Evolutionary forces act on promoter length: identification of enriched cis-regulatory elements

Mol Biol Evol. 2009 Jun;26(6):1299-307. doi: 10.1093/molbev/msp040. Epub 2009 Mar 3.


Transcription factors govern gene expression by binding to short DNA sequences called cis-regulatory elements. These sequences are typically located in promoters, which are regions of variable length upstream of the open reading frames of genes. Here, we report that promoter length and gene function are related in yeast, fungi, and plants. In particular, the promoters for stress-responsive genes are in general longer than those of other genes. Essential genes have, on the other hand, relatively short promoters. We utilize these findings in a novel method for identifying relevant cis-regulatory elements in a set of coexpressed genes. The method is shown to generate more accurate results and fewer false positives compared with other common procedures. Our results suggest that genes with complex transcriptional regulation tend to have longer promoters than genes responding to few signals. This phenomenon is present in all investigated species, indicating that evolution adjust promoter length according to gene function. Identification of cis-regulatory elements in Saccharomyces cerevisiae can be done with the web service located at http://enricher.zool.gu.se.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arsenic / pharmacology
  • Binding Sites / genetics
  • Computer Simulation
  • Data Interpretation, Statistical
  • Evolution, Molecular*
  • Fungi / genetics
  • Gene Expression Regulation, Fungal / drug effects
  • Genes, Fungal
  • Genes, Plant
  • Logistic Models
  • Models, Genetic*
  • Oligonucleotide Array Sequence Analysis
  • Plants / genetics
  • Promoter Regions, Genetic*
  • Saccharomyces cerevisiae / genetics
  • Stress, Physiological
  • Transcription Factors / genetics*


  • Transcription Factors
  • Arsenic