epigenetics

Inversion mutation

• usually occurs during crossing over

• The DNA of a single gene is cut in two places

• The cut portion is inverted 180*, then rejoined at the same place in the gene

• A large section of the gene is backwards

• Non-functional / different protein formed

Duplication

A whole gene or section of a gene is duplicated. Not harmful since the original version of the gene remains intact. The second copy can undergo mutations over time which can lead to evolutionary change

Translocation

A gene is cut in two places, and the section of the gene that is cut off attaches to a separate gene. The cut gene leads to a non-functional protein, and it is likely that the gene that has gained the section does too.

How can translocation lead to a tumour being formed

If a section of a proto-oncogene is translocated onto a gene controlling cell division, it could increase its expression. If a section of a tumour suppressor gene is translocated which means that the tumour suppressor gene will be faulty - the cell will continue to replicate with this fault gene.

Mutagens

• Physical - ionising radiation - x-rays, gamma rays

• Chemical

• Biological - HPV

Induced pluripotent stem cells

Pluripotent stem cells produced from adult somatic cells using transcription factors, which cause specific genes to be expressed which reprogram the cell to show characteristics of embryonic stem cells

Example of unipotent stem cells

Cardiomyocyte-forming unipotent cells

Transcription factor

A protein that helps control the process of transcription, either by activating or repressing the transcription of a particular gene

How do transcription factors work

• TF enters the nucleus through a nuclear pore

• Binds to the promoter region at the start of the gene

• This binding either allows or prevents the transcription of the gene, by either assisting the binding of RNA polymerase, or preventing it

• So either increases or decreases the rate of transcription of the gene

Promoter region

Section of DNA upstream of the coding region that is the binding site for transcription factors

Oestrogen stimulation pathway

• Oestrogen diffuses through the cell surface membrane into the cytoplasm, then diffuses through a nuclear pore into the nucleus

• Oestrogen binds to an ERa oestrogen receptor that is held within a protein complex, which causes it to undergo a conformational change in shape

• This causes it to detach from the protein complex and diffuses through towards the gene to be expressed

• It binds to a cofactor which enables it to bind to the promoter region of the gene, which stimulates RNA polymerase binding and gene transcription

Epigenetics

HERITABLE changes in gene function without changes to the base sequence of DNA

Epigenome

All chemical modifications to all histone proteins and DNA (except base changes)

Effect of acetylation of histones

DNA wraps less tightly around histones, so RNA polymerase and transcription factors can bind more easily, so gene expression is increased

Effect of methylation of DNA

Suppresses transcription

Why are therapies that aim to combat epigenetic changes promising

They are reversible, unlike mutations

Epigenetic causes of cancer

Changes in DNA methylation and histone acetylation lead tumour suppressor genes to be silenced and oncogenes to be activated

Tumour suppressor genes

Genes that code for proteins that prevent uncontrolled cell division, by repairing DNA, slowing the cell cycle at checkpoints, and signalling apoptosis if damage is irreparable

Proto-oncogene

Code for proteins that stimulate cell growth and differentiation

Oncogene

A mutated version of a proto-oncogene, which causes a cell to divide too quickly, as it causes constant activation of proteins that simulate cell growth and division, often leading to tumour formation

Epigenetic therapies for cancer

Removal of methyl groups on tumour suppressor genes. Removal of acetyl groups from histone proteins attached to oncogenes.

RNA interference

A form of post-transcriptional modification that occurs in the cytoplasm. A sequence-specific silencing of gene expression.

siRNA

Binds to mRNA that has been transcribed from target genes, as their base sequences are complementary. Each siRNA is attached to a protein complex that breaks down the mRNA that has been transcribed from the target genes, so translation cannot occur. The fragments of mRNA are then hydrolysed into nucleotides.

How is siRNA formed

Double stranded RNA is produced by RNA-dependent RNA polymerases, and hydrolysed into smaller fragments to form siRNAs, which bind to protein complexes, which use energy from the hydrolysis of ATP to separate the two strands of the siRNA, which exposes the nucleotide bases so they can pair with bases from the target mRNA molecule.

siRNAs in cancer treatment

They can target oncogenes that have been expressed or upregulated, to reduce the number of proteins produced that lead to cancer

Characteristics of malignant tumours

• Growing rapidly, invading and destroying surrounding tissues

• Secreting chemicals that cause the formation of blood vessels to supply the tumour with glucose, amino acids, growth factors, oxygen, etc

• Metastasis: cells breaking off tumours and spreading to other parts of the body, through the bloodstream or lymphatic system

Characteristics of benign tumours

• Grow slowly

• Do not invade other tissues, do not metastasise

• Do not usually grow back when removed

How can the genome of simple organisms be used to predict the proteome

• Use bioinformatics to identify genes from the genome

• Predict amino acid sequences of proteins

• Study which proteins are actively expressed in different conditions

Why are simple organisms (bacteria and viruses) used when predicting proteins from genomes

• relatively small genomes

• No introns

• Less complex gene regulation

How are genomes used to form vaccines

• Sequence the genome

• Use computational tools to predict the proteome

• Identify proteins that are expressed on the surface, are unique to the pathogen (so are not found in humans) and that will trigger an immune response

When sequencing the plasmodium genome for a malaria vaccine, scientists targeted genes that showed high variation between organisms. Why?

the high variation indicates a strong selective pressure on these genes, suggesting that they are antigen proteins found on the surface of the pathogen

What makes it hard to determine the proteome from the genome

• Non-coding DNA - introns and repetitive sequences

• Regulatory genes (that don’t code for proteins)

• Alternative splicing

• Post-translational modifications