9 Regulation of Gene Expression

Eukaryotic Epigenetic Regulation

Epigenetic changes are inheritable changes in gene expression that do not result from changes in the DNA sequence. Eukaryotic gene expression begins with control of access to the DNA. Transcriptional access to the DNA can be controlled in two general ways: chromatin remodeling and DNA methylation. Chromatin remodeling changes the way that DNA is associated with chromosomal histones. DNA methylation is associated with developmental changes and gene silencing.

The human genome encodes over 20,000 genes, with hundreds to thousands of genes on each of the 23 human chromosomes. The DNA in the nucleus is precisely wound, folded, and compacted into chromosomes so that it will fit into the nucleus. It is also organized so that specific segments can be accessed as needed by a specific cell type.

The first level of organization, or packing, is the winding of DNA strands around histone proteins. The DNA is wrapped around eight histone proteins to form structural units called nucleosome complexes, which can control the access of proteins to the DNA regions (Figure 3a). Under the electron microscope, this winding of DNA around histone proteins to form nucleosomes looks like small beads on a string (Figure 3b).

These beads (histone proteins) can move along the string (DNA) to expose different sections of the molecule. If DNA encoding a specific gene is to be transcribed into RNA, the nucleosomes surrounding that region of DNA can slide down the DNA to open that specific chromosomal region and allow for the transcriptional machinery (RNA polymerase) to initiate transcription (Figure 4).

How closely the histone proteins associate with the DNA is regulated by signals found on both the histone proteins and on the DNA. These signals are functional groups added to histone proteins or to DNA and determine whether a chromosomal region should be open or closed (Figure 4 depicts modifications to histone proteins and DNA). These tags are not permanent, but may be added or removed as needed. Some chemical groups (phosphate, methyl, or acetyl groups) are attached to specific amino acids in histone “tails” at the N-terminus of the protein. These groups do not alter the DNA base sequence, but they do alter how tightly wound the DNA is around the histone proteins. DNA is a negatively charged molecule and unmodified histones are positively charged; therefore, changes in the charge of the histone will change how tightly wound the DNA molecule will be. By adding chemical modifications like acetyl groups, the charge becomes less positive, and the binding of DNA to the histones is relaxed. Altering the location of nucleosomes and the tightness of histone binding opens some regions of chromatin to transcription and closes others.

The DNA molecule itself can also be modified by methylation. DNA methylation occurs within very specific regions called CpG islands. These are stretches with a high frequency of cytosine and guanine dinucleotide DNA pairs (CG) found in the promoter regions of genes. The cytosine member of the CG pair can be methylated (a methyl group is added). Methylated genes are usually silenced, although methylation may have other regulatory effects. In some cases, genes that are silenced during the development of the gametes of one parent are transmitted in their silenced condition to the offspring. Such genes are said to be imprinted. Parental diet or other environmental conditions may also affect the methylation patterns of genes, which in turn modifies gene expression. Changes in chromatin organization interact with DNA methylation. DNA methyltransferases appear to be attracted to chromatin regions with specific histone modifications. Highly methylated (hypermethylated) DNA regions with deacetylated histones are tightly coiled and transcriptionally inactive.

Epigenetic changes are not permanent, although they often persist through multiple rounds of cell division and may even cross generational lines. Chromatin remodeling alters the chromosomal structure (open or closed) as needed. If a gene is to be transcribed, the histone proteins and DNA in the chromosomal region encoding that gene are modified in a way that opens the promoter region to allow RNA polymerase and other proteins, called transcription factors, to bind and initiate transcription. If a gene is to remain turned off, or silenced, the histone proteins and DNA have different modifications that signal a closed chromosomal configuration. In this closed configuration, the RNA polymerase and transcription factors do not have access to the DNA and transcription cannot occur (Figure 5).

Post-transcriptional Eukaryotic RNA Regulation: mRNA Splicing

The newly transcribed eukaryotic mRNAs must undergo several processing steps before they can be transferred from the nucleus to the cytoplasm and translated into a protein. The additional steps involved in eukaryotic mRNA maturation create a molecule that is much more stable than a prokaryotic mRNA. For example, eukaryotic mRNAs last for several hours, whereas the typical prokaryotic mRNA lasts no more than five seconds.

The mRNA transcript is first coated in RNA-stabilizing proteins to prevent it from degrading while it is processed and exported out of the nucleus. This occurs while the pre-mRNA still is being synthesized by adding a special nucleotide “cap” to the 5′ end of the growing transcript. In addition to preventing degradation, factors involved in protein synthesis recognize the cap to help initiate translation by ribosomes.

Once elongation is complete, an enzyme then adds a string of approximately 200 adenine residues to the 3′ end, called the poly-A tail. This modification further protects the pre-mRNA from degradation and signals to cellular factors that the transcript needs to be exported to the cytoplasm.

Eukaryotic genes are composed of protein-coding sequences called exons (ex-on signifies that they are expressed) and intervening sequences called introns (int-ron denotes their intervening role). Introns are removed from the pre-mRNA during processing. Intron sequences in mRNA do not encode functional proteins. It is essential that all of a pre-mRNA’s introns be completely and precisely removed before protein synthesis so that the exons join together to code for the correct amino acids. If the process errs by even a single nucleotide, the sequence of the rejoined exons would be shifted, and the resulting protein would be nonfunctional. The process of removing introns and reconnecting exons is called splicing (Figure 6). Introns are removed and degraded while the pre-mRNA is still in the nucleus.

Alternative RNA Splicing

In the 1970s, genes were first observed that exhibited alternative RNA splicing. Alternative RNA splicing is a mechanism that allows different protein products to be produced from one gene when different combinations of introns (and sometimes exons) are removed from the transcript (Figure 7). This alternative splicing can be haphazard, but more often it is controlled and acts as a mechanism of gene regulation, with the frequency of different splicing alternatives controlled by the cell as a way to control the production of different protein products in different cells, or at different stages of development. Alternative splicing is now understood to be a common mechanism of gene regulation in eukaryotes; according to one estimate, 70% of genes in humans are expressed as multiple proteins through alternative splicing.

How could alternative splicing evolve? Introns have a beginning and ending recognition sequence, and it is easy to imagine the failure of the splicing mechanism to identify the end of an intron and find the end of the next intron, thus removing two introns and the intervening exon. In fact, there are mechanisms in place to prevent such exon skipping, but mutations are likely to lead to their failure. Such “mistakes” would more than likely produce a nonfunctional protein. Indeed, the cause of many genetic diseases is alternative splicing rather than mutations in a sequence. However, alternative splicing would create a protein variant without the loss of the original protein, opening up possibilities for adaptation of the new variant to new functions. Gene duplication has played an important role in the evolution of new functions in a similar way—by providing genes that may evolve without eliminating the original functional protein.

Gene Regulatory Networks

In the previous section, we discussed how alternative splicing allows a single gene to produce multiple proteins by rearranging its exons in different combinations. This is just one mechanism by which gene expression can be fine-tuned. However, gene regulation is rarely a simple, linear process. In most cases, the expression of a gene is influenced by many factors beyond splicing, such as signals from other genes, proteins, and even environmental cues. This interconnectedness is part of a larger system known as a gene regulatory network (GRN), where genes and their products interact to control the timing, location, and intensity of gene expression.

A gene regulatory network functions much like a complex communication system within cells, ensuring that genes are expressed only when needed. As part of this system, the expression of one gene can influence another. Gene products (e.g., mRNA, proteins) that promote the expression of other genes are broadly referred to as activators. For example, the protein product of one gene might bind to regulatory region of another gene, enhancing the production of mRNA. In contrast, gene products that inhibit the expression of other genes are broadly referred to as repressors. These interactions form feedback loops and pathways, coordinating gene activity across the cell or even throughout the organism. The result is a carefully regulated balance of gene expression, allowing cells to adapt to changes and maintain proper function.

What makes gene regulatory networks particularly powerful is their ability to integrate signals from both within the genome and the surrounding environment. For instance, in response to stress or a lack of nutrients, a cell might activate a set of genes that help it survive, while repressing others that aren’t immediately needed. Similarly, during development, a cascade of gene interactions ensures that cells differentiate into specialized types, such as muscle or nerve cells, at the right time and place.

When two genes interaction to affect the expression one another, the phenomenon is referred to as epistasis. Epistasis is common feature of gene regulatory networks. The interaction of two genes, however, can depend on the specific alleles (gene variants) present in an individual’s genome. One allele may modify or completely mask the expression of another gene, while a different allele for the same gene may have no affect at all. Such allelelic-specific interactions help explain why certain traits, like disease susceptibility, may not follow straightforward patterns of inheritance, as the combined effects of different alleles play a key role in determining the final outcome.

Gene expression is not just the product of an individual gene but the result of a vast and interconnected network of genes, proteins, and environmental factors working together. Gene regulatory networks represent the complexity and precision of biological systems, coordinating the expression of genes in response to internal and external signals to ensure that organisms function properly. Understanding these networks is key to unlocking the full picture of how genes influence traits, behaviors, and even responses to environmental changes.