ROD1 is a seedless target gene of hypoxia-induced miR-210

PLoS One. 2012;7(9):e44651. doi: 10.1371/journal.pone.0044651. Epub 2012 Sep 14.

Abstract

Most metazoan microRNA (miRNA) target sites have perfect pairing to the "seed" sequence, a highly conserved region centering on miRNA nucleotides 2-7. Thus, complementarity to this region is a necessary requirement for target prediction algorithms. However, also non-canonical miRNA binding can confer target regulation. Here, we identified a seedless target of miR-210, a master miRNA of the hypoxic response. We analyzed 20 genes that were inversely correlated to miR-210 expression and did not display any complementarity with miR-210 seed sequence. We validated ROD1 (Regulator of Differentiation 1, also named PTBP3, Polypyrimidine Tract Binding protein 3) as a miR-210 seedless transcript enriched in miR-210-containing RNA-induced silencing complexes. ROD1 was not indirectly targeted by a miR-210-induced miRNA. Conversely, we identified a "centered" miR-210 binding site in ROD1 involving 10 consecutive bases in the central portion of miR-210. Reporter assays showed that miR-210 inhibited ROD1 by the direct binding to this sequence, demonstrating that ROD1 is a bona fide seedless target of miR-210. As expected, both ROD1 mRNA and protein were down-modulated upon hypoxia in a miR-210 dependent manner. ROD1 targeting by miR-210 was biologically significant: the rescue of ROD1 inhibition significantly increased hypoxia-induced cell death. These data highlight the importance of ROD1 regulation by miR-210 for cell homeostasis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Apoptosis
  • Base Pairing
  • Base Sequence
  • Binding Sites
  • Cell Survival / genetics
  • Gene Expression Regulation*
  • HEK293 Cells
  • Humans
  • Hypoxia*
  • MicroRNAs / chemistry
  • MicroRNAs / genetics*
  • Polypyrimidine Tract-Binding Protein / chemistry
  • Polypyrimidine Tract-Binding Protein / genetics*
  • RNA Interference
  • Reproducibility of Results
  • Transcription, Genetic

Substances

  • MIRN210 microRNA, human
  • MicroRNAs
  • PTBP3 protein, human
  • Polypyrimidine Tract-Binding Protein

Grants and funding

This work was partly supported by Ministero della Salute and Associazione Italiana per la Ricerca sul Cancro (AIRC IG-11436). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.