing
RNA-Seq
lncRNA
Long non-coding RNA
ncRNA
Transcriptome
title_short Uncovering RNA Editing Sites in Long Non-Coding RNAs
title_full Uncovering RNA Editing Sites in Long Non-Coding RNAs
title_fullStr Uncovering RNA Editing Sites in Long Non-Coding RNAs
title_full_unstemmed Uncovering RNA Editing Sites in Long Non-Coding RNAs
title_sort Uncovering RNA Editing Sites in Long Non-Coding RNAs
dc.creator.none.fl_str_mv Picardi, Ernesto
D´Erchia, Anna Maria
Gallo, Angela
Montalvo Correa, Antonio
Pesole, Graziano
author Picardi, Ernesto
author_facet Picardi, Ernesto
D´Erchia, Anna Maria
Gallo, Angela
Montalvo Correa, Antonio
Pesole, Graziano
author_role author
author2 D´Erchia, Anna Maria
Gallo, Angela
Montalvo Correa, Antonio
Pesole, Graziano
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Universidad de Cantabria
dc.subject.none.fl_str_mv A-to-I editing
RNA editing
RNA-Seq
lncRNA
Long non-coding RNA
ncRNA
Transcriptome
topic A-to-I editing
RNA editing
RNA-Seq
lncRNA
Long non-coding RNA
ncRNA
Transcriptome
description RNA editing is an important co/post-transcriptional molecular process able to modify RNAs by nucleotide insertions/deletions or substitutions. In human, the most common RNA editing event involves the deamination of adenosine (A) into inosine (I) through the adenosine deaminase acting on RNA proteins. Although A-to-I editing can occur in both coding and non-coding RNAs, recent findings, based on RNA-seq experiments, have clearly demonstrated that a large fraction of RNA editing events alter non-coding RNAs sequences including untranslated regions of mRNAs, introns, long non-coding RNAs (lncRNAs), and low molecular weight RNAs (tRNA, miRNAs, and others). An accurate detection of A-to-I events occurring in non-coding RNAs is of utmost importance to clarify yet unknown functional roles of RNA editing in the context of gene expression regulation and maintenance of cell homeostasis. In the last few years, massive transcriptome sequencing has been employed to identify putative RNA editing changes at genome scale. Despite several efforts, the computational prediction of A-to-I sites in complete eukaryotic genomes is yet a challenging task. We have recently developed a software package, called REDItools, in order to simplify the detection of RNA editing events from deep sequencing data. In the present work, we show the potential of our tools in recovering A-to-I candidates from RNA-Seq experiments as well as guidelines to improve the RNA editing detection in non-coding RNAs, with specific attention to the lncRNAs.
publishDate 2014
dc.date.none.fl_str_mv 2014
2014-12-05
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
NA
http://purl.org/coar/version/c_be7fb7dd8ff6fe43
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/10902/5922
url http://hdl.handle.net/10902/5922
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Atribución 3.0 España
http://creativecommons.org/licenses/by/3.0/es/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Atribución 3.0 España
http://creativecommons.org/licenses/by/3.0/es/
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Frontiers
publisher.none.fl_str_mv Frontiers
dc.source.none.fl_str_mv Frontiers in Bioengineering and Biotechnology. 2014 Dec 5;2:64
reponame:UCrea Repositorio Abierto de la Universidad de Cantabria
instname:Universidad de Cantabria (UC)
instname_str Universidad de Cantabria (UC)
reponame_str UCrea Repositorio Abierto de la Universidad de Cantabria
collection UCrea Repositorio Abierto de la Universidad de Cantabria
repository.name.fl_str_mv
repository.mail.fl_str_mv
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