title: Genome-Wide Characterization of RNA Editing in Chicken Embryos Reveals Common Features among Vertebrates.
abstract: RNA editing results in a post-transcriptional nucleotide change in the RNA sequence that creates an alternative nucleotide not present in the DNA sequence. This leads to a diversification of transcription products with potential functional consequences. Two nucleotide substitutions are mainly described in animals, from adenosine to inosine (A-to-I) and from cytidine to uridine (C-to-U). This phenomenon is described in more details in mammals, notably since the availability of next generation sequencing technologies allowing whole genome screening of RNA-DNA differences. The number of studies recording RNA editing in other vertebrates like chicken is still limited. We chose to use high throughput sequencing technologies to search for RNA editing in chicken, and to extend the knowledge of its conservation among vertebrates. We performed sequencing of RNA and DNA from 8 embryos. Being aware of common pitfalls inherent to sequence analyses that lead to false positive discovery, we stringently filtered our datasets and found fewer than 40 reliable candidates. Conservation of particular sites of RNA editing was attested by the presence of 3 edited sites previously detected in mammals. We then characterized editing levels for selected candidates in several tissues and at different time points, from 4.5 days of embryonic development to adults, and observed a clear tissue-specificity and a gradual increase of editing level with time. By characterizing the RNA editing landscape in chicken, our results highlight the extent of evolutionary conservation of this phenomenon within vertebrates, attest to its tissue and stage specificity and provide support of the absence of non A-to-I events from the chicken transcriptome.
authors.affiliation: INRA, Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse, INP, ENSAT, Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse, INP, ENVT, Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France.
authors.forename: Laure
authors.initials: L
authors.lastname: Frésard
authors.affiliation: INRA, Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse, INP, ENSAT, Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse, INP, ENVT, Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Leroux
authors.affiliation: Agrocampus Ouest, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Élevage, Rennes, France; INRA, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Élevage, Rennes, France.
authors.forename: Pierre-François
authors.initials: PF
authors.lastname: Roux
authors.affiliation: INRA, Sigenae Biométrie et Intelligence Artificielle, Castanet-Tolosan, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Klopp
authors.affiliation: INRA, Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse, INP, ENSAT, Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse, INP, ENVT, Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Fabre
authors.affiliation: INRA, Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse, INP, ENSAT, Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse, INP, ENVT, Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France; INRA, GeT-PlaGe Genotoul, Castanet-Tolosan, France.
authors.forename: Diane
authors.initials: D
authors.lastname: Esquerré
authors.affiliation: INRA, Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse, INP, ENSAT, Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse, INP, ENVT, Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France; INRA, Sigenae Biométrie et Intelligence Artificielle, Castanet-Tolosan, France.
authors.forename: Patrice
authors.initials: P
authors.lastname: Dehais
authors.affiliation: INRA, Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse, INP, ENSAT, Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse, INP, ENVT, Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France; INRA, Sigenae Biométrie et Intelligence Artificielle, Castanet-Tolosan, France.
authors.forename: Anis
authors.initials: A
authors.lastname: Djari
authors.affiliation: INRA, Pôle d'Expérimentation Avicole de Tours, Nouzilly, France.
authors.forename: David
authors.initials: D
authors.lastname: Gourichon
authors.affiliation: Agrocampus Ouest, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Élevage, Rennes, France; INRA, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Élevage, Rennes, France.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Lagarrigue
authors.affiliation: INRA, Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse, INP, ENSAT, Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse, INP, ENVT, Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France.
authors.forename: Frédérique
authors.initials: F
authors.lastname: Pitel
mesh_terms: D000818:Animals; D002642:Chick Embryo; D002645:Chickens / Q000235:genetics*; D019295:Computational Biology; D004247:DNA / Q000737:chemistry; D019143:Evolution, Molecular; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D012313:RNA / Q000737:chemistry; D017393:RNA Editing; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA
chemical_list: D012313:RNA; D004247:DNA