Global analyses of the effect of different cellular contexts on microRNA targeting

Mol Cell. 2014 Mar 20;53(6):1031-1043. doi: 10.1016/j.molcel.2014.02.013. Epub 2014 Mar 13.


MicroRNA (miRNA) regulation clearly impacts animal development, but the extent to which development-with its resulting diversity of cellular contexts-impacts miRNA regulation is unclear. Here, we compared cohorts of genes repressed by the same miRNAs in different cell lines and tissues and found that target repertoires were largely unaffected, with secondary effects explaining most of the differential responses detected. Outliers resulting from differential direct targeting were often attributable to alternative 3' UTR isoform usage that modulated the presence of miRNA sites. More inclusive examination of alternative 3' UTR isoforms revealed that they influence ∼10% of predicted targets when comparing any two cell types. Indeed, considering alternative 3' UTR isoform usage improved prediction of targeting efficacy significantly beyond the improvements observed when considering constitutive isoform usage. Thus, although miRNA targeting is remarkably consistent in different cell types, considering the 3' UTR landscape helps predict targeting efficacy and explain differential regulation that is observed.

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

  • 3' Untranslated Regions*
  • Cell Line, Tumor
  • Gene Expression Regulation
  • HEK293 Cells
  • HeLa Cells
  • Hepatocytes / cytology
  • Hepatocytes / metabolism
  • Humans
  • MicroRNAs / genetics*
  • MicroRNAs / metabolism
  • Organ Specificity
  • Polymorphism, Genetic
  • RNA Stability*
  • Signal Transduction
  • Uridine / metabolism*


  • 3' Untranslated Regions
  • MicroRNAs
  • Uridine

Associated data

  • GEO/GSE52531
  • GEO/GSE52940