Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in prokaryotes, the catabolite activator protein or CAP directly interacts with the C-terminal domain of the alpha subunit of RNA polymerase to regulate gene expression. Strong evidence for direct interaction is the loss of function mutations in the activation domains of proteins that lead to suppression of transcriptional activity.

However, in some eukaryotic genes, regulation can happen via distal activation. Hence, the regulating elements may not lie in close proximity to the promoter or may not interact directly with the transcriptional machinery. Such interactions can be detected by (a) observing the rate of transcription in the presence or absence of the regulatory protein (b) mutations in the binding site of the regulatory protein that can disrupt gene expression (c) measuring the binding affinity between the regulatory protein and the promoter.

In addition, the transcription machinery also needs nucleosome remodelers to access the DNA within the chromatin. Hence, these nucleosome remodelers are also involved in regulating gene expression.