RT Journal Article
SR Electronic
T1 Genome-wide characterization of RNA editing in chicken: lack of evidence for non-A-to-I events
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 008912
DO 10.1101/008912
A1 Laure Frésard
A1 Sophie Leroux
A1 Pierre-François Roux
A1 Christophe Klopp
A1 Stéphane Fabre
A1 Diane Esquerré
A1 Patrice Dehais
A1 Anis Djari
A1 David Gourichon
A1 Sandrine Lagarrigue
A1 Frédérique Pitel
YR 2014
UL http://biorxiv.org/content/early/2014/09/09/008912.abstract
AB RNA editing corresponds to a post-transcriptional nucleotide change in the RNA sequence, creating 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 more and more described in mammals, notably since the availability of next generation sequencing technologies allowing a whole genome screening of RNA-DNA differences. The number of studies recording RNA editing in other vertebrates like chicken are still limited. We chose to use high throughput sequencing technologies to search for RNA editing in chicken, to understand to what extent this phenomenon is conserved in vertebrates.We performed RNA and DNA sequencing from 8 embryos. Being aware of common pitfalls inherent to sequence analyses leading to false positive discovery, we stringently filtered our datasets and found less 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 editing level increase with time.By characterizing the RNA editing landscape in chicken, our results highlight the extent of evolutionary conservation of this phenomenon within vertebrates, and provide support of an absence of non A-to-I events from the chicken transcriptome.