Identifying mRNA editing deaminase targets by RNA-Seq

Brad R. Rosenberg, Scott Dewell, F. Nina Papavasiliou

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

7 Scopus citations

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 demonstrated in vitro, identifying their physiological targets has proved challenging. Recent advances in ultra highthroughput 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.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages103-119
Number of pages17
DOIs
StatePublished - 2011
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume718
ISSN (Print)1064-3745

Keywords

  • APOBEC1
  • Adenosine deaminase
  • Cytidine deaminase
  • RNA editing
  • RNA-Seq

Fingerprint

Dive into the research topics of 'Identifying mRNA editing deaminase targets by RNA-Seq'. Together they form a unique fingerprint.

Cite this