A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets

Nat Methods. 2013 Mar;10(3):253-5. doi: 10.1038/nmeth.2341. Epub 2013 Jan 20.

Abstract

We introduce a biophysical model of miRNA-target interaction and infer its parameters from Argonaute 2 cross-linking and immunoprecipitation data. We show that a substantial fraction of human miRNA target sites are noncanonical and that predicted target-site affinity correlates well with the extent of target destabilization. Our model provides a rigorous biophysical approach to miRNA target identification beyond ad hoc miRNA seed-based methods.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Argonaute Proteins / genetics
  • Argonaute Proteins / metabolism*
  • Base Pairing
  • Binding Sites
  • Biophysical Phenomena*
  • Data Interpretation, Statistical
  • Databases, Genetic
  • Gene Targeting* / methods
  • HEK293 Cells
  • HeLa Cells
  • Humans
  • Immunoprecipitation
  • MicroRNAs / genetics*
  • MicroRNAs / metabolism
  • Models, Biological*
  • Probability
  • Protein Binding
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism
  • Transcriptome

Substances

  • AGO2 protein, human
  • Argonaute Proteins
  • MicroRNAs
  • RNA, Messenger