title: Impact of MicroRNA Levels, Target-Site Complementarity, and Cooperativity on Competing Endogenous RNA-Regulated Gene Expression.
abstract: 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.
authors.affiliation: Institute of Molecular Health Sciences, Swiss Federal Institute of Technology in Zurich (ETH Zurich), Otto-Stern-Weg 7, 8093 Zürich, Switzerland.
authors.forename: Rémy
authors.initials: R
authors.lastname: Denzler
authors.affiliation: Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Sean E
authors.initials: SE
authors.lastname: McGeary
authors.affiliation: Institute of Molecular Health Sciences, Swiss Federal Institute of Technology in Zurich (ETH Zurich), Otto-Stern-Weg 7, 8093 Zürich, Switzerland.
authors.forename: Alexandra C
authors.initials: AC
authors.lastname: Title
authors.affiliation: Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Vikram
authors.initials: V
authors.lastname: Agarwal
authors.affiliation: Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: dbartel@wi.mit.edu.
authors.forename: David P
authors.initials: DP
authors.lastname: Bartel
authors.affiliation: Institute of Molecular Health Sciences, Swiss Federal Institute of Technology in Zurich (ETH Zurich), Otto-Stern-Weg 7, 8093 Zürich, Switzerland. Electronic address: stoffel@biol.ethz.ch.
authors.forename: Markus
authors.initials: M
authors.lastname: Stoffel
mesh_terms: D000256:Adenoviridae / Q000235:genetics / Q000378:metabolism; D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D001667:Binding, Competitive; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D017930:Genes, Reporter; D022781:Hepatocytes / Q000166:cytology / Q000378:metabolism*; D008164:Luminescent Proteins / Q000235:genetics / Q000378:metabolism; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D010957:Plasmids / Q000737:chemistry / Q000378:metabolism; D061251:Primary Cell Culture; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D014170:Transformation, Genetic; D000097573:Red Fluorescent Protein
chemical_list: D001426:Bacterial Proteins; D008164:Luminescent Proteins; D035683:MicroRNAs; D012333:RNA, Messenger; D000097573:Red Fluorescent Protein; C054562:yellow fluorescent protein, Bacteria
keywords: base pair complementarity; competing endogenous RNA; cooperatively; gene regulation; miRNA; miRNA degradation; target abundance