An organism’s DNA contains genes with the instructions for building proteins. However, a layer of control is needed to dictate when, where, and to what extent each gene is used. This control is exerted by regulatory sequences, specific segments of DNA that function like molecular switches. They do not code for proteins but orchestrate complex patterns of gene activity. For instance, a gene for a digestive enzyme is switched on in the stomach but remains off in the brain, a process that allows cells to specialize and maintain health.
The Nature and Location of Regulatory Sequences
Regulatory sequences are composed of specific strings of nucleotides. They are part of the “non-coding” genome, which makes up the majority of our DNA. These sequences do not code for proteins, but instead are recognized and bound by molecules that control gene expression. While once considered “junk DNA,” it is now understood that these regions are rich with functional elements.
These control elements are cis-acting, meaning they influence the expression of genes on the same molecule of DNA. Their positions relative to the gene they regulate can vary. Many are found directly upstream of a gene’s protein-coding region, while others can be located downstream or within the gene itself in non-coding stretches called introns.
Some regulatory sequences can exert their influence from great distances, sometimes hundreds of thousands of nucleotide bases away from their target gene. In the cell nucleus, the DNA molecule can form loops, bringing these distant control regions into close physical proximity with the genes they manage. This three-dimensional organization of the genome is an important aspect of how these sequences function.
Principal Categories of Regulatory Elements
Regulatory elements fall into several categories. Promoters act as the “on” switch for a gene and are located immediately upstream. The promoter is the docking site where the transcription apparatus assembles. Specific sequences within the promoter, like the TATA box, serve as landmarks for this machinery to bind and prepare to transcribe the gene into messenger RNA (mRNA).
Enhancers act like volume knobs for gene activity, increasing the rate of transcription. They can be situated thousands of bases away from the gene they regulate, either upstream, downstream, or within an intron. Enhancers function by binding specific proteins that help to attract and stabilize the transcription machinery at the promoter, boosting gene output.
Silencers function as brakes on gene expression. When specific repressor proteins bind to these DNA sequences, they inhibit transcription. Like enhancers, silencers can be located at various distances from their target gene and work by interfering with the assembly of the transcription machinery. Insulator sequences serve as genetic fences, preventing an enhancer or silencer from influencing the wrong gene.
Mechanisms of Gene Expression Control
The function of regulatory sequences is mediated by their interaction with specialized proteins called transcription factors. These proteins scan the DNA molecule and bind to specific regulatory elements for which they have a chemical affinity. This binding is the event that initiates the process of either activating or repressing gene transcription.
Transcription factors that bind to enhancer sequences are typically called activators. Once attached to the DNA, these activator proteins help to recruit the main enzyme responsible for transcription, RNA polymerase, to the gene’s promoter. They facilitate the assembly of a large complex of proteins known as the basal transcription machinery, which is required to begin making an RNA copy of the gene.
Conversely, transcription factors known as repressors bind to silencer regions of DNA. Their presence can block gene expression in several ways. Some repressors physically obstruct the promoter region, preventing RNA polymerase and the basal transcription machinery from binding. Others interfere with the function of activator proteins, preventing them from effectively recruiting the transcription machinery.
Beyond direct interaction with the transcription machinery, these protein-DNA interactions can also influence the physical structure of the DNA itself. DNA in the nucleus is tightly packaged with proteins into a structure called chromatin. Regulatory proteins can recruit enzymes that modify this chromatin, causing it to either relax and become more accessible or condense and become more compact.
Consequences of Altered Regulatory Sequences
Since regulatory sequences control gene activity, mutations within them can have significant consequences. A mutation can alter a sequence so a transcription factor binds incorrectly. This can lead to a gene being expressed at the wrong time or at incorrect levels, disrupting cellular processes and leading to disease.
A clear example of this is found in certain types of thalassemia, a group of inherited blood disorders characterized by reduced production of hemoglobin. Some forms of the disease are not caused by mutations in the hemoglobin genes themselves, but by deletions or changes in their regulatory sequences. These alterations impair the genes’ ability to be switched on properly in developing red blood cells, leading to a deficiency in the hemoglobin protein.
Mutations in regulatory regions are also increasingly implicated in the development of cancer. For instance, a mutation in the promoter or an enhancer of an oncogene—a gene that promotes cell growth—can lead to its over-expression, contributing to uncontrolled cell division. Conversely, if a regulatory mutation silences a tumor suppressor gene, the cell loses a protective mechanism that would normally halt a cell’s progression toward becoming cancerous.