Human MicroRNA targets

PLoS Biol. 2004 Nov;2(11):e363. doi: 10.1371/journal.pbio.0020363. Epub 2004 Oct 5.


MicroRNAs (miRNAs) interact with target mRNAs at specific sites to induce cleavage of the message or inhibit translation. The specific function of most mammalian miRNAs is unknown. We have predicted target sites on the 3' untranslated regions of human gene transcripts for all currently known 218 mammalian miRNAs to facilitate focused experiments. We report about 2,000 human genes with miRNA target sites conserved in mammals and about 250 human genes conserved as targets between mammals and fish. The prediction algorithm optimizes sequence complementarity using position-specific rules and relies on strict requirements of interspecies conservation. Experimental support for the validity of the method comes from known targets and from strong enrichment of predicted targets in mRNAs associated with the fragile X mental retardation protein in mammals. This is consistent with the hypothesis that miRNAs act as sequence-specific adaptors in the interaction of ribonuclear particles with translationally regulated messages. Overrepresented groups of targets include mRNAs coding for transcription factors, components of the miRNA machinery, and other proteins involved in translational regulation, as well as components of the ubiquitin machinery, representing novel feedback loops in gene regulation. Detailed information about target genes, target processes, and open-source software for target prediction (miRanda) is available at Our analysis suggests that miRNA genes, which are about 1% of all human genes, regulate protein production for 10% or more of all human genes.

MeSH terms

  • 3' Untranslated Regions
  • Algorithms
  • Amino Acid Motifs
  • Amyloid beta-Protein Precursor / genetics
  • Animals
  • Chromosome Mapping
  • Computational Biology / methods*
  • Conserved Sequence
  • DNA, Complementary / metabolism
  • Disks Large Homolog 4 Protein
  • Fragile X Mental Retardation Protein / genetics
  • Gene Expression Regulation*
  • Gene Silencing
  • Humans
  • Intracellular Signaling Peptides and Proteins / chemistry
  • Introns
  • Membrane Proteins / chemistry
  • MicroRNAs / chemistry*
  • Models, Genetic
  • Models, Statistical
  • Molecular Sequence Data
  • Polyadenylation
  • Protein Binding
  • Protein Biosynthesis
  • Protein Structure, Tertiary
  • RNA / chemistry
  • RNA, Messenger / metabolism
  • Rats
  • Software


  • 3' Untranslated Regions
  • Amyloid beta-Protein Precursor
  • DLG4 protein, human
  • DNA, Complementary
  • Disks Large Homolog 4 Protein
  • Intracellular Signaling Peptides and Proteins
  • Membrane Proteins
  • MicroRNAs
  • RNA, Messenger
  • Fragile X Mental Retardation Protein
  • RNA