title: Uncovering RNA Editing Sites in Long Non-Coding RNAs.
abstract: 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.
authors.affiliation: Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari , Bari , Italy ; Institute of Biomembranes and Bioenergetics , Bari , Italy.
authors.forename: Ernesto
authors.initials: E
authors.lastname: Picardi
authors.affiliation: Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari , Bari , Italy ; Institute of Biomembranes and Bioenergetics , Bari , Italy.
authors.forename: Anna Maria
authors.initials: AM
authors.lastname: D'Erchia
authors.affiliation: RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù , Rome , Italy.
authors.forename: Angela
authors.initials: A
authors.lastname: Gallo
authors.affiliation: Department of Molecular Biology, Faculty of Medicine, University of Cantabria , Santander , Spain ; University Hospital Marqués de Valdecilla , Santander , Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Montalvo
authors.affiliation: Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari , Bari , Italy ; Institute of Biomembranes and Bioenergetics , Bari , Italy.
authors.forename: Graziano
authors.initials: G
authors.lastname: Pesole
keywords: A-to-I editing; RNA editing; RNA-Seq; lncRNA; long non-coding RNA; ncRNA; transcriptome