Transcription factors: specific DNA binding and specific gene regulation

Trends Genet. 2014 Jun;30(6):211-9. doi: 10.1016/j.tig.2014.04.002. Epub 2014 Apr 26.


Specific recognition of cis-regulatory regions is essential for correct gene regulation in response to developmental and environmental signals. Such DNA sequences are recognized by transcription factors (TFs) that recruit the transcriptional machinery. Achievement of specific sequence recognition is not a trivial problem; many TFs recognize similar consensus DNA-binding sites and a genome can harbor thousands of consensus or near-consensus sequences, both functional and nonfunctional. Although genomic technologies have provided large-scale snapshots of TF binding, a full understanding of the mechanistic and quantitative details of specific recognition in the context of gene regulation is lacking. Here, we explore the various ways in which TFs recognizing similar consensus sites distinguish their own targets from a large number of other sequences to ensure specific cellular responses.

Keywords: ChIP-seq; cis-regulation; gene expression; response element; transcription; transcription factor.

Publication types

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

MeSH terms

  • Animals
  • Binding Sites
  • Chromatin / genetics
  • Chromatin / metabolism
  • Gene Expression Regulation*
  • Humans
  • Protein Binding
  • Regulatory Sequences, Nucleic Acid
  • Signal Transduction
  • Transcription Factors / metabolism*
  • Transcription, Genetic


  • Chromatin
  • Transcription Factors