Gene expression is controlled by a number of features

In a nutshell

Every cell in your body carries the same genes, yet a neurone and a white blood cell look and behave nothing alike. This subtopic is about how a cell controls which of its genes are actually expressed, so that one genome can build hundreds of specialised cell types, and about what happens when that control fails and cells divide out of control (cancer).

It ties together four connected ideas: stem cells and specialisation, the control of transcription (transcription factors and oestrogen), epigenetic control and RNA interference, and how faults in all of these cause tumours.

Assumed knowledge: DNA and protein synthesis, the cell cycle and mitosis, gene mutation.

Core content

Cells specialise by expressing only part of their DNA

Every body cell has the same genome, so what makes a cell specialised is not the genes it has, but the genes it switches on.

During development, a cell transcribes and translates only part of its DNA. The genes whose proteins it needs are expressed; the rest are switched off. That difference in which genes are expressed is what gives a cell its structure and function, and it is called differential gene expression.

Everything in this note is a mechanism for turning that expression up or down: at the level of transcription (transcription factors, oestrogen, methylation, acetylation) or after it (RNA interference).

Stem cells and potency

A stem cell is an undifferentiated cell that can keep dividing to make more cells (self-renewal) and can differentiate into one or more specialised cell types.

An examiner point worth banking now: a stem cell both replaces itself by dividing and differentiates. Saying only that it "turns into other cells" misses the self-renewal half and loses a mark.

How far a stem cell can differentiate is its potency:

Pluripotent stem cells, because they divide in unlimited numbers and can form any body cell type, can be used in treating human disorders.

Use the word differentiate, not the GCSE word "specialise", when describing what a stem cell does.

Induced pluripotent stem (iPS) cells

iPS cells are made from a patient's own adult somatic (body) cells, such as skin cells, that are reprogrammed back into a pluripotent state.

The reprogramming works by switching on specific genes using appropriate protein transcription factors. These transcription factors activate the genes associated with pluripotency, so the specialised cell behaves like an embryonic stem cell again and can divide and differentiate into most body cell types.

Because they are made from the patient's own cells and no embryo is used, iPS cells have two big advantages: less risk of the cells being rejected by the immune system, and no ethical objection about destroying embryos.

Evaluating the use of stem cells

You are expected to evaluate stem cells in medicine, which means weighing benefits against risks using given information, not just listing facts.

Stem cells could treat disorders by replacing cells the body cannot replace itself: for example insulin-producing cells (type 1 diabetes), neurones (spinal injury, Parkinson's), retinal cells (macular degeneration) and cardiomyocytes (heart damage).

A strong evaluation reaches a judgement supported by the evidence given, and does not fall back on vague ethics ("playing God") or generic points ("more research is needed"), which examiners do not credit.

Regulation of transcription: transcription factors

A transcription factor is a protein that moves from the cytoplasm into the nucleus and binds to a specific base sequence of DNA (a promoter region), where it controls the rate of transcription of a target gene.

• An activator transcription factor stimulates transcription: it binds the promoter and helps RNA polymerase bind, so the gene is transcribed.
• Others inhibit transcription by preventing RNA polymerase binding.

The mark is in the mechanism, not the outcome: "the gene is switched on" on its own is not enough. You have to say the transcription factor binds to the promoter and this stimulates (or inhibits) RNA polymerase / transcription.

Oestrogen initiates transcription

Oestrogen is a steroid hormone. It is lipid-soluble, so it can cross the cell membrane, and it acts by switching on target genes.

The steps, in the order the marks are awarded:

1. Oestrogen is lipid-soluble, so it diffuses through the phospholipid bilayer of the cell-surface membrane into the cytoplasm.
2. It binds to a specific receptor, forming a hormone-receptor complex.
3. This complex acts as a transcription factor and moves into the nucleus.
4. It binds to the promoter of the target gene and stimulates RNA polymerase, so transcription of the gene begins.

Oestrogen only affects its target cells because only those cells have the specific oestrogen receptors. A cell with no receptor cannot respond, however much oestrogen reaches it.

Epigenetic control of gene expression

Epigenetics is heritable changes in gene function, without changes to the base sequence of DNA.

These changes are caused by changes in the environment and they inhibit transcription by one of two routes:

• increased methylation of the DNA, or
• decreased acetylation of associated histones.

DNA methylation. Methyl groups are added to the DNA (usually to cytosine bases) at the promoter. Increased methylation stops transcription factors binding to the promoter, so RNA polymerase cannot bind and the gene is not transcribed (switched off). Decreased methylation makes the promoter accessible again, so transcription can occur.

Histone acetylation. DNA is wound around histone proteins. Adding acetyl groups to histones changes how tightly the DNA is held:

Still don't get it? · why decreased acetylation switches a gene off

Think of the DNA as a long piece of thread and the histones as spools it is wound around. Two magnets pull the thread onto the spool: one magnet is the histone, the other is the thread itself. The harder they pull, the more tightly the thread is wound, and the more of it is buried where nothing can reach it.

Now the real version, one step at a time. Histones carry a positive charge. DNA carries a negative charge, from the phosphate groups in its backbone. Opposite charges attract, so the histones and the DNA pull together.

Acetyl groups are the dimmer switch on that attraction. Adding acetyl groups (increased acetylation) reduces the positive charge on the histones, so they pull on the DNA less, the DNA loosens, and transcription factors and RNA polymerase can reach it: the gene can be transcribed. Removing them (decreased acetylation) does the opposite: the positive charge rises, the attraction to the negative DNA gets stronger, the DNA winds up tightly around the histones, and nothing can get to it.

So for the marks: decreased acetylation means more positive charge on the histones, stronger attraction to the negatively charged DNA, DNA more tightly wound / condensed, transcription factors and RNA polymerase cannot bind, transcription is inhibited.

The four combinations pull in a consistent direction: whatever makes DNA less accessible switches genes off.

Two things make epigenetic changes different from a mutation: they do not change the base sequence of the DNA, and they are reversible and can be inherited (passed on through cell division, and sometimes to offspring). Because environmental factors can switch genes on and off this way, epigenetics matters for the development and treatment of disease, especially cancer (see below).

RNA interference (RNAi)

The controls above act on transcription. Expression can also be blocked after transcription, by stopping the mRNA being translated. This is RNA interference (RNAi), and it happens in eukaryotes and some prokaryotes.

Using siRNA (small interfering RNA):

1. Double-stranded RNA is cut into short fragments called siRNA.
2. An siRNA joins a protein complex and its two strands separate, leaving one single strand bound to the complex.
3. That single strand has a base sequence complementary to a target mRNA, so it guides the complex to that mRNA and binds it by complementary base pairing.
4. The mRNA is cut up and broken down, so it cannot be translated. No protein is made, and the gene is effectively silenced.

Still don't get it? · why siRNA blocks translation, not transcription

Imagine a factory (the cell) that makes a product from a printed instruction sheet. The master file is the DNA; a printout of one page is the mRNA; the finished product is the protein. siRNA does not touch the master file and does not stop the printer. It shreds the printout after it has been printed but before anyone builds from it.

Step by step: the gene is still transcribed, so the mRNA is still made. But siRNA finds that particular mRNA by matching its base sequence (complementary base pairing) and the protein complex destroys it. With the mRNA gone, the ribosome has nothing to read, so translation cannot happen.

For the marks, be precise about three things examiners specifically check: siRNA is complementary to the mRNA, it binds to (and leads to the breakdown of) the mRNA, and this prevents translation. It does not bind to the gene or DNA, and it does not stop transcription.

Gene expression and cancer

Cancer is uncontrolled cell division (uncontrolled mitosis) that produces a tumour. It happens when the genes that normally control division are disrupted, by mutation or by the epigenetic changes above.

Benign and malignant tumours differ mainly in whether they spread:

Tumour suppressor genes and oncogenes are the two gene types that go wrong:

• A tumour suppressor gene normally produces a protein that slows down cell division or causes the death (apoptosis) of damaged cells. If it is inactivated, that protein is not made, so division is no longer held back, and cells divide uncontrollably.
• A proto-oncogene normally codes for a protein that stimulates cell division in a controlled way. A mutation (or over-expression) turns it into an oncogene: it becomes permanently active, over-stimulating division. Cells divide uncontrollably.

Abnormal methylation causes cancer through exactly these genes:

• Increased (hyper)methylation of the promoter of a tumour suppressor gene inhibits its transcription, so the tumour suppressor protein is not made. Division is no longer controlled, so a tumour can form. (This is the route examiners most often ask for.)
• Decreased methylation of a proto-oncogene can over-express it, so it behaves like an oncogene and over-stimulates division.

Notice the phrasing carefully: it is the gene that is not transcribed, so the protein is not produced, and it is the protein that normally controls division. Saying "the suppressor gene stops dividing" is meaningless and scores nothing.

Increased oestrogen and breast cancer. Oestrogen acts as a transcription factor (see above) that can switch on genes controlling cell division. Increased oestrogen concentrations therefore raise transcription of these genes in breast tissue, driving more cell division. That extra division is linked to the development of some breast cancers, which is why some treatments work by reducing oestrogen production or by blocking oestrogen from binding its receptor.

Interpreting data on cancer

You are expected to evaluate evidence of correlations between genetic or environmental factors and cancer. A correlation is usually shown as a scatter graph:

Reading a graph like this well means three things:

• State the trend precisely: there is a positive correlation (higher fat intake is associated with a higher death rate).
• Use the data: point out that some points do not fit the trend (for example a country with high fat intake but a relatively low death rate), so the relationship is not perfect.
• Judge it honestly: a correlation does not prove that fat causes the cancer, because other factors may differ between countries. But do not dismiss real, published data with a rote "correlation is not causation" and nothing else, which examiners explicitly do not credit.

Worked examples

Model answer, a four-mark "explain how oestrogen switches on a target gene". Each numbered point is one creditable step, in order:

1. Oestrogen is lipid-soluble, so it diffuses through the phospholipid bilayer into the cytoplasm.
2. It binds to a specific receptor, forming a hormone-receptor complex.
3. The complex acts as a transcription factor and moves into the nucleus, where it binds to the promoter of the gene.
4. This stimulates RNA polymerase, so the gene is transcribed into mRNA (the gene is switched on).

Model answer, "explain how increased methylation of a tumour suppressor gene can lead to a tumour". Notice this needs a linked causal chain, not a definition:

1. Methyl groups are added to (the promoter of) the tumour suppressor gene.
2. This inhibits transcription of the gene, so the mRNA is not made.
3. So the tumour suppressor protein is not produced.
4. That protein normally slows cell division or causes apoptosis of damaged cells.
5. Without it, cell division is uncontrolled, so a tumour forms.

Model answer, evaluating the correlation graph. A question showing the scatter above and asking "do these data show that dietary fat causes breast cancer?" is answered by:

1. Describing the trend: as mean fat intake increases, the death rate generally increases, a positive correlation.
2. Referring to the data that do not fit (the anomalous points), so the correlation is not perfect.
3. Concluding that the data show a correlation but not that fat causes the cancer, because the countries differ in other factors (a controlled investigation would be needed to establish cause).

Common exam mistakes

• Writing that a "lack of the suppressor gene" or that "the gene stops dividing" causes cancer. The gene is not transcribed, so the protein is not produced, and it is the protein that normally inhibits division or triggers apoptosis. Name the protein.
• Saying siRNA "prevents transcription" or "binds to the gene / DNA". siRNA acts after transcription: it is complementary to the mRNA, binds and destroys the mRNA, and so prevents translation.
• Describing a gene as just "switched on" or "switched off" with no mechanism. For transcription factors you must say they bind to the promoter and stimulate or inhibit RNA polymerase / transcription.
• Saying cancer is "uncontrolled cell growth". The credited term is uncontrolled (or rapid) cell division / mitosis. "Growth" is not accepted as a substitute for division.
• Describing metastasis as "the tumour moves around the body". Cells break off a malignant tumour and spread in the blood or lymph to form secondary tumours elsewhere.
• Contrasting the wrong way round, or only describing one tumour type. The key point is that benign tumours cannot metastasise or invade neighbouring tissues, while malignant ones can.
• Saying epigenetic changes alter the DNA. By definition they change gene function without changing the base sequence of the DNA.
• For oestrogen, not explaining why it affects only some cells: only target cells have the specific oestrogen receptor.
• Using "active site" or "similar" for a transcription factor or receptor. The site is a binding site, and shapes that fit are complementary, not "similar" (this is not enzyme action).
• Defining a stem cell only as one that "turns into other cells". It must also be able to divide / replace itself (self-renewal).
• Dismissing given correlation data with a rote "correlation does not mean causation" while failing to state that the correlation is positive or to use the data.

Key definitions

• Stem cell: an undifferentiated cell that can keep dividing (self-renew) and can differentiate into one or more specialised cell types.
• Totipotent cell: a cell that can divide and produce any type of body cell; found only for a limited time in early mammalian embryos.
• Pluripotent cell: a cell that can divide in unlimited numbers and can become any type of body cell.
• Multipotent cell: a cell that can divide to form a limited number of different cell types.
• Unipotent cell: a cell that can divide to form only one type of cell.
• Transcription factor: a protein that moves from the cytoplasm into the nucleus and binds to a specific region (promoter) of DNA to stimulate or inhibit transcription of a target gene.
• Epigenetics: heritable changes in gene function, without changes to the base sequence of DNA.
• RNA interference (RNAi): the inhibition of translation of a target mRNA by a short single strand of RNA (siRNA) that is complementary to the mRNA, binds to it and leads to its breakdown.
• Benign tumour: a tumour whose cells cannot invade neighbouring tissues or spread to other parts of the body (cannot metastasise).
• Malignant tumour: a cancerous tumour whose cells invade neighbouring tissues and metastasise to form secondary tumours elsewhere.
• Tumour suppressor gene: a gene that produces a protein that slows cell division or causes the death (apoptosis) of damaged cells.
• Oncogene: a mutated or over-expressed proto-oncogene whose protein permanently stimulates cell division, causing uncontrolled division.

Specification

• I can explain that cells become specialised because they express (transcribe and translate) only part of their DNA.
• I can state what totipotent, pluripotent, multipotent and unipotent cells can produce, and where each is found (including cardiomyocytes from unipotent cells).
• I can describe how induced pluripotent stem (iPS) cells are produced from adult somatic cells using protein transcription factors.
• I can evaluate the use of stem cells in treating human disorders.
• I can explain how transcription factors move from the cytoplasm to the nucleus and stimulate or inhibit transcription of target genes.
• I can explain the role of oestrogen (a steroid hormone) in initiating transcription.
• I can explain epigenetic control by increased methylation of DNA and decreased acetylation of histones, and state that these are heritable and do not change the base sequence.
• I can explain how translation can be inhibited by RNA interference (RNAi) using siRNA.
• I can describe the main characteristics of benign and malignant tumours.
• I can explain the roles of tumour suppressor genes, oncogenes, abnormal methylation, and increased oestrogen concentrations in the development of tumours.
• I can interpret data on gene expression and evaluate correlations between genetic or environmental factors and cancer.

Related notes

• Alteration of the sequence of bases in DNA (gene mutation)
• Using genome projects
• DNA and protein synthesis
• All cells arise from other cells (the cell cycle and cancer)