Regulation| mRNA Transcription in Eukaryotes

Regulation| mRNA Transcription in Eukaryotes

Most active eukaryotic cells transcribe a common (basal) set of structural genes that maintain routine (housekeeping) cellular functions. In some cells, specific structural genes are transcribed and translated, giving the tissue or organ its unique properties. For example, the genes that encode the α and β subunits of adult hemoglobin are expressed only in the cells that develop into red blood cells. The numbers of cell-specific mRNA transcripts range from a few sequences in some cells to dozens of different sequences in others. The ability of cells to turn on (activate) or turn off (repress) transcription of particular structural genes is essential for maintaining cell specificity, for conserving cellular energy, and for enabling cells to respond to developmental cues or environmental changes.

There are a number of diverse, highly specific processes that activate or repress the transcription of various eukaryotic structural genes. In general, the control of transcription in eukaryotes is mediated by proteins that ar collectively classified as transcription factors. Many transcription factors bind directly to DNA sequences that are frequently less than 10 bp in length. The naming of these protein-binding sites is idiosyncratic. However, for the most part, they are called boxes, DNA modules, initiator elements, or response elements. Unlike the situation in prokaryotes, operons are almost never found in the genomes of eukaryotes. Consequently, each eukaryotic structural gene has its own set of response elements. Moreover, in addition to DNA–protein interactions, protein–protein associations are important for regulating eukaryotic transcription.

Regulation| mRNA Transcription in Eukaryotes
Activation and deactivation of a bacterial operon. An activator protein (Act) binds to an activating site and enhances the rate of transcription of the operon. When an effector molecule (E) binds to the activator protein, the Act–E complex does not bind to the activating site. The rate of transcription of the operon is diminished when the activating site is not occupied by the activating protein.

In addition to specific response elements, a representative eukaryotic structural gene has a promoter sequence that binds to a core set of proteins that are minimally required for transcription initiation. A eukaryotic promoter consists of a TATA sequence (TATA box, or Hogness box), a CCAAT sequence (“cat” box), and a sequence of repeated GC nucleotides (GC box) that lie about -25, -75, and -90 bp, respectively, from the site of initiation of transcription (+1) . The first step in the initiation of transcription of eukaryotic structural genes with a TATA promoter is the binding of transcription factor IID (TFIID, or TATA-binding protein [TBP]), which is a complex of at least 14 proteins, to an available TATA sequence.

Subsequently, other transcription factors bind to TFIID and the DNA adjacent to the TATA box. Then, RNA polymerase II, which is oriented toward the structural gene, binds to the transcription complex. With the aid of additional transcription factors, transcription is initiated at the correct starting point (the +1 nucleotide) . Clearly, if a TATA sequence is deleted or grossly altered, then transcription of the structural gene cannot occur. Transcription factors that are specific for the CCAAT and GC response elements have been identified. In addition, enhancer sequences that increase the rate of transcription of structural genes are located hundreds or even thousands of base pairs from the +1 base pair. Folding, looping, or bending of the chromosomal DNA may bring DNA regions, which in the elongated state are far apart, close to one another. Also, transcription factors that bind to certain enhancers or response elements may form a chain of proteins that create bridges from one DNA site to another.

Regulation| mRNA Transcription in Eukaryotes
Promoter and initiator elements of some eukaryotic structural genes. The negative numbers designate the locations of nucleotide pairs in the DNA that lie upstream from the site of initiation (+1) of transcription. The right-angled arrow indicates the site of initiation and the direction of transcription. The locations of the transcription elements are not drawn to scale.

Some repressed (nonexpressed) structural genes are activated by a cascade of events that is triggered by a specific extracellular signal, such as a temperature increase or the presence of a hormone. For example, a hormone that is released into the circulatory system comes into contact with a specific cell type that has a receptor on its outer surface that binds the hormone and facilitates the entry of the hormone into the cell. Once inside the cell, the hormone interacts with a cytoplasmic protein and changes the conformation of the protein. In this altered state, the protein is now able to enter the nucleus, where it binds to an exclusive response element that initiates transcription of the target gene.

Some proteins bind to response elements and prevent transcription. For example, there is a class of about 18 vertebrate genes that are actively transcribed in nerve cells (neurons) and turned off in nonneuronal cells. Each of these neuron-active genes has a 24-bp response element that lies upstream of its transcription initiation site. This DNA sequence is called a neuron-restrictive silencer element (NRSE). In nonneuronal cells, a protein called neuron-restrictive silencer factor (NRSF) is synthesized, binds to each NRSE, and prevents transcription of each member of this set of genes. Conversely, NRSF is not produced by neuronal cells, and therefore, each gene with an NRSE is transcribed.

Regulation| mRNA Transcription in Eukaryotes
Formation of an RNA polymerase II transcription initiation complex at a TATA box. Transcription factor TFIID binds to a TATA box, and in sequence, other transcription factors and RNA polymerase II bind to form a protein aggregate that is responsible for initiating transcription. The right-angled arrow indicates the site of initiation and the direction of transcription.

On the whole, the regulation of transcription in eukaryotes is complex. A structural gene may have a number of different response elements that can be activated in different cell types by different signals at different times in the life cycle of an organism. Alternatively, some structural genes are under the preferential control of a unique transcription factor. For the off state, specific proteins can interact with certain response elements and prevent transcription, or in a more general way, some proteins obstruct transcription by binding to the transcription complex either before initiation or during the elongation process.

More generalized control of gene expression that influences larger regions of the chromosomes is mediated by the state of chromosome structure. A very large amount of chromosomal DNA must be packaged into the nucleus of a eukaryotic cell. To facilitate this, the DNA is bound by specific proteins called histones that interact with each other to compact (condense) the chromosomes into a smaller volume. DNA with its associated packaging proteins is known as chromatin. Some regions of the chromosomes are tightly packed (heterochromatin), while other regions are less condensed (euchromatin). Highly condensed DNA is less accessible to regulatory proteins that activate transcription, and therefore, the genes in these regions are usually not expressed or are expressed only at a low level. Chromatin structure, however, is dynamic, and condensed regions can be “relaxed” by the addition of chemical groups, such as an acetyl group to amino acids in the packaging proteins or methyl groups to specific sites in the nucleotide sequences to which the proteins bind. Unpacking of the chromatin generally increases transcription of genes in the region.