Junk DNA

A Journey Through the Dark Matter of the Genome

Nessa Carey

• Publisher: Icon Books
• Year: 2015
• Print ISBN:
  9781848318267
• eBook ISBN:
  9781848318274
• Topic: Biological Sciences
• Subtopic: Genetics & Genomics
• Index: Biological Sciences

From the author of the acclaimed The Epigenetics Revolution ('A book that would have had Darwin swooning' – Guardian) comes another thrilling exploration of the cutting edge of human science.For decades after the structure of DNA was identified, scientists focused purely on genes, the regions of the genome that contain codes for the production of proteins. Other regions – 98% of the human genome – were dismissed as 'junk'. But in recent years researchers have discovered that variations in this 'junk' DNA underlie many previously intractable diseases, and they can now generate new approaches to tackling them.Nessa Carey explores, for the first time for a general audience, the incredible story behind a controversy that has generated unusually vituperative public exchanges between scientists. She shows how junk DNA plays an important role in areas as diverse as genetic diseases, viral infections, sex determination in mammals, human biological complexity, disease treatments, even evolution itself – and reveals how we are only now truly unlocking its secrets, more than half a century after Crick and Watson won their Nobel prize for the discovery of the structure of DNA in 1962.

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.¹

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.² 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.³

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.⁴

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.

Because of the Human Genome Project, we know where all the genes are positioned relative to one another, and their sequences. This, together with enormous improvements in the technologies used to sequence DNA, has made it much faster and cheaper to find the mutations underlying even very rare genetic diseases.

But the completion of the human genome sequence has had impact far beyond identifying the mutations that cause disease. It’s changing many of our ideas about some of the most fundamental ideas that have held sway in biology since we first understood that DNA was our genetic material.

When considering how our cells work, almost every scientist over the last six decades has been focused on the impacts of proteins. But from the moment the human genome was sequenced, scientists have had to face a rather puzzling dilemma. If proteins are so all-important, why is only 2 per cent of our DNA devoted to coding for amino acids, the building blocks of proteins? What on earth is the other 98 per cent doing?

2. When Dark Matter Turns Very Dark Indeed

The astonishing percentage of the genome that didn’t code for proteins was a shock. But it was the scale of the phenomenon that was surprising, not the phenomenon itself. Scientists had known for many years that there were stretches of DNA that didn’t code for proteins. In fact, this was one of the first big surprises after the structure of DNA itself was revealed. But hardly anyone anticipated how important these regions would prove to be, nor that they would provide the explanation for certain genetic diseases.

At this point it’s worth looking in a little more detail at the building blocks of our genome. DNA is an alphabet, and a very simple one at that. It is formed of just four letters – A, C, G and T. These are also known as bases. But because our cells contain so much DNA, this simple alphabet carries an incredible amount of information. Humans inherit 3 billion of the bases that make up our genetic code from our mother, and a similar set from our father. Imagine DNA as a ladder, with each base representing a rung, and each rung being 25cm from the next. The ladder would stretch 75 million kilometres, roughly from earth to Mars (depending on the relative positions of their orbits on the day the ladder was put in place).

To think of it another way, the complete works of Shakespeare are reported to contain 3,695,990 letters.¹ This means we inherit the equivalent of just over 811 books the length of the Bard’s canon from mum and the same number from dad. That’s a lot of information.

If we extend our alphabet analogy a bit further, the DNA alphabet encodes words of just three letters each. Each three-letter word acts as the placeholder for a specific amino acid, the building blocks of proteins. A gene can be thought of as a sentence of three-letter words, which acts as the code for a sequence of amino acids forming a protein. This is summarised in Figure 2.1.

Each cell usually contains two copies of any given gene. One was inherited from the mother and one from the father. But although there are only two copies of each gene in a cell, that same cell can create thousands and thousands of the protein molecules encoded by a specific gene.

This is because there are two amplification mechanisms built into gene expression. The sequence of bases in the DNA doesn’t act as the direct template for the protein. Instead, the cell makes copies of the gene. These copies are very similar to the DNA gene itself, but not identical. They have a slightly different chemical composition and are known as RNA (ribonucleic acid, instead of the deoxyribonucleic acid in DNA). Another difference is that in RNA, the base T is replaced by the base U. DNA is formed of two strands joined together via pairs of bases. We could visualise this as looking a little like a railway track. The two rails are held together by a base on one rail linking to a base on the other, as if the bases were holding hands. They only link up in a set pattern. T holds hands with A, C holds hands with G. Because of this arrangement, we tend to refer to DNA in terms of base pairs. RNA is a single-stranded molecule, just one rail. The key differences between DNA and RNA are shown in Figure 2.2. A cell can make thousands of RNA copies of a DNA gene really quickly, and this is the first amplification step in gene expression.

Figure 2.1 The relationship between a gene and a protein. Each three-letter sequence in the gene codes for one building block in the protein.

The RNA copies of a gene are transported away from the DNA to a different part of the cell, called the cytoplasm. In this distinct region of the cell, the RNA molecules act as the placeholders for the amino acids that form a protein. Each RNA molecule can act as a template multiple times, and this introduces the second amplification step in gene expression. This is shown diagrammatically in Figure 2.3.

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Table of contents

• Copyright Page
• Dedication
• Acknowledgements
• Notes on Nomenclature
• An Introduction to Genomic Dark Matter
• 1. Why Dark Matter Matters
• 2. When Dark Matter Turns Very Dark Indeed
• 3. Where Did All the Genes Go?
• 4. Outstaying an Invitation
• 5. Everything Shrinks When We Get Old
• 6. Two is the Perfect Number
• 7. Painting with Junk
• 8. Playing the Long Game
• 9. Adding Colour to the Dark Matter
• 10. Why Parents Love Junk
• 11. Junk with a Mission
• 12. Switching It On, Turning It Up
• 13. No Man’s Land
• 14. Project ENCODE – Big Science Comes to Junk DNA
• 15. Headless Queens, Strange Cats and Portly Mice
• 16. Lost in Untranslation
• 17. Why LEGO is Better Than Airfix
• 18. Mini Can Be Mighty
• 19. The Drugs Do Work (Sometimes)
• 20. Some Light in the Darkness
• Notes
• Appendix: Human Diseases in which Junk DNA Has Been Implicated
• Index