Because the first committed step of gene expression is the transcription of the gene, a large fraction of genetic control takes place at this step, especially through the initiation of transcription. Genetic control schemes may be classified in several ways.
The first method of classification is according to their physiological effect on gene expression, either positive or negative. In positive control, the control element or pathway stimulates gene expression. The effect of a mutation “knocking out” the control gene is therefore to decrease the level of gene expression. In this classification, a promoter sequence would be a positive control element, because removing it would decrease transcription. A positive control element is like the ignition switch in a car: removing it means that the car can't go. By contrast, in negative control, a control element acts to reduce or repress gene expression. The effect of a mutation “knocking out” a positive control gene would be to increase the level of expression. A negative control element is like the brakes in a car: removing it means that the car keeps moving. Several steps in the expression of a single gene may be controlled in positive and/or negative fashion. This can lead to finely tuned gene expression.
The location and manner in which a control element acts genetically determine a second classification. Cis‐acting control elements affect gene expression from the same chromosome only. A promoter, for example, is a cis‐acting element, because mutating it affects the level of gene expression from that chromosome only. In the preceding analogy, the brake on a car is cis‐acting, because removing it affects the ability of only a single car to stop. Trans‐acting control elements affect gene expression from a chromosome other than the one encoding them. For example, the δ subunit of RNA polymerase is trans‐acting, because mutating it can affect the expression of genes from another chromosome. In general, but not always, cis‐acting genes are DNA sequences that act as sites for regulation, and trans‐acting genes code for proteins or other diffusible control molecules that act on these sites. By analogy, a red light is trans‐acting because it stops several cars.
The third way in which gene expression schemes may be classified is by determining at which step of gene expression the control elements function. As mentioned previously, much of the overall genetic control in all organisms is transcriptional because RNA synthesis is the first committed step to gene expression. Control can also be post‐transcriptional, that is, at any of the steps after transcription, including RNA processing, mRNA translation, protein metabolism, and so forth.