Base-pairing probability in the microRNA stem region affects the binding and editing specificity of human A-to-I editing enzymes ADAR1-p110 and ADAR2

RNA Biol. 2018;15(7):976-989. doi: 10.1080/15476286.2018.1486658. Epub 2018 Jul 24.

Abstract

Adenosine deaminases acting on RNA (ADARs) catalyze the deamination of adenosine (A) to inosine (I). A-to-I RNA editing targets double-stranded RNA (dsRNA), and increases the complexity of gene regulation by modulating base pairing-dependent processes such as splicing, translation, and microRNA (miRNA)-mediated gene silencing. This study investigates the genome-wide binding preferences of the nuclear constitutive isoforms ADAR1-p110 and ADAR2 on human miRNA species by RNA immunoprecipitation of ADAR-bound small RNAs (RIP-seq). Our results suggest that secondary structure predicted by base-pairing probability in the mainly double-stranded region of a pre-miRNA or mature miRNA duplex may determine ADAR isoform preference for binding distinct subpopulations of miRNAs. Furthermore, we identify 31 unique editing sites with statistical significance, 19 sites of which are novel editing sites. Editing sites are enriched in the seed region responsible for target recognition by miRNAs, and isoform-specific nucleotide motifs in the immediate vicinity and opposite of editing sites are consistent with previous studies, and further reveal that ADAR2 may edit A/C bulges more frequently than ADAR1-p110 in the context of miRNA.

Keywords: ADAR; RIP-seq; RNA editing; binding preference; double-stranded RNA binding protein; miRNA; miRNA manqué.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine / genetics
  • Adenosine Deaminase / chemistry
  • Adenosine Deaminase / genetics
  • Adenosine Deaminase / metabolism*
  • Base Pairing*
  • Deamination
  • Genome-Wide Association Study
  • HeLa Cells
  • Humans
  • Inosine / genetics
  • Isoenzymes / chemistry
  • Isoenzymes / genetics
  • Isoenzymes / metabolism
  • MicroRNAs / chemistry
  • MicroRNAs / genetics
  • MicroRNAs / metabolism*
  • Nucleotide Motifs
  • Protein Structure, Secondary
  • RNA Editing*
  • RNA-Binding Proteins / chemistry
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism*

Substances

  • Isoenzymes
  • MicroRNAs
  • RNA-Binding Proteins
  • Inosine
  • ADAR protein, human
  • ADARB1 protein, human
  • Adenosine Deaminase
  • Adenosine

Grant support

This work was partially supported by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) and the Cell Innovation Project (MEXT) to KU-T, by Nestlé Nutrition Council of Japan (NNCJ) to JG and research funds from the Yamagata Prefectural Government and the City of Tsuruoka to JG and MT.