Impact of MicroRNA Levels, Target-Site Complementarity, and Cooperativity on Competing Endogenous RNA-Regulated Gene Expression

Mol Cell. 2016 Nov 3;64(3):565-579. doi: 10.1016/j.molcel.2016.09.027. Epub 2016 Oct 27.


Expression changes of competing endogenous RNAs (ceRNAs) have been proposed to influence microRNA (miRNA) activity and thereby regulate other transcripts containing miRNA-binding sites. Here, we find that although miRNA levels define the extent of repression, they have little effect on the magnitude of the ceRNA expression change required to observe derepression. Canonical 6-nt sites, which typically mediate modest repression, can nonetheless compete for miRNA binding, with potency ∼20% of that observed for canonical 8-nt sites. In aggregate, low-affinity/background sites also contribute to competition. Sites with extensive additional complementarity can appear as more potent, but only because they induce miRNA degradation. Cooperative binding of proximal sites for the same or different miRNAs does increase potency. These results provide quantitative insights into the stoichiometric relationship between miRNAs and target abundance, target-site spacing, and affinity requirements for ceRNA-mediated gene regulation, and the unusual circumstances in which ceRNA-mediated gene regulation might be observed.

Keywords: base pair complementarity; competing endogenous RNA; cooperatively; gene regulation; miRNA; miRNA degradation; target abundance.

Publication types

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

MeSH terms

  • Adenoviridae / genetics
  • Adenoviridae / metabolism
  • Animals
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Binding, Competitive
  • Gene Expression Regulation*
  • Gene Regulatory Networks*
  • Genes, Reporter
  • Hepatocytes / cytology
  • Hepatocytes / metabolism*
  • Luminescent Proteins / genetics
  • Luminescent Proteins / metabolism
  • Male
  • Mice
  • Mice, Inbred C57BL
  • MicroRNAs / genetics*
  • MicroRNAs / metabolism
  • Plasmids / chemistry
  • Plasmids / metabolism
  • Primary Cell Culture
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism
  • Transformation, Genetic


  • Bacterial Proteins
  • Luminescent Proteins
  • MicroRNAs
  • RNA, Messenger
  • red fluorescent protein
  • yellow fluorescent protein, Bacteria