Prediction of cis-regulatory elements using binding site matrices--the successes, the failures and the reasons for both

Curr Opin Genet Dev. 2005 Aug;15(4):395-402. doi: 10.1016/j.gde.2005.05.002.


Protein-DNA interactions control many aspects of animal development and cellular responses to the environment. Although profiling of individual transcription factor binding sites is not a reliable guide for predicting the position of cis-regulatory elements in large genomes, modelling the evolution and the organization of regulatory elements has provided enough information to make some successful predictions. For vertebrate genomes, the field is limited by the lack of sufficient experimental data upon which to build reliable models. Nonetheless, a combination of experimental, computational and comparative data is likely to reveal aspects of complex regulatory networks in vertebrates, just as it has already done for simple eukaryotic genomes.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Animals
  • Base Sequence
  • Binding Sites / genetics
  • Conserved Sequence / genetics
  • Enhancer Elements, Genetic / genetics*
  • Evolution, Molecular
  • Gene Expression Regulation, Developmental
  • Humans
  • Molecular Sequence Data
  • Sequence Homology, Nucleic Acid
  • Transcription Factors / metabolism*


  • Transcription Factors