Discriminative Prediction of A-To-I RNA Editing Events from DNA Sequence

PLoS One. 2016 Oct 20;11(10):e0164962. doi: 10.1371/journal.pone.0164962. eCollection 2016.

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.

MeSH terms

  • Adenosine / metabolism*
  • Animals
  • Base Sequence
  • Computational Biology / methods*
  • Computer Simulation
  • DNA / genetics*
  • Genome, Human / genetics
  • Humans
  • Inosine / metabolism*
  • Machine Learning
  • Mice
  • RNA Editing*

Substances

  • Inosine
  • DNA
  • Adenosine

Grants and funding

This work was supported by the Crafoord, Novo Nordisk, Knut & Alice Wallenberg, and Albert Påhlsson foundations, as well as The Medical Faculty in Lund and The Swedish Research Council. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.