3.8.2.2 Regulation of transcription and translation

In eukaryotes, transcription of target genes can be stimulated or inhibited when specific transcriptional factors move from the cytoplasm into the nucleus. The general principles involved in controlling gene expression by controlling transcription are as follows:

• For transcription to begin the gene must be switched on by specific molecules (transcriptional factors) that move from the cytoplasm into the nucleus
• Each transcriptional factor has a site that binds to a specific bas sequence of the DNA in the nucleus
• When it binds it causes this region of DNA to begin the process of transcription
• mRNA is produced and the information it carries is translated into a polypeptide (this is translation)
• When a gene is not being expressed (it is switched off), the site on the transcriptional factor that binds to DNA is not active
• As the site is inactive it cannot cause transcription and polypeptide synthesis.

So we need to know a bit about the role of the steroid hormone oestrogen in initiating transcription. Well, hormones like oestrogen can switch on a gene and start transcription by combining with a receptor site on the transcriptional factor. This then activates the DNA binding site on the transcriptional factor (by causing it to change shape):

• Oestrogen, a lipid-soluble molecule, diffuses easily through the phospholipid bilayer of cell-surface membranes
• Once inside the cytoplasm oestrogen binds with a site on a receptor molecule of the transcriptional factor. They are complimentary to one another
• By binding with the site the oestrogen changes the shape of the DNA binding site on the transcriptional factor, activating it
• It can now bind to DNA
• The transcriptional factor enters the nucleus (through a nuclear pore) and binds to a specific base sequence of DNA
• This stimulates transcription of the gene that makes up that portion of DNA

Whilst genes determine the features of an organism, the environment can influence the expression of these genes. It is now believed that environmental factors can cause heritable changes in gene function without changing the base sequence of DNA. This process is known as epigenetics. This provides explanations as to how environmental influences such as diets, stress, toxins (etc), can alter the genetic inheritance of an organism's offspring. So, now about how it works. Basically, we already know that DNA is wrapped around proteins called histones. We now know that both the DNA and histones are covered in chemicals (tags). These chemicals/tags form the epigenome. The epigenome determines the shape of the DNA-histone complex. E.g it keeps genes that are inactive tightly packed in arrangement ensuring they cannot be read (epigenetic silencing). It can also unwrap genes so the DNA is exposed and can be easily transcribed (switching on these particular genes). Unlike DNA, the epigenome is not fixed (it is flexible). It is flexible because its chemical tags respond to environmental changes, factors such as stress and diet can cause the chemical tags to adjust the wrapping/unwrapping, switching genes on/off.

The epigenome of a cell is an accumulation of the signals it has received during its lifetime. It acts a bit like a cellular memory. In early development the signals come from within the cells of the foetus. The nutrition provided by the mother is important in shaping the epigenome at this stage (this is why it is imperative that pregnant woman keep a good diet and don't smoke etc).After birth environmental factors affect the epigenome (although signals, such as hormones, from within the body can still influence it). These factors cause the epigenome to activate/inhibit a specific set of genes. The environmental signal stimulates proteins to carry its message inside the cell from where it is passed by a series of other proteins into the nucleus. Here the message passes to a specific protein which can be attached to a specific sequence of bases on the DNA. Once attached the protein can change:

• acetylation of histones, leading to the activation/inhibition of a gene
• methylation of DNA by attractive enzymes that can add/remove methyl groups.

Okaaay so what does any of that actually mean. Well, when the association of histones with DNA is weak the DNA-histone complex is less condensed meaning that the DNA is accessible by transcriptional factors which can initiate transcription (basically, the gene is switched on). When the association is stronger, the reverse occurs and the gene is switched off. Condensation of the DNA histone complex inhibits transcription. It can be brought about by decreased acetylation of the histones or by methylation of DNA. So how do these processes work?

Decreased acetylation of associated histones
Acetylation is the process whereby an acetyl group is transferred to a molecule. In this case, acetylcoenzyme A donates an acetyl group. Deacetylation is the removal of an acetyl group from a molecule. Decreased acetylation increase the positive charges on histones as acetyl groups are negatively charged. This increases the attraction of the histones to the phosphate groups of DNA. The association between DNA and histones becomes stronger and the genes are switched off.

Increased methylation of DNA
Methylation is the addition of a methyl group to a molecule. In this case a methyl group is added to the cytosine bases of the DNA. It inhibits transcription in the following ways:

• prevents the binding of transcriptional factors to DNA
• attracts proteins that condense the DNA-histone complex by inducing the deacetylation of histones.

Epigenetic changes can be responsible for certain diseases. Altering the epigenetic process can cause abnormal activation/silencing of a gene. In some cases the activation of a normally inactive gene can cause cancer. In other cases, the inactivation (silencing) of a usually active gene causes a disease.

In specific sections of DNA (near promoter regions) that have no methylation in normal cells. In cancer cells these regions become highly methylated causing genes that should be active to switch off.

Whilst epigenetics do not alter the sequence of bases in a DNA molecule they can increase the incidence of mutations. For example, some active genes help to repair DNA (preventing cancers). Individuals with various types of inherited cancer have increased methylation of these genes causing the gene to be switched off. As a result, the damage to base sequences in DNA are not repaired. This can lead to the development of cancer.

It's not all bad news though, we can also use epigenetic treatments to counteract the epigenetic changes that cause certain genes to be activated/silenced. The treatments use drugs to inhibit certain enzymes involved in either histone acetylation or DNA methylation. E.g. drugs that inhibit enzymes that cause DNA methylation can reactivate silenced genes. 

Epigenetics have also been used in diagnostics tests to detect the early stages of diseases such as cancer/brain disorders/arthritis. The tests can identify the level of DNA methylation and histone acetylation at an early stage of disease. This allows patients to seek treatment asap.

RNA interference
This is the last little bit in this section. Basically, in eukaryotes (and some prokaryotes!) the translation of mRNA produced by a gene can be inhibited by breaking mRNA down before its coded information can be translated into a polypeptide.One type of RNA molecule that may be involved is small interfering RNA (siRNA). This mechanism involved small double-stranded sections of siRNA and operates as follows:

• An enzyme cuts large double stranded RNA molecules into smaller sections known as siRNA
• One of the two siRNA strands combines with an enzyme
• The siRNA molecule guides the enzyme to a mRNA molecule by pairing up its bases with the complimentary ones on a section of the mRNA molecule
• Once in position the enzyme cuts the mRNA into smaller sections
• the mRNA is no longer capable of being translated into a polypeptide meaning that the gene has not beed expressed (so it has been silenced/blocked)