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The regulation of gene activity is a crucial factor in coordinating development, growth and acclimation to environmental changes. By this means, metabolic processes are adjusted according to cellular needs by changing gene expression patterns. In the genome of the model plant
Arabidopsis thaliana,
more than 7% of the genes are estimated to encode proteins directly involved in gene regulation. Transcription factors (TFs) are able to bind to specific
DNA
motifs named
cis
-elements and control the expression of target genes. The regulation may be either activation, stimulation, inhibition or suppression. The activation of genes is mediated by well-coordinated protein–protein interactions between transcription factors and a various number of cofactors. The gene activation networks are still poorly understood. In order to address the involved protein–DNA and protein–protein interactions, a number of methods have been developed that efficiently address
cis
-element interacting partners. This chapter describes two powerful methods: the yeast one-hybrid system and the yeast two-hybrid system. In combination these techniques provide the ability to identify
cis
-element-binding transcription factors and their upstream interaction partners.
