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Identifying mRNA Editing Deaminase Targets by RNA-Seq

  • Brad R. Rosenberg
  • Scott Dewell
  • F. Nina PapavasiliouEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 718)

Abstract

RNA editing deaminases act on a variety of targets in different organisms. A number of such enzymes have been shown to act on mRNA, with the resultant nucleotide changes modifying a transcript’s information content. Though the deaminase activity of mRNA editing enzymes is readily demonstratedin vitro, identifying their physiological targets has proved challenging. Recent advances in ultra high-throughput sequencing technologies have allowed for whole transcriptome sequencing and expression profiling (RNA-Seq). We have developed a system to identify novel mRNA editing deamination targets based on comparative analysis of RNA-Seq data. The efficacy and utility of this approach is demonstrated for APOBEC1, a cytidine deaminase with a known and well-characterized mRNA editing target in the mammalian small intestine.

Key words

RNA editing Cytidine deaminase Adenosine deaminase APOBEC1 RNA-Seq 

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Brad R. Rosenberg
    • 1
  • Scott Dewell
    • 2
  • F. Nina Papavasiliou
    • 1
    Email author
  1. 1.Laboratory of Lymphocyte BiologyThe Rockefeller UniversityNew YorkUSA
  2. 2.Genomics Resource CenterThe Rockefeller UniversityNew YorkUSA

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