Control of gene expression

What are transcription factors?

• Proteins that physically bind to the ‘promoter’ regions upstream of genes to activate (or inhibit) the transcription of the gene (they usually do this by helping RNA polymerase to bind or by stopping RNA polymerase from binding). 

• They bind during transcription to the exposed DNA strand  

•  Transcription factors are globular proteins therefore they are synthesised in the ribosomes (free ribosomes as they are internal proteins, not to be secreted outside of the cell). Transcription factors are produced in the cytoplasm, but operate within the nucleus, therefore, to control the action of transcription factors, their movement between these two locations can be controlled. 

What is oestrogen, and what does it do?

• Can control the transcription of around 100 different genes 

• Oestrogen is a steroid hormone, meaning it is lipid-based and hydrophobic  

How does oestrogen work to control transcription factors?

• Oestrogen can diffuse directly through the cell surface membrane phospholipid bilayer into the cytoplasm 

• In the cytoplasm it binds to an internal oestrogen receptor (a protein with a complementary shape to oestrogen) 

• Binding to the receptor causes the receptor to undergo a conformational shape change 

• The receptor is now able to diffuse through a nuclear pore into the nucleus 

• The new shape of the receptor allows it to bind, in combination with other proteins, to the DNA of the promoter region of the gene to be expressed 

• This stimulates RNA polymerase binding and gene transcription (where the receptor acts as the transcription factor) 

How can expression of a gene be reduced?

Expression of a gene can be reduced by either preventing transcription (transcription factors), and hence preventing the production of mRNA, or by the breakdown of mRNA before its genetic code can be translated

Epigenetics

The study of how environmental factors can cause heritable changes in gene activity without changing the base sequence of DNA. An important concept is that the shape of the DNA-histone complex, including how tightly wound the DNA is around the histone proteins, can be changed 

Suggest how an androgen receptor (AR) could stimulate gene expression (within the nucleus) [2

1. AR is a transcription factor 

2. Binds to DNA/promoter

3. Stimulates RNA polymerase

What is methylation of DNA?

• Increased methylation of DNA inhibits transcription 

• When methyl groups (CH3) are added to DNA, they attach to only the cytosine bases 

• This prevents transcription factors from binding and attracts proteins that condense the DNA-histone complex. In this way, methylation prevents a section of DNA from being transcribed by making it inaccessible to transcription factors 

Gene expression through epigenetics

• Factors such as diet, stress and toxins can add epigenetic (chemical tags) to the DNA, and this can control gene expression in eukaryotes  

• A single layer of chemical tags on the DNA is called the epigenome, and this impacts the shape of the DNA-histone complex and whether the DNA is tightly wound so won’t be expressed, or is unwound so will be expressed 

• If the DNA is tightly wound, then transcription factors cannot bind. Chromatin can be tightly packed – this makes the DNA inaccessible to transcription factors and RNA polymerase, therefore turning the expression of the gene off 

In terms of A+M, which processes happen to make DNA expressed, or not expressed?

Gene expression

• decreased methylation of DNA

• increased acetylation of histones

Genes not expressed

• increased methylation

• decreased acetylation

What is acetylation of histone proteins?

• Increased acetylation of associated histone proteins on DNA increases transcription. (Histone acetylation results in loose packing of nucleosomes. Transcription factors can bind to the DNA, and genes are expressed) 

• If acetyl groups are added to the DNA then the histones become less positively charged and are less attracted to the negatively charged phosphate group on DNA (effectively decreases the electrostatic attraction between the DNA and histone proteins) 

• This makes the DNA and histones less strongly associated/attracted and therefore it is easy for the transcription factors to bind  

Epigenome

• The complete collection of chemical modifications that a cell's chromatin experiences in its ‘lifetime’. This includes turning genes on/off, DNA methylation, acetylation of histone proteins

What does the enzyme histone deacetylase do, and what effect what a non-competitive inhibitor have on it?

• The enzyme histone deacetylase (HDAC) removes acetyl groups from histone proteins, making them less acetylated.

• When a new drug acts as a non-competitive inhibitor of HDAC, it prevents the removal of these acetyl groups, leading to increased histone acetylation. This results in a looser chromatin structure, which can increase gene expression. 

Tumour suppressor genes

• These genes produce proteins that slow down cell division, repair DNA, or cause programmed cell death (apoptosis) 

• If a mutation results in the tumour suppressor gene, it will not produce the proteins to carry out this function - cell division would continue, and mutated cells would not be identified and destroyed  

• p53 is one of the most common tumour suppressor genes involved in causing cancer 

Abnormal methylation

• Tumour suppressor genes could become hypermethylated, meaning an increased number of methyl groups attached to it. This results in the gene being inactivated and becomes turned off. 

• The opposite could occur in oncogenes, as they may be hypomethylated (or increased in acetylation of histones). This results in the oncogene being permanently switched on, tumours form 

• Increased methylation of the tumour suppressor gene’s promoter region will lead to an inactivation of the tumour suppressor gene (decreased gene expression, tumour expressor gene turned off) 

Differences between benign and malignant tumours

• benign grow slowly, malignant grow rapidly

• benign do not spread to other areas of the body (because they are adhesive and surrounded by a capsule of tissue.) Malignant tumours spread to neighbouring cells via metastasis through the bloodstream or lymphatic system

• benign tumours are specialised cells, malignant tumours have de-differentiated and are no longer specialised

Oncogenes

these genes are formed from mutated proto-oncogenes and are permanently switched on/over-expressed – resulting in cell division that is uncontrolled, creation of tumours 

Proto-oncogenes

a gene that stimulate cells to divide regularly by producing proteins stimulate cell division - can cause cancer if mutated