A novel computational strategy to identify A-to-I RNA editing sites by RNA-Seq data: de novo detection in human spinal cord tissue.

RNA editing is a post-transcriptional process occurring in a wide range of organisms. In human brain, the A-to-I RNA editing, in which individual adenosine (A) bases in pre-mRNA are modified to yield inosine (I), is the most frequent event. Modulating gene expression, RNA editing is essential for ce...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Ernesto Picardi, Angela Gallo, Federica Galeano, Sara Tomaselli, Graziano Pesole
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d3be0c80369044bf87b5025dcd7d66d3
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:d3be0c80369044bf87b5025dcd7d66d3
record_format	dspace
spelling	oai:doaj.org-article:d3be0c80369044bf87b5025dcd7d66d32021-11-18T07:06:35ZA novel computational strategy to identify A-to-I RNA editing sites by RNA-Seq data: de novo detection in human spinal cord tissue.1932-620310.1371/journal.pone.0044184https://doaj.org/article/d3be0c80369044bf87b5025dcd7d66d32012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22957051/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203RNA editing is a post-transcriptional process occurring in a wide range of organisms. In human brain, the A-to-I RNA editing, in which individual adenosine (A) bases in pre-mRNA are modified to yield inosine (I), is the most frequent event. Modulating gene expression, RNA editing is essential for cellular homeostasis. Indeed, its deregulation has been linked to several neurological and neurodegenerative diseases. To date, many RNA editing sites have been identified by next generation sequencing technologies employing massive transcriptome sequencing together with whole genome or exome sequencing. While genome and transcriptome reads are not always available for single individuals, RNA-Seq data are widespread through public databases and represent a relevant source of yet unexplored RNA editing sites. In this context, we propose a simple computational strategy to identify genomic positions enriched in novel hypothetical RNA editing events by means of a new two-steps mapping procedure requiring only RNA-Seq data and no a priori knowledge of RNA editing characteristics and genomic reads. We assessed the suitability of our procedure by confirming A-to-I candidates using conventional Sanger sequencing and performing RNA-Seq as well as whole exome sequencing of human spinal cord tissue from a single individual.Ernesto PicardiAngela GalloFederica GaleanoSara TomaselliGraziano PesolePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 9, p e44184 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ernesto Picardi Angela Gallo Federica Galeano Sara Tomaselli Graziano Pesole A novel computational strategy to identify A-to-I RNA editing sites by RNA-Seq data: de novo detection in human spinal cord tissue.
description	RNA editing is a post-transcriptional process occurring in a wide range of organisms. In human brain, the A-to-I RNA editing, in which individual adenosine (A) bases in pre-mRNA are modified to yield inosine (I), is the most frequent event. Modulating gene expression, RNA editing is essential for cellular homeostasis. Indeed, its deregulation has been linked to several neurological and neurodegenerative diseases. To date, many RNA editing sites have been identified by next generation sequencing technologies employing massive transcriptome sequencing together with whole genome or exome sequencing. While genome and transcriptome reads are not always available for single individuals, RNA-Seq data are widespread through public databases and represent a relevant source of yet unexplored RNA editing sites. In this context, we propose a simple computational strategy to identify genomic positions enriched in novel hypothetical RNA editing events by means of a new two-steps mapping procedure requiring only RNA-Seq data and no a priori knowledge of RNA editing characteristics and genomic reads. We assessed the suitability of our procedure by confirming A-to-I candidates using conventional Sanger sequencing and performing RNA-Seq as well as whole exome sequencing of human spinal cord tissue from a single individual.
format	article
author	Ernesto Picardi Angela Gallo Federica Galeano Sara Tomaselli Graziano Pesole
author_facet	Ernesto Picardi Angela Gallo Federica Galeano Sara Tomaselli Graziano Pesole
author_sort	Ernesto Picardi
title	A novel computational strategy to identify A-to-I RNA editing sites by RNA-Seq data: de novo detection in human spinal cord tissue.
title_short	A novel computational strategy to identify A-to-I RNA editing sites by RNA-Seq data: de novo detection in human spinal cord tissue.
title_full	A novel computational strategy to identify A-to-I RNA editing sites by RNA-Seq data: de novo detection in human spinal cord tissue.
title_fullStr	A novel computational strategy to identify A-to-I RNA editing sites by RNA-Seq data: de novo detection in human spinal cord tissue.
title_full_unstemmed	A novel computational strategy to identify A-to-I RNA editing sites by RNA-Seq data: de novo detection in human spinal cord tissue.
title_sort	novel computational strategy to identify a-to-i rna editing sites by rna-seq data: de novo detection in human spinal cord tissue.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/d3be0c80369044bf87b5025dcd7d66d3
work_keys_str_mv	AT ernestopicardi anovelcomputationalstrategytoidentifyatoirnaeditingsitesbyrnaseqdatadenovodetectioninhumanspinalcordtissue AT angelagallo anovelcomputationalstrategytoidentifyatoirnaeditingsitesbyrnaseqdatadenovodetectioninhumanspinalcordtissue AT federicagaleano anovelcomputationalstrategytoidentifyatoirnaeditingsitesbyrnaseqdatadenovodetectioninhumanspinalcordtissue AT saratomaselli anovelcomputationalstrategytoidentifyatoirnaeditingsitesbyrnaseqdatadenovodetectioninhumanspinalcordtissue AT grazianopesole anovelcomputationalstrategytoidentifyatoirnaeditingsitesbyrnaseqdatadenovodetectioninhumanspinalcordtissue AT ernestopicardi novelcomputationalstrategytoidentifyatoirnaeditingsitesbyrnaseqdatadenovodetectioninhumanspinalcordtissue AT angelagallo novelcomputationalstrategytoidentifyatoirnaeditingsitesbyrnaseqdatadenovodetectioninhumanspinalcordtissue AT federicagaleano novelcomputationalstrategytoidentifyatoirnaeditingsitesbyrnaseqdatadenovodetectioninhumanspinalcordtissue AT saratomaselli novelcomputationalstrategytoidentifyatoirnaeditingsitesbyrnaseqdatadenovodetectioninhumanspinalcordtissue AT grazianopesole novelcomputationalstrategytoidentifyatoirnaeditingsitesbyrnaseqdatadenovodetectioninhumanspinalcordtissue
_version_	1718423946482679808

A novel computational strategy to identify A-to-I RNA editing sites by RNA-Seq data: de novo detection in human spinal cord tissue.

Ejemplares similares