Epigenetics

Epigenetic Mechanisms

Epigenetic changes are heritable changes in gene expression that, unlike mutations, do not change the base sequence of DNA. These changes occur via the attachment or removal of tags (chemical groups) to the DNA or the histone proteins.

The long-term persistence of changes in gene expression is an important characteristic of epigenetic effects.

During embryonic development, epigenetic modifications are transferred from cell to cell. For example, epigenetic changes in adult muscle cells prevent the expression of genes that are not needed for the function of the muscle since the expression would be wasteful.

Some epigenetic changes, such as the ones mentioned above, are relatively permanent during an individual’s lifespan, while others may be reversible during the individual’s life.

In multicellular organisms that undergo sexual reproduction, some epigenetic modifications may be passed from the parents to the offspring. This type of inheritance is called transgenerational epigenetic inheritance.

Environmental factors such as stress, toxins, and agents in cigarette smoke can result in epigenetic changes to DNA and affect gene expression.

Epigenetic Modification

The three most common chemical modifications involved in epigenetic regulation of gene expression are DNA methylation, chromatin remodelling, and covalent histone modification.

DNA methylation

One method that eukaryotes use to suppress gene expression is called DNA methylation.Methylation of DNA is when methyl groups (--CH₃) are covalently attached to the carbon at the number 5 position of the cytosine base on the DNA by an enzyme called DNA methyltransferase, forming 5-methylcytosine. The methylated cytosine is usually connected to a neighbouring guanine residue via a phosphodiester bond on the same strand. These dinucleotides of cytosine and guanine are called CpG islands.

Fig. 1 - A schematic diagram of DNA methylation as well as chemical structure of 5-methylcytosine

DNA methylation usually inhibits the transcription of genes in eukaryotes, especially when it occurs near the gene’s promoter region. There are many CpG islands located near the promoter in both vertebrates and invertebrates.

In the housekeeping genes (essential genes for most cells’ viability in multicellular organisms, such as the gene for RNA polymerase gene), the CpG islands are mainly unmethylated. As a result, housekeeping is expressed in almost all cell types. On the other hand, some tissue-specific genes that are highly regulated may be suppressed by the methylation of CpG islands.

There are two ways by which methylation of CpG islands inhibits DNA transcription:

1. First, methylation may influence regulatory transcription factors (TFs) binding to the DNA. For instance, the presence of the methyl group may prevent the binding of an activatory TF to the enhancer region. This would inhibit the recruitment of RNA polymerase to the promoter and inhibit transcription initiation.

2. Second, methylation suppresses the expression of genes via proteins called methyl-CpG-binding proteins. These proteins can specifically recognise and bind to methylated CpG groups. After that, these proteins would recruit other proteins that inhibit transcription. For example, they may recruit a histone deacetylase to the methylated CpG region near the promoter, which would remove acetyl groups from the histones and make it more difficult for the histones to be removed from the DNA.

Chromatin remodelling

In eukaryotic cells, different areas within the chromatin can have different conformations. Areas of chromatin that are densely packed and have a closed structure are called heterochromatin. Due to its dense organisation, transcription of genes within the heterochromatin is very difficult or near impossible.

More open areas of the chromatin are known as euchromatin. Due to their open conformation, DNA polymerase and TFs can access euchromatin genes more easily than heterochromatin. As a result, the genes in euchromatin are expressed more than the genes located in heterochromatin.

The chromatin can be remodelled. One way to perform this is via ATP-dependent chromatin remodelling. This process is carried out by protein complexes that can recognise nucleosomes.

These complexes contain a catalytic ATPase subunit called DNA translocase, which can use the energy released from ATP hydrolysis to change the position or composition of nucleosomes, which can make the chromatin more or less condensed.

Histone covalent modification

Histone complexes are structures that DNA double helix is wrapped around in nucleosomes. Each of these complexes is composed of eight histone core proteins that consist of a globular domain and a flexible charged amino-terminal tail.

The amino-terminal tails protrude away from the chromatin while the DNA twists around the globular domains. The amino-terminal tails contain particular amino acids that are subject to various covalent modifications such as acetylation, methylation and phosphorylation.

Histone modification affects the interactions within the nucleosomes. Let’s take acetylation, for example. We briefly mentioned histone acetylation when we were discussing DNA methylation. During histone acetylation, an acetyl group (CH₃CO-) is added to a positively charged lysine residue in the amino-terminal tail of a histone core protein by histone acetyltransferase. This attachment eliminates the positive charge on the lysine side chain, disrupting the electrostatic attraction between positively charged histones and negatively charged DNA strands. As a result, the DNA becomes less tightly bound to the histone proteins and becomes more accessible to RNA polymerase and TFs.

Fig. 2 - This diagram shows the process of histone acetylation and its effect on DNA accessibility by the transcription machinery

Histone acetylation is a reversible modification, and the acetyl group can be removed from the histone core proteins by the enzyme histone deacetylase. Decreased acetylation means lysine is in its positively charged state and has a stronger attraction to the DNA molecule, causing the association between DNA and histones to be stronger, so the DNA is not available to transcription factors. Therefore mRNA production is not initiated, and the gene is switched off - it cannot be transcribed or translated.

Transgenerational epigenetic inheritance

As discussed earlier, epigenetic effects result in DNA and chromosomal modifications that alter gene expression. Some of these epigenetic modifications may be reversible during an individual’s lifespan, but others may be permanent or even get passed on to the next generation. For instance, it has been shown that gestational diabetes in a pregnant mother can increase the likelihood of the daughter developing gestational diabetes in the future. These high glucose concentrations cause epigenetic changes in the daughter’s DNA.

Despite the cellular mechanism that searches and clears epigenetic changes in the DNA of sperm and egg cells, some modifications may escape and get passed on.

Dosage compensation

Dosage compensation describes the phenomenon which ensures the level of sex gene expression (such as those on the X chromosome) are the same in both males and females, even though males and females have different numbers of sex chromosomes.

Genomic imprinting

Genomic imprinting refers to marking a segment of DNA where the mark is retained and recognized throughout the organism’s life, inheriting the marked DNA. Genomic imprinting occurs before fertilization and mainly involves a modification in a single gene or chromosome during gametogenesis.

Depending on whether the imprinting occurs during the sperm or the egg cell formation, each offspring expresses only one of the two alleles. This phenomenon is termed monoallelic expression.

Epigenetics and Disease

Epigenetic modifications are a regulated process, forming part of healthy development. Changing any of the epigenetic mechanisms might result in aberrant gene activation or silencing and cause certain disorders. Such changes have been linked to various disorders, one of which is cancer.

Cancer Epigenetics

As we discussed earlier, epigenetic changes do not affect the base sequence in the DNA. However, they can increase the rate of mutations.

Epigenetic changes are linked to cancer development. They are present in tumour cells and often cooperate with genetic alterations that drive the properties of cancer cells.

TSGs

Tumour suppressor genes (TSGs) code for proteins that slow down cell division. They can be thought of as stop breaks in the cell cycle. TSGs can trigger cell death (apoptosis) if mistakes in the process of DNA replication are detected.

If a mutation occurs in TSGs, the protein produced would be non-functional. This would lead to uncontrolled cell division and unregulated proliferation. Examples of important TSGs in the cells are the p53 retinoblastoma genes. Other examples include the BRCA1 and BRCA2 genes linked to breast cancer development.

TSGs can become inactivated by three pathways:

1. Loss-of-function mutation.

2. Complete deletion.

3. Suppression by epigenetic changes.

Epigenetic silencing of TSGs can occur by deregulation of the machinery responsible for epigenetic modifications. For instance, it may involve inappropriate methylation of CpG islands within the promoter region of TSGs, thereby suppressing their transcription.

Proto-oncogenes

Proto-oncogenes are another set of genes that are important in the pathophysiology of tumours. Proto-oncogenes are normal genes that promote cell proliferation and can be thought of as gas pedals that accelerate the cell cycle. An example of oncogenes would be the ras protein.

When proto-oncogenes’ activity is enhanced due to mutation, they become oncogenes and result in uncontrolled cell proliferation. Epigenetic changes can also increase the expression of proto-oncogenes. For instance, acetylation of the histone complexes around proto-oncogenes makes the DNA less tightly bound to the histone complex and more accessible by the transcription machinery. Increased expression of proto-oncogenes would have an oncogenic effect on the cell and result in uncontrolled cell division.