Molecular Genetics 5: Mutations and Epigenetics
Learning Objectives
- Explain how DNA repair mechanisms maintain genome stability and how mutations arise through spontaneous and induced genetic change
- Compare the major classes of mutations and predict their effects on genes, proteins, and phenotypes
- Define epigenetics and distinguish between changes in DNA sequence and epigenetic modifications that influence gene expression
- Describe how DNA methylation, histone modification, and chromatin structure regulate access to genetic information
- Explain the roles of epigenetic regulation in development, cell differentiation, imprinting, and transgenerational inheritance
- Evaluate the contribution of genetic mutations and epigenetic changes to human disease, particularly cancer and complex traits
Modern epigenetics builds on these early insights by examining how protein interactions in eukaryotic cells affect gene expression. These interactions don’t alter the DNA sequence itself but instead modify the proteins and molecular structures that regulate how genes are used. Such changes can be stable and heritable, influencing how cells differentiate and maintain their identity across generations
The concept of epigenetic inheritance — where chromatin modifications and gene expression patterns are passed on alongside DNA — suggests a second layer of biological information. Waddington referred to this as genetic assimilation, a controversial idea that some saw as a return to Lamarckian thinking. Lamarck had proposed that traits acquired during an organism’s life could be inherited. Though later dismissed in favour of Darwin’s natural selection and Mendel’s genetics, the idea of environmentally influenced inheritance has resurfaced in light of epigenetic research.
One striking example comes from the small Swedish town of Överkalix, where detailed historical records revealed that environmental conditions experienced by grandparents, such as famine or abundance, could affect the health and longevity of their grandchildren, in a sex-specific manner. This raised the provocative possibility that acquired traits might indeed be passed down through generations.
A sample of Bygren’s data is shown in the table below.
| Grandparent | Food supply | Grandson relative risk of death from cardio disease and diabetes | Grand-daughter relative risk of death from cardio disease and diabetes |
|---|---|---|---|
| Grandfather | Poor | -35% | No change |
| Grandfather | Abundant | +67% | No change |
| Grandmother | Poor | No change | -49% |
| Grandmother | Abundant | No change | +113% |
Table 11.1. Epigenetic inheritance based on Bygren's Overkaliix data. Source: Epigenetics by Gerald Bergstrom, published by LibreTexts Biology, and used under a Creative Commons Attribution 4.0 International.
Alongside epigenetic inheritance, another key mechanism driving biological change is mutation. Mutations are random changes in the sequence of bases in DNA. While the word might conjure images of Ninja Turtles, most mutations are far less dramatic. In fact, everyone carries dozens or even hundreds of mutations in their DNA. From an evolutionary perspective, mutations are essential—they are the ultimate source of all new genetic variation in any species.
Mutations can occur spontaneously or be induced by external factors. Spontaneous mutations arise naturally, often due to errors during DNA replication or cell division. Induced mutations, on the other hand, result from exposure to mutagens such as chemicals (e.g. those in cigarette smoke) or radiation (e.g. X-rays or ultraviolet light). Different mutagens damage DNA in different ways. For instance, UV radiation can cause abnormal bonding between adjacent nucleotides, creating distortions in the DNA helix that, if unrepaired, lead to mutation. These changes can disrupt normal replication, transcription, and translation processes.
In 1927, Hermann Muller demonstrated the effects of induced mutations by exposing fruit flies to X-rays, visibly altering their chromosomes. His work helped establish mutagenesis as a powerful force in both evolution and disease. While some mutations are harmful, leading to cancer or genetic disorders, others are neutral or even beneficial, providing the raw material for natural selection to act upon.
Together, epigenetic regulation and genetic mutation form the foundation of how organisms develop, adapt, and evolve. As we delve deeper into these mechanisms, we gain a clearer picture of the dynamic and multilayered nature of inheritance.
Mutations
DNA replication is a highly accurate process, but mistakes can occasionally occur, such as a DNA polymerase inserting a wrong base. Uncorrected mistakes may sometimes lead to serious consequences, such as cancer. Repair mechanisms correct the mistakes. In rare cases, mistakes are not corrected, leading to mutations; in other cases, repair enzymes are themselves mutated or defective.
Most of the mistakes during DNA replication are promptly corrected by the proofreading ability of DNA polymerase itself (Figure 11.2). In proofreading, the DNA pol reads the newly added base before adding the next one, so a correction can be made. The polymerase checks whether the newly added base has paired correctly with the base in the template strand. If it is the right base, the next nucleotide is added. If an incorrect base has been added, the enzyme makes a cut at the phosphodiester bond and releases the wrong nucleotide. This is performed by the 3' exonuclease action of DNA pol. Once the incorrect nucleotide has been removed, it can be replaced by the correct one.
Some errors are not corrected during replication but are instead corrected after replication is completed; this type of repair is known as mismatch repair (Figure 11.3). Specific repair enzymes recognise the mispaired nucleotide and excise part of the strand that contains it; the excised region is then resynthesised. If the mismatch remains uncorrected, it may lead to more permanent damage when the mismatched DNA is replicated. How do mismatch repair enzymes recognise which of the two bases is the incorrect one? In E. coli, after replication, the nitrogenous base adenine acquires a methyl group; the parental DNA strand will have methyl groups, whereas the newly synthesized strand lacks them. Thus, DNA polymerase is able to remove the wrongly incorporated bases from the newly synthesised, non-methylated strand. In eukaryotes, the mechanism is not very well understood, but it is believed to involve recognition of unsealed nicks in the new strand, as well as a short-term continuing association of some of the replication proteins with the new daughter strand after replication has completed.
Another type of repair mechanism, nucleotide excision repair, is similar to mismatch repair, except that it is used to remove damaged bases rather than mismatched ones. The repair enzymes replace abnormal bases by making a cut on both the 3' and 5' ends of the damaged base (Figure 11.4). The segment of DNA is removed and replaced with the correctly paired nucleotides by the action of DNA pol. Once the bases are filled in, the remaining gap is sealed with a phosphodiester linkage catalysed by DNA ligase. This repair mechanism is often employed when UV exposure causes the formation of pyrimidine dimers.
A well-studied example of mistakes not being corrected is seen in people suffering from xeroderma pigmentosa (Figure 11.5). Affected individuals have skin that is highly sensitive to UV rays from the sun. When individuals are exposed to UV light, pyrimidine dimers, especially those of thymine, are formed; people with xeroderma pigmentosa are not able to repair the damage. These are not repaired because of a defect in the nucleotide excision repair enzymes, whereas in normal individuals, the thymine dimers are excised and the defect is corrected. The thymine dimers distort the structure of the DNA double helix, and this may cause problems during DNA replication. People with xeroderma pigmentosa may have a higher risk of contracting skin cancer than those who don't have the condition.
Errors during DNA replication are not the only reason why mutations arise in DNA. Mutations, variations in the nucleotide sequence of a genome, can also occur because of damage to DNA. Such mutations may be of two types: induced or spontaneous. Induced mutations are those that result from an exposure to chemicals, UV rays, x-rays, or some other environmental agent. For example, Charlotte Auerbach and J.M Robson discovered the mutation-inducing effects of mustard gas. Spontaneous mutations occur without any exposure to any environmental agent; they are a result of natural reactions taking place within the body.
Mutations may have a wide range of effects. Point mutations are those mutations that affect a single base pair. The most common nucleotide mutations are substitutions, in which one base is replaced by another. These substitutions can be of two types, either transitions or transversions. Transition substitution refers to a purine or pyrimidine being replaced by a base of the same kind; for example, a purine such as adenine may be replaced by the purine guanine. Transversion substitution refers to a purine being replaced by a pyrimidine, or vice versa; for example, cytosine, a pyrimidine, is replaced by adenine, a purine. Some point mutations are not detectable in the final product; these are known as silent mutations. Silent mutations are usually due to a substitution in the third base of a codon, which often represents the same amino acid as the original codon. Other point mutations can result in the replacement of one amino acid by another, which may alter the function of the protein. Point mutations that generate a stop codon can terminate a protein early.
Some mutations can result in an increased number of copies of the same codon. These are called trinucleotide repeat expansions and result in repeated regions of the same amino acid. Mutations can also be the result of the addition of a base, known as an insertion, or the removal of a base, also known as deletion. If an insertion or deletion results in the alteration of the translational reading frame (a frameshift mutation), the resultant protein is usually nonfunctional. Sometimes a piece of DNA from one chromosome may get translocated to another chromosome or to another region of the same chromosome; this is also known as translocation. These mutation types are shown in Figure 11.6.
A frameshift mutation that results in the insertion of three nucleotides is often less deleterious than a mutation that results in the insertion of one nucleotide. Mutations in repair genes have been known to cause cancer. Many mutated repair genes have been implicated in certain forms of pancreatic cancer, colon cancer, and colorectal cancer. Mutations can affect either somatic cells or germ cells. If many mutations accumulate in a somatic cell, they may lead to problems such as the uncontrolled cell division observed in cancer. If a mutation takes place in germ cells, the mutation will be passed on to the next generation, as in the case of haemophilia and xeroderma pigmentosa.
Epigenetics
Our behaviour and environment can have long-term effects on gene expression, linked with changes in chromatin structure. Those changes can influence traits over the course of a lifetime and even, in some cases, be inherited by offspring.
The mechanism by which we pass acquired traits to our children is not due to typical Mendelian inheritance. Instead, this inheritance is dependent on mechanisms outside of or on top of the rules of genetics we’ve discussed so far. The mechanism has thus been named epigenetic inheritance. A closer look reveals that epigenetic inheritance results from the regulation of gene expression through changes in chromatin structure that are transmitted to daughter cells during cell division.
Those epigenetic modifications are heritable through mitosis, so individual somatic cells can share epigenetic marks with other cells of the same lineage – meaning, other cells that came from the same parent cell during development. This type of epigenetic inheritance influences cell fate during the early development of multicellular organisms as well as certain complex genetic phenotypes, including obesity and cancer. In some cases, epigenetic modifications are also maintained through meiosis (so epigenetic marks can be shared from parent to offspring). Inter-generational epigenetic inheritance is linked with cardiovascular disease and stress response in humans and other mammals and other complex phenotypes. Collectively, the combination of epigenetic marks found in a cell is called the epigenome.
Eukaryotic gene expression is more complex than prokaryotic gene expression because the processes of transcription and translation are physically separated. Unlike prokaryotic cells, eukaryotic cells can regulate gene expression at many different levels. Epigenetic changes are heritable 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 remodelling and DNA methylation. Chromatin remodelling changes the way that DNA is associated with chromosomal histones. DNA methylation is associated with developmental changes and gene silencing.
Epigenetic Control: Regulating Access to Genes within the Chromosome
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 organised so that specific segments can be accessed as needed by a specific cell type.
The first level of organisation, or packing, is the winding of DNA strands around histone proteins. Histones package and order DNA into structural units called nucleosome complexes, which can control the access of proteins to the DNA regions. Under the electron microscope, this winding of DNA around histone proteins to form nucleosomes looks like small beads on a string.
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 11.8).
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 11.9 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 organisation 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 remodelling 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 11.9).
Acetylation and deacetylation of histones is a method for decreasing and increasing their affinity for DNA. This can be controlled (Figure 11.10) by the recruitment of histone deacetylase (HDAC) to particular genes via repressor/co-repressor complexes. The deacetylase forces tight winding of the targeted DNA to the histones, precluding access by RNA polymerases or general transcription factors. Another recruiter of HDAC are MBD proteins, which bind to methylated DNA. DNA methylation in mammals usually occurs on CpG dinucleotide sequences. This methylation appears to have the effect of blocking access of transcription factors and enzymes to the DNA. It can do so directly, or by recruiting MBD (methyl-CpG-binding domain) proteins. In either case, methylation is a long-term method of locking up genes and is the mechanism for turning off genes that would never be used in a particular cell type (e.g. haemoglobin in neurons).
Epigenetics during development
Most, but not all, epigenetic marks are removed in the zygote. So as the embryo begins to develop, it starts with almost a clean slate, epigenetically. This likely contributes to the totipotency of the early embryonic cells. Totipotency describes the ability of a cell to divide and give rise to any other cell type. The cells are called totipotent stem cells. But as the fertilised egg divides, daughter cells become committed to a particular cell fate, beginning 4-5 days post-fertilization with the differentiation of trophoblast cells and embryonic stem cells of the inner cell mass (shown in yellow and red, respectively, in Figure 11.11).
This commitment is correlated with a loss of some potential: the trophoblast cells develop into much of the placenta but cannot develop into cells of the embryo proper. Likewise, the embryonic stem cells of the inner cell mass cannot give rise to the trophoblastic structures. These embryonic cells are thus called pluripotent rather than totipotent.
We’ve already seen an example of epigenetics in the module on Sex: X-chromosome inactivation is a form of epigenetic inheritance. In individuals with more than one X chromosome (most commonly XX genotypes, but also XXX, XXY, or other less common genotypes), only one X chromosome is typically active in each cell. The additional X chromosome(s) are highly condensed, and most (but not all) of genes are transcriptionally inactive. The condensed X chromosome is visible under the microscope as a structure called a Barr body, which is a densely staining region within the nucleus. An example of a Barr body stained is shown in Figure 11.12.
Which X chromosome is inactivated occurs randomly in individual cells early in embryogenesis. However, the inactivation is inherited, with the same X chromosome consistently inactive in daughter cells after cell division. X-inactivation depends on the action of a long non-coding RNA molecule called Xist. Xist molecules coat the to-be-inactivated X chromosome, recruiting additional protein factors and ultimately leading to the remodelling of the X chromatin. The inactivated X chromosome shows high levels of DNA methylation around the promoters of silenced genes as well as low levels of histone acetylation.
The phenotype of a calico cat is a visually striking example of how silencing of part of the genome is inherited through replication and mitosis: the patches of colour result from epigenetic silencing of one or the other of the X chromosomes in a cell with XX genotype. Patches include cells that were derived from the same parent cell.
On average, because the X chromosomes are inactivated randomly, about 50% of the cells in the body of an XX individual will be inactivated for each X chromosome. But in some individuals, X inactivation is skewed, with more than 75% of cells inactivating the chromosome inherited from one parent. Interestingly, this appears to play a role in the variable expressivity of some X-linked genetic traits, including red-green colour-blindness and diseases like Haemophilia B, Duchenne muscular dystrophy, and Fabry syndrome. The skewed inactivation of a healthy allele increases the severity of the disease, and the skewed inactivation of a disease-associated allele lessens the severity and reduces symptoms.
Imprinted genes are differently expressed depending on the parent-of-origin for each allele. For some imprinted genes, only (or almost only) the maternal copy of a gene is expressed, and for others, only (or almost only) the paternal copy is expressed. The other allele was silenced with DNA methylation and histone modification.
For most genes, epigenetic marks are cleared in the zygote. But for imprinted genes, epigenetic marks are reprogrammed in the egg or the sperm, and the egg- or sperm-specific epigenetic marks are maintained in the zygote beyond the stage of development when most other epigenetic marks are removed. Imprinting is maintained throughout the lifespan and is only reset during gametogenesis when new egg- or sperm-specific epigenetic marks are reprogrammed for the next generation. Figure 11.13 shows this for a maternally imprinted gene. Paternal imprinting is similar but with the paternal allele silenced.
The phenomenon of imprinting appears to have evolved independently in flowering plants and mammals; about 1% of human genes are imprinted. Many imprinted genes appear to be involved in growth rate, metabolism, brain function, and behaviour, with imprinted genes linked to phenotypes like body size and behaviours like risk-taking and impulsive behaviour.
In humans, several genetic diseases are caused by a disruption in imprinting. For example, Beckwith-Wiedemann syndrome is caused by a disruption in imprinted genes on Chromosome 11. These genes include the growth factor IGF2, which is normally only expressed from the paternal chromosome. Altered DNA methylation, duplication of the paternal chromosome, and other changes result in two copies of the gene being expressed. Among other signs associated with the syndrome, children with Beckwith-Wiedemann syndrome tend to be larger in size than their same-age peers.
Angelman syndrome is linked with a loss of function of the gene UBE3A on Chromosome 15. UBE3A is imprinted and in cells of the central nervous system, only the maternal copy of the gene is expressed. Children with Angelman syndrome show intellectual disability, small head size, and, often, a happy and excitable personality. These traits are linked with a deletion or loss of function in the maternal chromosome, which leaves patients without a functional copy of the gene in cells of the central nervous system. Mutations in the paternal allele will not cause Angelman syndrome.
Epigenetic changes are influenced by behaviour and environment
Over the course of a lifetime, diet, behaviour, and environment contribute to the accumulation of epigenetic marks. For example, some nutrients in the diet are a source of methyl groups that are eventually part of S-adenosyl methionine (SAM/SAMe), which in turn donates methyl groups to methylate cytosine or methylate histones. Nutrients like folate and choline are examples, and SAMe itself can be purchased as a dietary supplement. Other nutrients may promote or inhibit the action of DNA methyltransferase or histone modifiers. Examples include molecules like resveratrol (found in red wine, activates HDACs), curcumin (found in turmeric, inhibits HATs), and diallyl disulfide (found in garlic and onions, inhibits HDACs). Stress, drug use, trauma, and lifestyle choices have also been shown to impact the epigenome.
Environmental effects can add up over time. Identical twins, who share 100% of their DNA, are phenotypically similar but not actually indistinguishable from one another. Identical twins tend to have very similar epigenomes early in life. However, as identical twins age, their genomes stay the same, but their epigenomes diverge. This likely contributes to identical twins becoming more dissimilar as they age.
These environmental effects on the epigenome likely influence the incomplete penetrance of some genetic traits. For example, the methylation of a gene called REELIN appears to be linked with the development of schizophrenia. Schizophrenia is a psychiatric disorder that manifests in early adulthood. The phenotype shows a strong genetic component, but twin studies reveal that less than 50% of identical twins are concordant for schizophrenia. Differences in methylation status between twins may account for at least some of this difference.
Epigenetic changes are also linked with cancer. Loss-of-function mutation of tumour suppressor genes contributes to oncogenesis. However, in some cases, the DNA sequence of tumour suppressor genes is unchanged, but the gene is highly methylated, resulting in loss of function without underlying mutation. Acetylation of genes that drive the cell cycle can play a role in the uncontrolled growth associated with cancer. A number of HDAC inhibitors have been approved for the treatment of cancer.
Transgenerational epigenetics
The examples discussed above all involve mitotic inheritance of epigenetic marks, with maintenance of the epigenome in somatic cells of a single individual. As was discussed earlier, most epigenetic marks are erased during gametogenesis or in the fertilised egg (zygote). However, some epigenetic marks escape this zygotic reprogramming. These allow epigenetic information to be passed through meiotic cell division from parent to offspring – a mechanism for Lamarckian inheritance of acquired traits.
There are many known examples of transgenerational epigenetic inheritance in non-mammalian species, where the epigenome can be manipulated and tracked for many generations. For example, in the plant Arabidopsis thaliana, a mustard weed used as a model organism in the genetics lab, DNA methylation induced in one generation can be measured for at least 8 generations of offspring.
In mice, a “tail kink” phenotype (Figure 11.14) is associated with a mutation of a gene called AxinFu, but whether the tail kink phenotype is penetrant depends on the methylation status of the gene. The phenotype can be inherited across generations. In contrast, in humans, many of the traits suspected to be affected by epigenetics are likely multifactorial, and causative genes may or may not yet be linked with the phenotype. Many studies are retrospective analyses of human populations, tracking traits associated with environmental factors over the course of several generations.
Some of the most commonly cited of these retrospective studies track the descendants of individuals who were exposed to famine in utero. These studies include the Dutch famine winter of 1944-1945, food scarcity in the Överkalix municipality in Sweden, the Ukrainian famine of 1932-1933, and the Chinese famine of 1959-1961.
Exposure to famine as a foetus increased the risk for obesity and other metabolic disorders, Type 2 diabetes, schizophrenia, and depression. It also altered the risk of disease in their children and grandchildren.
Other large-scale retrospective studies track the descendants of women treated with diethylstilbesterol (DES) during pregnancy. DES is a synthetic estrogen that was used to prevent miscarriage in pregnant women in the 1940’s-1960’s (Figure 11.15). By the 1970s, however, studies had shown that DES was not effective in preventing miscarriage and, even worse, was causing vaginal and breast cancers and reproductive anomalies in “DES daughters” – children born to women treated with DES. Follow-up studies have shown that DES grandchildren are also affected: DES grandchildren born to DES daughters are more likely to be born premature, and DES grandsons born to DES daughters appear to have an increased risk of certain anomalies of the reproductive tract. It is not clear whether the grandchildren born to DES sons are similarly affected.
Multigenerational retrospective studies like the famine and DES studies can be very powerful in linking phenotypes to environmental stressors. And, with modern genome sequencing tools, both mutations and changes to DNA methylation can be compared across generations. However, it can be difficult to distinguish between true transgenerational epigenetic inheritance and the direct effects of environmental exposure.You may have heard that when a baby is born, ovaries already contain all the eggs the baby will have in their lifetime (this is not true for sperm, which are produced lifelong after puberty). Those future egg cells form very early during foetal development: as early as 8 weeks post-fertilization.
So as soon as those primitive ovaries form during development, exposure during pregnancy potentially exposes three generations to a stressor: the pregnant parent (P or F0 generation), the foetus (F1 generation), and, potentially, the future eggs of the foetus (F2 generation). This is illustrated in Figure 11.16, which shows three generations in the same image: parent, foetus, and the eggs of the foetus, illustrated by the blue star.Because of this, to show true transgenerational epigenetic inheritance – with the maintenance of epigenetic marks through meiosis – retrospective studies of environmental stress must track great-grandchildren from pregnant women and grandchildren from non-pregnant women and/or men.
Cancer and Gene Regulation
Cancer is not a single disease but includes many different diseases. In cancer cells, mutations modify cell-cycle control and cells don’t stop growing as they normally would. Mutations can also alter the growth rate or the progression of the cell through the cell cycle. One example of a gene modification that alters the growth rate is increased phosphorylation of cyclin B, a protein that controls the progression of a cell through the cell cycle and serves as a cell-cycle checkpoint protein.
For cells to move through each phase of the cell cycle, the cell must pass through checkpoints. This ensures that the cell has properly completed the step and has not encountered any mutation that will alter its function. Many proteins, including cyclin B, control these checkpoints. The phosphorylation of cyclin B, a post-translational event, alters its function. As a result, cells can progress through the cell cycle unimpeded, even if mutations exist in the cell and its growth should be terminated. This post-translational change of cyclin B prevents it from controlling the cell cycle and contributes to the development of cancer.
Cancer: Disease of Altered Gene Expression
Cancer can be described as a disease of altered gene expression. There are many proteins that are turned on or off (gene activation or gene silencing) that dramatically alter the overall activity of the cell. A gene that is not normally expressed in that cell can be switched on and expressed at high levels. This can be the result of gene mutation or changes in gene regulation.
Changes in epigenetic regulation, transcription, RNA stability, protein translation, and post-translational control can be detected in cancer. While these changes don’t occur simultaneously in one cancer, changes at each of these levels can be detected when observing cancer at different sites in different individuals. Therefore, changes in histone acetylation (epigenetic modification that leads to gene expression), activation of transcription factors by phosphorylation, increased RNA stability, increased translational control, and protein modification can all be detected at some point in various cancer cells. Scientists are working to understand the common changes that give rise to certain types of cancer or how a modification might be exploited to destroy a tumour cell.
Tumour Suppressor Genes, Oncogenes, and Cancer
In normal cells, some genes function to prevent excess, inappropriate cell growth. These are tumour-suppressor genes, which are active in normal cells to prevent uncontrolled cell growth. There are many tumour-suppressor genes in cells. The most studied tumour-suppressor gene is p53, which is mutated in over 50 percent of all cancer types. The p53 protein itself functions as a transcription factor. It can bind to sites in the promoters of genes to initiate transcription. Therefore, the mutation of p53 in cancer will dramatically alter the transcriptional activity of its target genes.
Proto-oncogenes are positive cell-cycle regulators. When mutated, proto-oncogenes can become oncogenes and cause cancer. Overexpression of the oncogene can lead to uncontrolled cell growth. This is because oncogenes can alter transcriptional activity, stability, or protein translation of another gene that directly or indirectly controls cell growth. An example of an oncogene involved in cancer is a protein called myc. Myc is a transcription factor that is aberrantly activated in Burkett’s Lymphoma, a cancer of the lymph system. Overexpression of myc transforms normal B cells into cancerous cells that continue to grow uncontrollably. High B-cell numbers can result in tumours that can interfere with normal bodily function. Patients with Burkett’s lymphoma can develop tumours on their jaw or in their mouth that interfere with the ability to eat.
Cancer and Epigenetic Alterations
Silencing genes through epigenetic mechanisms is also very common in cancer cells. There are characteristic modifications to histone proteins and DNA that are associated with silenced genes. In cancer cells, the DNA in the promoter region of silenced genes is methylated on cytosine DNA residues in CpG islands. Histone proteins that surround that region lack the acetylation modification that is present when the genes are expressed in normal cells. This combination of DNA methylation and histone deacetylation (epigenetic modifications that lead to gene silencing) is commonly found in cancer. When these modifications occur, the gene present in that chromosomal region is silenced. Increasingly, scientists understand how epigenetic changes are altered in cancer. Because these changes are temporary and can be reversed — for example, by preventing the action of the histone deacetylase protein that removes acetyl groups, or by DNA methyl transferase enzymes that add methyl groups to cytosines in DNA — it is possible to design new drugs and new therapies to take advantage of the reversible nature of these processes. Indeed, many researchers are testing how a silenced gene can be switched back on in a cancer cell to help re-establish normal growth patterns.
Genes involved in the development of many other illnesses, ranging from allergies to inflammation to autism, are thought to be regulated by epigenetic mechanisms. As our knowledge of how genes are controlled deepens, new ways to treat diseases like cancer will emerge.
Cancer and Transcriptional Control
Alterations in cells that give rise to cancer can affect the transcriptional control of gene expression. Mutations that activate transcription factors, such as increased phosphorylation, can increase the binding of a transcription factor to its binding site in a promoter. This could lead to increased transcriptional activation of that gene that results in modified cell growth. Alternatively, a mutation in the DNA of a promoter or enhancer region can increase the binding ability of a transcription factor. This could also lead to the increased transcription and aberrant gene expression that is seen in cancer cells.
Researchers have been investigating how to control the transcriptional activation of gene expression in cancer. Identifying how a transcription factor binds, or a pathway that activates where a gene can be turned off, has led to new drugs and new ways to treat cancer. In breast cancer, for example, many proteins are overexpressed. This can lead to increased phosphorylation of key transcription factors that increase transcription. One such example is the overexpression of the epidermal growth-factor receptor (EGFR) in a subset of breast cancers. The EGFR pathway activates many protein kinases that, in turn, activate many transcription factors which control genes involved in cell growth. New drugs that prevent the activation of EGFR have been developed and are used to treat these cancers.
Cancer and Post-transcriptional Control
Changes in the post-transcriptional control of a gene can also result in cancer. Recently, several groups of researchers have shown that specific cancers have altered expression of miRNAs. Because miRNAs bind to the 3' UTR of RNA molecules to degrade them, overexpression of these miRNAs could be detrimental to normal cellular activity. Too many miRNAs could dramatically decrease the RNA population, leading to a decrease in protein expression. Several studies have demonstrated a change in the miRNA population in specific cancer types. It appears that the subset of miRNAs expressed in breast cancer cells is quite different from the subset expressed in lung cancer cells or even from normal breast cells. This suggests that alterations in miRNA activity can contribute to the growth of breast cancer cells. These types of studies also suggest that if some miRNAs are specifically expressed only in cancer cells, they could be potential drug targets. It would, therefore, be conceivable that new drugs that turn off miRNA expression in cancer could be an effective method to treat cancer.
Cancer and Translational/Post-translational Control
There are many examples of how translational or post-translational modifications of proteins arise in cancer. Modifications are found in cancer cells from the increased translation of a protein to changes in protein phosphorylation to alternative splice variants of a protein. An example of how the expression of an alternative form of a protein can have dramatically different outcomes is seen in colon cancer cells. The c-Flip protein, a protein involved in mediating the cell-death pathway, comes in two forms: long (c-FLIPL) and short (c-FLIPS). Both forms appear to be involved in initiating controlled cell-death mechanisms in normal cells. However, in colon cancer cells, expression of the long form results in increased cell growth instead of cell death. Clearly, the expression of the wrong protein dramatically alters cell function and contributes to the development of cancer.
New Drugs to Combat Cancer: Targeted Therapies
Scientists are using what is known about the regulation of gene expression in disease states, including cancer, to develop new ways to treat and prevent disease development. Many scientists are designing drugs on the basis of the gene expression patterns within individual tumours. This idea, that therapy and medicines can be tailored to an individual, has given rise to the field of personalized medicine. With an increased understanding of gene regulation and gene function, medicines can be designed to specifically target diseased cells without harming healthy cells. Some new medicines, called targeted therapies, have exploited the overexpression of a specific protein or the mutation of a gene to develop a new medication to treat disease. One such example is the use of anti-EGF receptor medications to treat the subset of breast cancer tumours that have very high levels of the EGF protein. Undoubtedly, more targeted therapies will be developed as scientists learn more about how gene expression changes can cause cancer.
Career Connection
Geneticist
Many diseases arise from genetic mutations that prevent synthesising critical proteins. One such disease is Lowe disease (or oculocerebrorenal syndrome, because it affects the eyes, brain, and kidneys). In Lowe disease, there is a deficiency in an enzyme localised to the Golgi apparatus. Children with Lowe disease are born with cataracts, typically develop kidney disease after the first year of life, and may have intellectual disabilities.
A mutation on the X chromosome causes Lowe disease. The X chromosome is one of the two human sex chromosomes, as these chromosomes determine a person's sex. Females possess two X chromosomes while males possess one X and one Y chromosome. In females, the genes on only one of the two X chromosomes are expressed. Females who carry the Lowe disease gene on one of their X chromosomes are carriers and do not show symptoms of the disease. However, males only have one X chromosome and the genes on this chromosome are always expressed. Therefore, males will always have Lowe disease if their X chromosome carries the Lowe disease gene. Geneticists have identified the mutated gene's location, as well as many other mutation locations that cause genetic diseases. Through prenatal testing, a pregnant person can find out if the foetus they are carrying may be afflicted with one of several genetic diseases.
Geneticists analyse prenatal genetic test results and may counsel pregnant people on available options. They may also conduct genetic research that leads to new drugs or foods or perform DNA analyses for forensic investigations.
A permanent, heritable change in the nucleotide sequence of a cell's genome.
The immediate repair mechanism where DNA polymerase's 3' exonuclease activity detects, removes, and replaces mispaired bases before proceeding with replication.
An enzyme-driven repair pathway that scans, excises, and replaces mispaired nucleotides incorporated during replication.
A DNA repair pathway that cuts and removes damaged bases or bulky distortions (such as UV-induced thymine dimers) and resynthesises the gap.
A point mutation where a purine is replaced by another purine, or a pyrimidine is replaced by another pyrimidine.
A point mutation where a purine is replaced by a pyrimidine, or vice versa.
Heritable changes in gene expression and cellular phenotype that persist through mitosis and meiosis without altering the underlying DNA nucleotide sequence.
The collective combination of all chemical tags and epigenetic modifications found on the DNA and histones in a cell.
Highly basic, conserved eukaryotic nuclear proteins around which DNA winds to form nucleosome complexes.
The fundamental subunit of eukaryotic chromatin, consisting of ~146 bp of DNA wrapped 1.65 times around an octamer of core histone proteins.
The most versatile stem cells, present only in the earliest stages of development, capable of giving rise to any cell type in the body as well as extraembryonic tissues (the placenta).
An unspecialised cell that is capable of dividing indefinitely to self-renew and can differentiate into one or more specialised cell types under appropriate biochemical cues.
Stem cells derived from the inner cell mass of the blastocyst that can differentiate into virtually any cell type across the three primary germ layers, but cannot form an entire organism.
