1The idea in one paragraph

A gene does nothing until it is expressed: transcribed into mRNA and translated into a protein that then does a job. Every cell in your body has the same genes, but each expresses only some of them, and that choice is what makes a liver cell different from a nerve cell. Cells set the choice at several points. Proteins called transcription factors bind to DNA near a gene and switch its transcription on or off. The mRNA is broken down after a set time, which limits how much protein is made. And chemical epigenetic tags, methyl groups on DNA and on histones, lock genes on or off for long periods, can be copied into daughter cells, and are altered by the environment. Some tags even pass to offspring, which is why a liger and a tigon look different although they have the same parent species.

2Gene expression: from gene to phenotype

Gene expression is the process by which the information in a gene has an effect on the phenotype. In most cases it has three stages, and Figure 1 follows them.

1. Transcription: the base sequence of the gene is copied into mRNA.
2. Translation: the mRNA is used to make a polypeptide, which folds into a protein.
3. The protein acts. Very often the protein is an enzyme, and its product is the thing you can see.

Take the dark pigment melanin in skin and hair. The gene for the enzyme tyrosinase is transcribed in pigment cells; the mRNA is translated into tyrosinase; tyrosinase catalyses a step in making melanin from the amino acid tyrosine. If the gene is expressed, the hair is pigmented. If it is not, or if the enzyme made is faulty, there is no melanin, and the animal is albino. The gene's effect on the phenotype runs entirely through the protein.

Because every step can be sped up or slowed down, the cell has several places to control expression. The amber labels in Figure 1 mark the three this subtopic covers.

3Regulating transcription: promoters, enhancers and transcription factors

Transcription factors are proteins that bind to specific base sequences in DNA and so control whether a gene is transcribed. Figure 2 shows where they bind.

The promoter is a base sequence just before (upstream of) the gene, where RNA polymerase binds to start transcription. In eukaryotes, RNA polymerase cannot bind to a promoter on its own. A set of transcription factors must bind first and bring it in. So the promoter is where the decision to transcribe is made.

Enhancers are base sequences that increase the rate of transcription of a gene. They can be a long way from the gene, thousands of bases away. A transcription factor that binds to an enhancer and increases transcription is an activator. The DNA between the enhancer and the promoter bends into a loop, bringing the activator into contact with the proteins at the promoter, where it helps RNA polymerase to bind and start. Other transcription factors, repressors, bind to DNA and reduce transcription.

Why so many layers? Because the combination is the point. A cell transcribes a gene strongly only when the right combination of factors is bound, and which factors a cell makes depends on its type and the signals it has received. A liver cell makes the factors that switch on liver genes; a nerve cell makes different ones.

Transcription factors bind to specific base sequences. A gene is transcribed only when the right factors are bound at its promoter and enhancers.

4Regulating translation: how long the mRNA lasts

Once an mRNA is made, it is translated again and again, each time making another copy of the protein. It is translated until it is broken down by enzymes called nucleases. In human cells, an mRNA may last from a few minutes to several days. So controlling the rate of degradation of mRNA controls how much protein is made from it.

Figure 3 compares two mRNAs whose transcription stops at the same moment. mRNA A has a half-life of 30 minutes: half of it is broken down every half-hour. mRNA B has a half-life of 8 hours.

A short-lived mRNA suits a protein the cell needs only briefly, such as one that responds to a signal: when transcription stops, protein production stops within an hour or so. A long-lived mRNA suits a protein needed steadily, and keeps being translated long after transcription has ended.

5Epigenesis: why cells with one genome differ

A human body has hundreds of cell types, and all of them (apart from a few, such as red blood cells, which lose their nucleus) carry the same DNA. They differ because they express different genes. Epigenesis is the development of patterns of differentiation in the cells of a multicellular organism: in the embryo, cells in different positions receive different signals, switch on different sets of genes, and become different types of cell.

The key fact, and the one the guide asks you to stress: epigenetic changes do not alter the base sequence of DNA. They change which genes are expressed, so they change the phenotype of the cell. They do not change its genotype. A skin cell and a liver cell from one person have identical genotypes and very different phenotypes.

6Genome, transcriptome and proteome

Three words separate what a cell has from what it uses.

No cell expresses all of its genes, and the pattern of expression is what decides how a cell differentiates. An example from three human cells:

All three genomes contain all four genes. The transcriptomes and proteomes differ. Genes like ATP synthase, needed by every cell, are expressed everywhere; genes that make a cell specialised are expressed only in that cell type.

7Epigenetic tags: methylation of DNA and of histones

The long-term settings that keep a liver cell a liver cell are held by epigenetic tags: chemical groups attached to DNA or to histones that change gene expression without changing the base sequence. The guide names two, both methylation (addition of a methyl group, –CH₃). Figure 4 shows both.

Methylation of cytosine in a promoter. Methyl groups can be added to cytosine bases in DNA. When the cytosines in a gene's promoter are heavily methylated, transcription factors and RNA polymerase cannot bind there, so the gene downstream is repressed: it is not transcribed and not expressed. The base is still cytosine and still pairs with guanine; the sequence is unchanged. Only the tag is new.

Methylation of histones. Methyl groups can also be added to particular amino acids in the histone proteins of nucleosomes. Depending on which amino acid is tagged, this can make the chromatin pack more tightly, so the DNA cannot be reached and transcription is repressed, or pack more loosely, so transcription is activated. You do not need to know how.

8Epigenetic inheritance

Tags survive cell division. When DNA is replicated, enzymes copy the methylation pattern onto the new strand, and histone tags are re-established on the new nucleosomes. So when a differentiated cell divides by mitosis, its daughter cells inherit its pattern of tags, and with it the same pattern of gene expression. A dividing skin cell produces skin cells, not liver cells, although both kinds of cell have the same DNA.

This is epigenetic inheritance: a change in phenotype passed on to daughter cells, or sometimes to offspring, without any change in the nucleotide sequence of DNA. It happens when tags remain in place through mitosis (to daughter cells) or through meiosis (to gametes, and so to the next generation).

9The environment changes the tags

Tags are not fixed at birth. They can be added or removed during life, and the environment is one of the things that changes them. That gives the environment a route to alter gene expression, and so the phenotype, without mutation.

Air pollution. Studies of people exposed to polluted air, for example fine particles from traffic exhaust, have found changes in the methyl tags on DNA in their cells, including in blood cells, compared with people breathing cleaner air.

Diet and smoking are other factors known to change tags. The mechanism is always the same: the environment changes tags, tags change expression, and expression changes phenotype.

10Resetting the tags between generations: ligers and tigons

If every tag passed from parent to child, a child would inherit the parents' differentiated states, which would be a disaster: the zygote must be able to become every cell type. So during the making of eggs and sperm, and again just after fertilisation, most epigenetic tags are removed and the genome is reset.

Most, but not all. A small number of genes keep tags that record which parent they came from, so only the copy from the mother, or only the copy from the father, is expressed. This is called genomic imprinting, and it means that the same allele can have a different effect depending on which parent passed it on.

The guide's example is the hybrids of lions and tigers, which have the same two parent species but opposite parents of each sex (Figure 5).

• A liger has a lion father and a tiger mother. Ligers grow far larger than either parent species.
• A tigon has a tiger father and a lion mother. Tigons are about the size of their parents, or smaller.

If only the DNA sequence mattered, ligers and tigons would be alike, because each has one set of lion chromosomes and one set of tiger chromosomes. They differ because of imprinted growth genes. The usual explanation is this. Some genes that promote growth are expressed only from the father's copy, and some that restrain growth only from the mother's copy. In lions, the father's growth-promoting genes are strongly expressed, and the mother's restraining genes are strong enough to balance them. In tigers, both effects are weaker. A liger inherits the strong push from a lion father with only the weak restraint of a tiger mother, so it keeps growing. A tigon inherits a weak push from a tiger father and a strong restraint from a lion mother, so its growth is held back. The phenotypic difference has an epigenetic origin: it comes from tags that survived the reset.

11Monozygotic twin studies

Monozygotic (identical) twins develop from one zygote that split, so they have identical genomes. Any difference between them therefore comes from the environment, or from chance, and not from their DNA sequence. That makes them ideal for studying the effect of the environment on gene expression.

A well-known study published in 2005 by Mario Fraga and colleagues compared identical twin pairs of different ages. Young twin pairs had very similar patterns of DNA methylation. Older pairs differed much more, and pairs who had spent more of their lives apart, with different lifestyles, tended to differ the most. Figure 6 shows the shape of that finding with invented data.

Read it as a Paper 1B question would ask you to. The difference in methylation between twins increases with the age of the pair, roughly steadily, from about 0.6 units at age 3 to about 4.6 at age 72. Because the twins' base sequences are identical, the growing difference must be in the tags, built up by different environments (and some chance) over a lifetime. The data show a correlation with age; they do not by themselves show which environmental factors are responsible.

12External factors that switch genes: a hormone and a biochemical

Cells change their pattern of expression in response to things outside them. The guide asks for one hormone and one biochemical.

A hormone: oestradiol. Oestradiol is a steroid hormone, made mainly in the ovaries. Figure 7 shows how it acts.

Oestradiol is lipid-soluble, so it diffuses through the plasma membrane of any cell. It has an effect only in target cells, which have a receptor protein for it. Oestradiol binds to the receptor, and the hormone–receptor complex, in the nucleus, binds to specific base sequences in the DNA near its target genes. There it acts as a transcription factor, activating transcription. In cells of the uterus lining, for example, the genes switched on cause the cells to grow and divide, which is how oestradiol thickens the endometrium in the menstrual cycle (D3.1). The hormone does not change the genes; it changes which are read.

A biochemical: lactose in E. coli. The bacterium E. coli can use the sugar lactose as a source of energy, but only if it makes a protein to take lactose into the cell and the enzyme lactase (strictly, β-galactosidase) to break it into glucose and galactose. Making them with no lactose about would waste energy and amino acids, so the genes are switched on only when lactose is present (Figure 8).

• No lactose. A repressor protein binds to a base sequence between the promoter and the genes, called the operator. It blocks RNA polymerase, so the genes are not transcribed.
• Lactose present. Lactose (strictly, a molecule the cell makes from it) binds to the repressor and changes its shape, so the repressor can no longer bind the operator. It comes off, RNA polymerase transcribes the genes, and the proteins for using lactose are made.
• Lactose used up. The repressor, now free of lactose, binds the operator again and transcription stops. Because bacterial mRNA is short-lived (section 4), production of the enzymes stops soon after.

Both examples use the same principle as section 3: a protein that binds a specific DNA sequence, whose binding is changed by a molecule from outside.