Junk DNA: A Journey Through the Dark Matter of the Genome (2 page)

But a great deal of our junk DNA is not simply structural. It doesn’t code for proteins, but it does code for a different type of molecule, called RNA. A large class of this junk DNA forms factories in the cell, helping to produce proteins. Other types of RNA molecules transport the raw material for protein production to the factory sites.

Other regions of junk DNA are genetic interlopers, derived from the genomes of viruses and other microorganisms that have integrated into human chromosomes, like genetic sleeper agents. These remnants of long-dead organisms carry potential dangers to the cell, the individual and sometimes even to wider populations. Mammalian cells have developed multiple mechanisms to keep these viral elements silent, but these systems can break down. When they do, the effects can range from relatively benign – changing the coat colour of a particular strain of mice – to much more dramatic, such as an increased risk of cancer.

A major role of junk DNA, only recognised in the main in the last few years, is to regulate gene expression. Sometimes this can have a huge and noticeable effect in an individual. One particular piece of junk DNA is absolutely vital for ensuring healthy gene expression patterns in female animals. Its effects are seen in a whole range of situations. A mundane example is the control of the colour patterns of tortoiseshell cats. At its most extreme, the same mechanism also explains why female identical twins may present with different symptoms of a genetically inherited disease. In some cases, this can be so extreme that one twin is severely affected with a life-threatening disorder while the other is completely healthy.

Thousands and thousands of regions of junk DNA are suspected to regulate networks of gene expression. They act like the stage directions for the genetic script, but directions of a complexity we could never envisage in the theatre. Forget about ‘Exit,
pursued by a bear’. These would be more along the lines of ‘If performing
Hamlet
in Vancouver and
The Tempest
in Perth, then put the stress on the fourth syllable of this line of
Macbeth
. Unless there’s an amateur production of
Richard III
in Mombasa and it’s raining in Quito.’

Researchers are only just beginning to unravel the subtleties and interconnections in the vast networks of junk DNA. The field is controversial. At one extreme we have scientists claiming experimental proof is lacking to support sometimes sweeping claims. At the other are those who feel there is a whole generation of scientists (if not more) trapped in an outdated model and unable to see or understand the new world order.

Part of the problem is that the systems we can use to probe the functions of junk DNA are still relatively underdeveloped. This can sometimes make it hard for researchers to use experimental approaches to test their hypotheses. We have only been working on this for a relatively short space of time. But sometimes we need to remember to step back from the lab bench and the machines that go ping. Experiments surround us every day, because nature and evolution have had billions of years to try out all sorts of changes. Even the brief geological moment that represents the emergence and spread of our own species has been sufficient time to create a greater range of experiments than those of us who wear lab coats could ever dream of testing. Consequently, throughout much of this book we will explore the darkness by using the torch of human genetics.

There are many ways to begin shining a light on the dark matter of our genome, so let’s start with an odd but unassailable fact to anchor us. Some genetic diseases are caused by mutations in junk DNA, and there is probably no better starting point for our journey into the hidden genomic universe than this.

1. Why Dark Matter Matters

Sometimes life seems to be cruel in the troubles it piles onto a family. Consider this example. A baby boy was born; let’s call him Daniel. He was strangely floppy at birth, and had trouble breathing unassisted. With intensive medical care Daniel survived and his muscle tone improved, allowing him to breathe unaided and to develop mobility. But as he grew older it became apparent that Daniel had pronounced learning disabilities that would hold him back throughout life.

His mother Sarah loved Daniel and cared for him every day. As she entered her mid-30s this became more difficult because Sarah developed strange symptoms. Her muscles became very stiff, to the extent that she would have trouble releasing items after grasping them. She had to give up her highly skilled part-time job as a ceramics restorer. Her muscles also began to waste away noticeably. Yet she found ways to cope. But when she was only 42 years old Sarah died suddenly from a cardiac arrhythmia, a catastrophic disruption in the electrical signals that keep the heart beating in a coordinated way.

It fell to Sarah’s mother, Janet, to look after Daniel. This was challenging for her, and not just because of her grandson’s difficulties and the grief she was suffering over the early death of her daughter. Janet had developed cataracts in her early 50s and as a consequence her vision wasn’t that great.

It seemed as if the family had suffered a very unfortunate combination of unrelated medical problems. But specialists began to notice something rather unusual. This pattern – cataracts in one individual, muscle stiffness and cardiac defects in their daughter
and floppy muscles and learning disabilities in the grandchildren – occurred in multiple families. These individual families lived all over the world and none of them were related to each other.

Scientists realised they were looking at a genetic disease. They named it myotonic dystrophy (myotonic means muscle tone, dystrophy means wasting). The condition occurred in every generation of an affected family. On average there was a one in two chance of a child being affected if their parent had the condition. Males and females were equally at risk and either could pass it on to their children.
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These inheritance characteristics are very typical of diseases caused by mutations in a single gene. A mutation is simply a change from the normal DNA sequence. We typically inherit two copies of every gene in our cells, one from our mother and one from our father. The pattern of inheritance in myotonic dystrophy, where the disease appears in each generation, is referred to as dominant. In dominant disorders, only one of the two copies of a gene carries the mutation. It is the copy inherited from the affected parent. This mutated gene is able to cause the disease even though the cells also contain a normal copy. The mutated gene somehow ‘dominates’ the action of the normal gene.

But myotonic dystrophy also had characteristics that were very different from a typical dominant disorder. For a start, dominant disorders don’t normally get worse as they are passed on from parent to child. There is no reason why they should, because the affected child inherits the same mutation as the affected parent. Patients with myotonic dystrophy also developed symptoms at earlier ages as the disorder was passed on down the generations, which again is unusual.

There was another way in which myotonic dystrophy was different from the normal genetic pattern. The severe congenital form of the disease, the one that affected Daniel, was only ever found in the children of affected mothers. Fathers never passed on this really severe form.

In the early 1990s a number of different research groups identified the genetic change that causes myotonic dystrophy. Fittingly for an unusual disease, it was a very unusual mutation. The myotonic dystrophy gene contains a small sequence of DNA that is repeated multiple times.
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The small sequence is made from three of the four ‘letters’ that make up the genetic alphabet used by DNA. In the myotonic dystrophy gene, this repeated sequence is formed by the letters C, T and G (the other letter in the genetic alphabet is A).

In people without the myotonic dystrophy mutation, there can be anything from five to around 30 copies of this CTG motif, one after the other. Children inherit the same number of repeats as their parents. But when the number of repeats gets larger, greater than 35 or thereabouts, the sequence becomes a bit unstable and may change in number when it is passed on from parent to child. Once it gets above 50 copies of the motif, the sequence becomes really unstable. When this happens, parents can pass on much bigger repeats to their children than they themselves possess. As the repeat length increases, the symptoms become more severe and are obvious at an earlier age. That’s why the disease gets worse as it passes down the generations, such as in the family that opened this chapter. It also became apparent that usually only mothers passed on the really big repeats, the ones that led to the severe congenital phenotype.

This ongoing expansion of a repeated sequence of DNA was a very unusual mutation mechanism. But the identification of the expansion that causes myotonic dystrophy shone a light on something even more unusual.

Knitting with DNA

Until quite recently, mutations in gene sequences were thought to be important not because of the change in the DNA itself but because of their downstream consequences. It’s a little like a mistake in a knitting pattern. The mistake doesn’t matter when it’s
just a notation on a piece of paper. The mistake only becomes a problem when you knit something and end up with a hole in your sweater or three sleeves on your cardigan because of the error in the knitting code.

A gene (the knitting pattern) ultimately codes for a protein (the sweater). It’s proteins that we think of as the molecules in our cells that do all the work. They carry out an enormous number of functions. These include the haemoglobin in our red blood cells that carries oxygen around our bodies. Another protein is insulin, which is released from the pancreas to encourage muscle cells to take in glucose. Thousands and thousands of other proteins carry out the dizzying range of functions that underlie life.

Proteins are made from building blocks called amino acids. Mutations generally change the sequence of these amino acids. Depending on the mutation and where it lies in the gene, this can lead to a number of consequences. The abnormal protein may carry out the wrong function in a cell, or may not be able to work at all.

But the myotonic dystrophy mutation doesn’t change the amino acid sequence. The mutated gene still codes for exactly the same protein. It was incredibly difficult to understand how the mutation led to a disease, when there was nothing wrong with the protein.

It would be tempting to write off the myotonic dystrophy mutation as some bizarre outlier with no impact for the majority of biological circumstances. That way we could put it to one side and forget about it. But it’s not alone.

Fragile X syndrome is the commonest form of inherited learning disability. Mothers don’t usually have any symptoms but they pass the condition on to their sons. The mothers carry the mutation but are not affected by it. Like myotonic dystrophy, this disorder is also caused by increases in the length of a three-letter sequence. In this case, the sequence is CCG. And just like myotonic dystrophy, this increase doesn’t change the sequence of the protein encoded by the Fragile X gene.

Friedreich’s ataxia is a form of progressive muscle wasting in which symptoms normally appear in late childhood or early adolescence. In contrast to myotonic dystrophy, the parents are usually unaffected by the disorder. Both the mother and father are carriers. Each parent possesses one normal and one abnormal copy of the relevant gene. But if a child inherits a mutated copy from each parent, the child develops the disease. Friedreich’s ataxia is also caused by an increase in a three-letter sequence, GAA in this case. And once again it doesn’t change the sequence of the protein encoded by the affected gene.
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These three genetic diseases, so different in their family histories, symptoms and inheritance patterns, nevertheless told scientists something quite consistent: there are mutations that can cause disease without changing the amino acid sequence of proteins.

An impossible disease

An even more startling discovery was made a few years later. There is another inherited wasting disorder in which the muscles of the face, shoulders, and upper arms gradually weaken and degenerate. The disease is named after this pattern – it’s called facioscapulohumeral muscular dystrophy. Perhaps unsurprisingly, this is usually shortened to FSHD. Symptoms are usually detectable by the time a patient is in their early 20s. Like myotonic dystrophy, the disease is dominant and passed from affected parent to child.
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Scientists spent years looking for the mutation that causes FSHD. Eventually, they tracked it down to a repeated DNA sequence. But in this case the mutation is very different from the three-letter repeats found in myotonic dystrophy, fragile X syndrome and Friedreich’s ataxia. It is a stretch of over 3,000 letters. We can call this a block. In people who don’t suffer from FSHD, there are from eleven to about 100 blocks, one after another. But patients with FSHD have a small number of blocks, ten at most.
That was unexpected. But the real shock for the researchers was that they really struggled to find a gene near the mutation.

Genetic diseases have given us great new insights into biology over the last hundred years or so. It’s easy to underestimate how hard-won some of that knowledge was. The identification of the mutations described here usually represented over a decade of work for significant numbers of people. It was entirely dependent on access to families who were willing to give blood samples and trace their family histories to help scientists home in on the key individuals to analyse.

The reason this kind of analysis was so difficult was because researchers were normally looking for a very small change in a very large landscape, hunting for a single specific acorn in a forest. This all became much easier from 2001 onwards, after the release of the human genome sequence. The genome is the entire sequence of DNA in our cells.