Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions

Nat Struct Mol Biol. 2006 Sep;13(9):849-51. doi: 10.1038/nsmb1138. Epub 2006 Aug 20.


We use Caenorhabditis elegans to test proposed general rules for microRNA (miRNA)-target interactions. We show that G.U base pairing is tolerated in the 'seed' region of the lsy-6 miRNA interaction with its in vivo target cog-1, and that 6- to 8-base-pair perfect seed pairing is not a generally reliable predictor for an interaction of lsy-6 with a 3' untranslated region (UTR). Rather, lsy-6 can functionally interact with its target site only in specific 3' UTR contexts. Our findings illustrate the difficulty of establishing generalizable rules of miRNA-target interactions.

Publication types

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

MeSH terms

  • 3' Untranslated Regions / chemistry
  • 3' Untranslated Regions / genetics
  • 3' Untranslated Regions / metabolism
  • Animals
  • Base Pairing / genetics*
  • Base Sequence
  • Caenorhabditis elegans / cytology
  • MicroRNAs / metabolism*
  • Molecular Sequence Data


  • 3' Untranslated Regions
  • MicroRNAs