Regulation of RNA editing by RNA-binding proteins in human cells

Commun Biol. 2019 Jan 14;2:19. doi: 10.1038/s42003-018-0271-8. eCollection 2019.

Abstract

Adenosine-to-inosine (A-to-I) editing, mediated by the ADAR enzymes, diversifies the transcriptome by altering RNA sequences. Recent studies reported global changes in RNA editing in disease and development. Such widespread editing variations necessitate an improved understanding of the regulatory mechanisms of RNA editing. Here, we study the roles of >200 RNA-binding proteins (RBPs) in mediating RNA editing in two human cell lines. Using RNA-sequencing and global protein-RNA binding data, we identify a number of RBPs as key regulators of A-to-I editing. These RBPs, such as TDP-43, DROSHA, NF45/90 and Ro60, mediate editing through various mechanisms including regulation of ADAR1 expression, interaction with ADAR1, and binding to Alu elements. We highlight that editing regulation by Ro60 is consistent with the global up-regulation of RNA editing in systemic lupus erythematosus. Additionally, most key editing regulators act in a cell type-specific manner. Together, our work provides insights for the regulatory mechanisms of RNA editing.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adenosine / genetics
  • Adenosine Deaminase / genetics*
  • Adenosine Deaminase / metabolism*
  • Alu Elements
  • Autoantigens / genetics
  • Gene Expression Regulation, Neoplastic*
  • Gene Knockdown Techniques
  • Hep G2 Cells
  • Humans
  • Inosine / genetics
  • K562 Cells
  • Lupus Erythematosus, Systemic / genetics
  • RNA Editing / genetics*
  • RNA, Small Cytoplasmic / genetics
  • RNA-Binding Proteins / genetics*
  • RNA-Binding Proteins / metabolism*
  • Ribonucleoproteins / genetics
  • Sequence Analysis, RNA
  • Transcription, Genetic
  • Transfection

Substances

  • Autoantigens
  • RNA, Small Cytoplasmic
  • RNA-Binding Proteins
  • RO60 protein, human
  • Ribonucleoproteins
  • Inosine
  • ADAR protein, human
  • Adenosine Deaminase
  • Adenosine