title: Discriminative Prediction of A-To-I RNA Editing Events from DNA Sequence.
abstract: RNA editing is a post-transcriptional alteration of RNA sequences that, via insertions, deletions or base substitutions, can affect protein structure as well as RNA and protein expression. Recently, it has been suggested that RNA editing may be more frequent than previously thought. A great impediment, however, to a deeper understanding of this process is the paramount sequencing effort that needs to be undertaken to identify RNA editing events. Here, we describe an in silico approach, based on machine learning, that ameliorates this problem. Using 41 nucleotide long DNA sequences, we show that novel A-to-I RNA editing events can be predicted from known A-to-I RNA editing events intra- and interspecies. The validity of the proposed method was verified in an independent experimental dataset. Using our approach, 203 202 putative A-to-I RNA editing events were predicted in the whole human genome. Out of these, 9% were previously reported. The remaining sites require further validation, e.g., by targeted deep sequencing. In conclusion, the approach described here is a useful tool to identify potential A-to-I RNA editing events without the requirement of extensive RNA sequencing.
authors.affiliation: Department of Clinical Sciences in Malmö, Unit of Molecular Metabolism, Lund University Diabetes Centre, CRC, Malmö, Sweden.
authors.forename: Jiangming
authors.initials: J
authors.lastname: Sun
authors.affiliation: Department of Clinical Sciences in Malmö, Unit of Diabetes and Endocrinology, Lund University Diabetes Centre, CRC, Malmö, Sweden.
authors.forename: Yang
authors.initials: Y
authors.lastname: De Marinis
authors.affiliation: Department of Clinical Sciences in Malmö, Unit of Diabetes and Endocrinology, Lund University Diabetes Centre, CRC, Malmö, Sweden.
authors.forename: Peter
authors.initials: P
authors.lastname: Osmark
authors.affiliation: Department of Clinical Sciences in Malmö, Unit of Molecular Metabolism, Lund University Diabetes Centre, CRC, Malmö, Sweden.
authors.forename: Pratibha
authors.initials: P
authors.lastname: Singh
authors.affiliation: Department of Clinical Sciences in Malmö, Unit of Molecular Metabolism, Lund University Diabetes Centre, CRC, Malmö, Sweden.
authors.forename: Annika
authors.initials: A
authors.lastname: Bagge
authors.affiliation: Department of Clinical Sciences in Malmö, Unit of Molecular Metabolism, Lund University Diabetes Centre, CRC, Malmö, Sweden.
authors.forename: Bérengère
authors.initials: B
authors.lastname: Valtat
authors.affiliation: Department of Clinical Sciences in Malmö, Unit of Diabetes and Endocrinology, Lund University Diabetes Centre, CRC, Malmö, Sweden.
authors.forename: Petter
authors.initials: P
authors.lastname: Vikman
authors.affiliation: Department of Clinical Sciences in Malmö, Unit of Molecular Metabolism, Lund University Diabetes Centre, CRC, Malmö, Sweden.|Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Lund, Sweden.
authors.forename: Peter
authors.initials: P
authors.lastname: Spégel
authors.affiliation: Department of Clinical Sciences in Malmö, Unit of Molecular Metabolism, Lund University Diabetes Centre, CRC, Malmö, Sweden.
authors.forename: Hindrik
authors.initials: H
authors.lastname: Mulder
mesh_terms: D000241:Adenosine / Q000378:metabolism*; D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004247:DNA / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D007288:Inosine / Q000378:metabolism*; D000069550:Machine Learning; D051379:Mice; D017393:RNA Editing
chemical_list: D007288:Inosine; D004247:DNA; D000241:Adenosine