The activity of most genes in eukaryotic cells is regulated primarily at the point of transcriptional initiation. Analyses of mutations that affect a gene's function without changing the sequence of its product provided insight into this level of regulation. Through these mutations, researchers defined cis-acting DNA regulatory elements and trans-acting transcription factors.
The eukaryotic genome contains three classes of genes, each associated with a different type of promoter and transcribed by a different RNA polymerase. Class I genes encode the rRNAs. Class III genes encode the tRNAs as well as other small RNA molecules. Class II genes, by far the largest class, encode all proteins.
Two types of cis-acting regulatory regions--promoters and enhancers--are associated with class II genes. All class II promoters are located at the 5' end of the gene they influence. The enhancers have a more variable location in relation to the genes they control.
The binding of nonspecific basal factors to promoters is a prerequisite for the transcription of a gene. Basal factors alone allow a low, nonspecific basal level of gene transcription.
The association of transcription factors with enhancer elements can modulate levels of transcriptional initiation. Activation is mediated by transcription factors called activators, which bind to enhancers, and coactivators, which bind to activators. Activators and coactivators can interact with basal factors at the promoter to increase transcription levels above the basal level. Repressors can compete with activators for enhancer binding or quench the ability of activators to carry out their function. Corepressors operate by binding to DNA-bound transcription factors. Many transcription factors can function as either activators or repressors, depending on the situation. Activators and repressors that bind directly to DNA typically form homodimers and/or heterodimers. Formation of these dimers is a prerequisite for them to function as transcription factors.
Although promoters and enhancers are the most common and best characterized types of cis-acting regulatory elements, there are other elements that do not fit into either of these classes. One such element is the locus control region associated with the b-globin gene cluster. Another is the insulator, which restricts the genomic region over which an enhancer can operate.
The regulation of transcription is a complex process dependent on the interactions of multiple enhancer elements with many competing transcription factors, and responsive to signals originating within and outside the cell. The integration of signals and regulatory components determines the precise level of transcription of a particular gene in a particular cell at a particular time.
The structure of chromatin around a gene contributes to the regulation of transcription. Normal chromatin structure prevents runaway transcription from genes that are not under activation. The unraveling of the DNA in chromatin is an initial step in activation. Hypercompaction of chromatin domains causes transcriptional silencing by blocking access to the promoter and enhancers of a gene and thereby preventing its activation even in the presence of activator proteins.
Genomic imprinting is an example of epigenetic control over gene expression. Imprinting operates on the copy of a gene received from one parent but not the other. DNA methylation plays a role in the maintenance of imprinting from one mammalian somatic cell generation to the next.
Although the regulation of most genes depends primarily on controls over transcription, in some cases, further regulation down the path to protein production also plays a role. Modulation of gene function can occur through changes in RNA splicing or RNA stability, mRNA editing, changes in the efficiency of translation, and chemical modification of the gene product.
