trans meets cis in MADS science

Trends Plant Sci. 2006 May;11(5):224-31. doi: 10.1016/j.tplants.2006.03.008. Epub 2006 Apr 17.


The interaction between a transcription factor and its binding site at the DNA is an integral part of transcriptional regulatory networks, which is fundamental for an understanding of biological processes. An example is the family of MADS domain transcription factors, which represent key regulators of processes in yeast, animals and plants. However, despite our extensive knowledge of these transcription factors, limited information is available on the cis-elements to which these proteins bind or how these elements are defined. Here, we discuss the current understanding of MADS protein binding sites and compare data from various organisms. This information can help us in developing algorithms to predict binding sites for MADS domain transcription factors, which would be a significant step forward in the identification of "down-stream" target genes and the elucidation of transcriptional networks.

Publication types

  • Review

MeSH terms

  • Base Sequence
  • Binding Sites / physiology
  • Computational Biology
  • Consensus Sequence
  • Gene Expression Regulation, Plant
  • MADS Domain Proteins / chemistry
  • MADS Domain Proteins / physiology*
  • Plant Proteins / chemistry
  • Plant Proteins / physiology*
  • Regulatory Elements, Transcriptional*
  • Sequence Analysis, DNA
  • Trans-Activators / physiology
  • Transcriptional Activation


  • MADS Domain Proteins
  • Plant Proteins
  • Trans-Activators