Genome-wide quantification of ADAR adenosine-to-inosine RNA editing activity

Nat Methods. 2019 Nov;16(11):1131-1138. doi: 10.1038/s41592-019-0610-9. Epub 2019 Oct 21.

Abstract

Adenosine-to-inosine (A-to-I) RNA editing by the adenosine deaminase that acts on RNA (ADAR) enzymes is a common RNA modification, preventing false activation of the innate immune system by endogenous double-stranded RNAs. Methods for quantification of ADAR activity are sought after, due to an increasing interest in the role of ADARs in cancer and autoimmune disorders, as well as attempts to harness the ADAR enzymes for RNA engineering. Here, we present the Alu editing index (AEI), a robust and simple-to-use computational tool devised for this purpose. We describe its properties and demonstrate its superiority to current quantification methods of ADAR activity. The AEI is used to map global editing across a large dataset of healthy human samples and identify putative regulators of ADAR, as well as previously unknown factors affecting the observed Alu editing levels. These should be taken into account in future comparative studies of ADAR activity. The AEI tool is available at https://github.com/a2iEditing/RNAEditingIndexer.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine / genetics*
  • Adenosine Deaminase / analysis*
  • Alu Elements
  • Animals
  • Base Sequence
  • Humans
  • Inosine / genetics*
  • Mice
  • RNA Editing*
  • RNA-Binding Proteins / analysis*

Substances

  • RNA-Binding Proteins
  • Inosine
  • ADAR1 protein, human
  • Adenosine Deaminase
  • Adenosine