Not every gene codes for an enzyme or structural protein. A regulatory gene produces a product—usually a transcription factor or non-coding RNA—that controls whether other genes are turned on or off. These genes sit at the top of regulatory hierarchies and coordinate complex developmental and physiological programs.

Classic examples include the lac repressor in bacteria and the homeobox genes that pattern animal body axes. Mutations in regulatory genes often have wide-ranging effects because they alter the expression of many downstream targets. Dosage and timing are critical; too much or too little regulator can disrupt entire pathways.

Modern genomics has revealed that a large fraction of the genome is devoted to regulatory functions. Mapping the interactions between regulatory genes and their targets remains a major effort in systems biology and disease research.

• Gene that controls expression of other genes
• Often encodes transcription factors
• Coordinates developmental and metabolic programs
• Mutations can have broad phenotypic effects