Translating ceRNA Susceptibilities into Correlation Functions

Biophys J. 2017 Jul 11;113(1):206-213. doi: 10.1016/j.bpj.2017.05.042.

Abstract

Competition to bind microRNAs induces an effective positive cross talk between their targets, which are therefore known as "competing endogenous RNAs" (ceRNAs). Although such an effect is known to play a significant role in specific situations, estimating its strength from data and experimentally in physiological conditions appears to be far from simple. Here, we show that the susceptibility of ceRNAs to different types of perturbations affecting their competitors (and hence their tendency to cross talk) can be encoded in quantities as intuitive and as simple to measure as correlation functions. This scenario is confirmed by extensive numerical simulations and validated by re-analyzing phosphatase and tensin homolog's cross-talk pattern from The Cancer Genome Atlas breast cancer database. These results clarify the links between different quantities used to estimate the intensity of ceRNA cross talk and provide, to our knowledge, new keys to analyze transcriptional data sets and effectively probe ceRNA networks in silico.

Publication types

  • Validation Study

MeSH terms

  • Algorithms*
  • Binding, Competitive*
  • Breast Neoplasms / metabolism
  • Computer Simulation
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism
  • Databases, Genetic
  • Gene Expression Profiling
  • Humans
  • Kinetics
  • MicroRNAs / chemistry
  • MicroRNAs / metabolism*
  • Models, Biological*
  • Models, Molecular*
  • Nuclear Proteins / chemistry
  • Nuclear Proteins / metabolism
  • RNA-Binding Proteins / chemistry
  • RNA-Binding Proteins / metabolism
  • Stochastic Processes
  • Tensins / chemistry
  • Tensins / metabolism
  • Transcription, Genetic / physiology

Substances

  • DNA-Binding Proteins
  • MicroRNAs
  • Nuclear Proteins
  • PPP1R10 protein, human
  • RNA-Binding Proteins
  • Tensins