In considering gene regulation in both bacteria and eukaryotes, we must distinguish between the DNA sequences that are transcribed and the DNA sequences that regulate the expression of other sequences. Structural genes encode proteins that are used in metabolism or biosynthesis or that play a structural role in the cell. The products of regulatory genes, either RNA or proteins, interact with other DNA sequences and affect the transcription or translation of those sequences. In many cases, the products of regulatory genes are DNA-binding proteins (although RNA molecules also affect gene expression). Bacteria and eukaryotes use regulatory genes to control the expression of many of their structural genes. However, a few structural genes, particularly those that encode essential cellular functions, are expressed continually and are therefore said to be constitutive. Constitutive genes are not regulated.

We will also encounter DNA sequences that are not transcribed at all, but still play a role in regulating genes and other nucleotide sequences. These regulatory elements affect the expression of DNA sequences to which they are physically linked. Regulatory elements are common in both bacterial and eukaryotic cells, and much of gene regulation in both types of organisms takes place through the action of proteins produced by regulatory genes that recognize and bind to regulatory elements.

The regulation of gene expression can occur through processes that stimulate gene expression, termed positive control, or through processes that inhibit gene expression, termed negative control. Bacteria and eukaryotes use both positive and negative control mechanisms to regulate their genes.