As Figure 2.4 shows, a protein is encoded from modular blocks of information. This modularity gives the cell a lot of flexibility in how it processes the RNA. It can vary the modules which it joins together from a messenger RNA molecule, creating a range of final messengers that code for related but non-identical proteins. This is shown in Figure 2.5.
Figure 2.4 In step 1, DNA is copied into RNA. In step 2, the RNA is processed so that only the amino acid-coding regions, denoted by boxes containing letters, are joined together. The intervening junk regions are removed from the mature messenger RNA molecule.
The bits of gobbledegook between the parts of a gene that code for amino acids were originally considered to be nothing but nonsense or rubbish. They were referred to as junk or garbage DNA, and pretty much dismissed as irrelevant. As mentioned earlier, from here on in, we’ll use the term ‘junk’ to denote any DNA that doesn’t code for protein.
Figure 2.5 An RNA molecule can be processed in different ways. As a result, different amino acid-coding regions can be joined together. This allows different versions of a protein molecule to be produced from one original DNA gene.
But we now know that they can have a very big impact. In Friedreich’s ataxia, which we met in Chapter 1, the disorder is caused by an abnormally expanded stretch of GAA repeats in one of the junk regions, between two sections that encode amino acids. This raised the perfectly reasonable question — if the mutation doesn’t affect the amino acid sequence, why do people with this mutation develop such debilitating symptoms?
The mutation in the Friedreich’s ataxia gene occurs in the junk region between the first two amino acid-coding regions. In Figure 2.5, this would be between regions ‘D’ and ‘E’. A normal gene contains from five to 30 GAA repeats but a mutated gene contains from 70 up to 1,000 repeated GAA motifs.{6} Researchers showed that when cells contained this expanded repeat, they stopped producing the messenger RNA encoded by the gene. Because they didn’t make messenger RNA, they couldn’t make the protein either. If you don’t send out the copies of the knitting patterns, the soldiers don’t get socks.
In fact, the cells didn’t even make the long, unprocessed RNA copy of the gene.{7} The big GAA expansion acts as a ‘sticky’ region, which prevents good copying of the DNA. It’s analogous to trying to photocopy a 50-page document, when pages four to twelve have been glued together. They won’t feed into the copier, and the process grinds to a halt, for that particular document. In the case of the Friedreich’s ataxia gene, no copying means no RNA, which means no protein.
It’s not completely clear why lack of the protein encoded by the Friedreich’s ataxia gene causes the disease symptoms. The protein seems to be involved in preventing iron overload in the parts of the cell that generate energy.{8} When a cell fails to produce the protein, the iron rises to toxic levels. Some cell types seem to be more sensitive than others to iron levels, and these include the ones affected in the disease.
A related but different mechanism accounts for Fragile X syndrome, the form of learning disability we encountered in Chapter 1. The mutation in Fragile X syndrome is the expansion of a CCG three-base repeat. Similarly to the Friedreich’s ataxia mutation, there are usually fifteen to 65 copies of the repeat on a normal chromosome. On a chromosome carrying the Fragile X mutation there are from around 200 to several thousand copies.{9},{10} But the expansion lies in a different part of the gene in Fragile X compared with Friedreich’s ataxia. The mutation is found before the first amino acid-coding region, essentially in the junk to the left of block ‘D’ in Figure 2.5. When the junk repeat gets very large, no messenger RNA is produced, and consequently there is no protein produced from this gene.{11}
The function of the Fragile X protein is to carry lots of different RNA molecules around in the cell. This gets them to the correct locations, influences how these RNAs are processed and how they generate proteins. If there is no Fragile X protein, the other RNA molecules aren’t properly regulated, and this plays havoc with the normal functioning of the cell.{12} For reasons that aren’t clear, the neurons in the brain seem particularly sensitive to this effect, hence the learning disability in this disorder.
An everyday analogy may help with visualising this. In the UK, a relatively small amount of snow can incapacitate the transport networks. The snow covers the roads and the railway tracks, preventing cars and trains from moving. When this happens, people can’t get to their place of work and this creates all sorts of problems. Schools can’t open, deliveries aren’t made, banks can’t dispense cash, etc. One starting event — the snow — has all sorts of consequences because it ruins the transport systems in society. A similar thing happens in Fragile X syndrome. Just like snow on the roads and railway tracks, the effect of the mutation is to mess up a transport system in the cell, with multiple knock-on effects.
Switching off the expression of a specific gene is the key step in the pathology of both Friedreich’s ataxia and Fragile X syndrome. Support for this hypothesis has been provided by very rare cases of both disorders. There are small numbers of patients where the repeat in the junk regions is of the same small size found in most healthy people. In these patients, there are mutations that change the sequence in the amino acid-coding regions. These particular amino acid sequence changes actually make it impossible for the cell to produce the protein. In other words, it doesn’t matter why the protein isn’t expressed. If it’s not expressed, the patients have the symptoms.
So far it might seem like there’s a nice straightforward theme emerging. We could speculate that expansions in the junk regions are only important because they create abnormal DNA. This DNA isn’t handled properly by the cells, resulting in a lack of specific important proteins. We could suggest that normally these junk regions are unimportant, with no significant role in the cell.
But there is something that argues against this. The normal range of repeats in both the Fragile X and Friedreich’s ataxia genes is found in all human populations, and has been retained throughout human evolution. If these regions were completely nonsensical we would expect them to have changed randomly over time, but they haven’t. This suggests that the normal repeats have some function.
But the real grit in this genetic oyster comes from myotonic dystrophy, the disorder that opened Chapter 1. The myotonic dystrophy expansion gets bigger as it passes down the generations. A parent’s chromosome may contain the sequence CTG repeated 100 times, one after another. But when they pass this on to their child, this may have expanded so the child’s chromosome has the sequence CTG repeated 500 times. As the number of CTG repeats gets larger, the disease becomes more and more severe. This isn’t what we would expect if the expansion just switches off the nearby gene. All cells of someone with myotonic dystrophy contain two copies of the gene. One carries the normal number of repeats, and the other carries the expanded number. So, one copy of the gene should always be producing the normal amount of protein. That would mean that the most the overall levels of the protein should drop would be about 50 per cent.
We could hypothesise that as the repeat gets longer there is progressively less gene expression from the mutant version of the gene. This could lead to a gradual decline in the amount of protein produced overall. This could range from a 1 per cent drop overall for fairly small expansions, to a 50 per cent final decrease for the large ones. This could lead to different symptoms. The problem is that there aren’t really any inherited genetic diseases like this. We just don’t see disorders where very minor variations in expression have such a big effect (all patients with the expansion develop symptoms), but with such fine tuning between patients (the symptoms becoming more extreme as the expansion lengthens).