Conserved Seed Pairing, Often Flanked by Adenosines, Indicates That Thousands of Human Genes Are microRNA Targets

Cell. 2005 Jan 14;120(1):15-20. doi: 10.1016/j.cell.2004.12.035.

Abstract

We predict regulatory targets of vertebrate microRNAs (miRNAs) by identifying mRNAs with conserved complementarity to the seed (nucleotides 2-7) of the miRNA. An overrepresentation of conserved adenosines flanking the seed complementary sites in mRNAs indicates that primary sequence determinants can supplement base pairing to specify miRNA target recognition. In a four-genome analysis of 3' UTRs, approximately 13,000 regulatory relationships were detected above the estimate of false-positive predictions, thereby implicating as miRNA targets more than 5300 human genes, which represented 30% of our gene set. Targeting was also detected in open reading frames. In sum, well over one third of human genes appear to be conserved miRNA targets.

Publication types

  • Letter
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • 3' Untranslated Regions / genetics
  • Adenosine / genetics
  • Adenosine / metabolism*
  • Amino Acid Sequence
  • Animals
  • Chickens
  • Dogs
  • Gene Expression Regulation / genetics
  • Gene Targeting / methods
  • Humans
  • Mice
  • MicroRNAs / genetics*
  • Molecular Sequence Data
  • Nucleic Acid Hybridization / physiology
  • Nucleotides / metabolism*
  • RNA, Messenger / genetics
  • Rats

Substances

  • 3' Untranslated Regions
  • MicroRNAs
  • Nucleotides
  • RNA, Messenger
  • Adenosine