The Language of the Genes

by Steve Jones

  Research on human mutation once involved frustration ameliorated by anecdotes like these. It has been turned on its head by the advance of molecular biology. In the old days, the 1980s, the only way to study it was to find a

  patient with an inherited disease and to try to work out what had gone wrong in the protein. The change in the DNA was quite unknown. This was as true for haemophilia as for any other gene. In fact, haemophilia seemed a rather simple error. Different patients showed rather different symptoms, but the mode of inheritance was simple and all seemed to share the same disease.

  Now whole sections of DNA from normal and haemophiliac families can be compared to show what has happened and, like the genetic map itself, things have got more complicated. Molecular biology has made geneticists' lives much less straightforward. First, uncontrollable bleeding is not one disease, but several. To make a clot is a complicated business that involves several steps. Proteins are arranged in a cascade which responds to the damage, produces and then mobilises the material needed and assembles it into a barrier. A dozen or more different genes scattered all over the DNA take part in the production line.

  Two are particularly likely to go wrong. One makes factor VIII in the clotting cascade. Errors in that gene lead to haemophilia A, which accounts for nine tenths of all cases of the disease. The other common type — haemophilia B — involves factor IX. In a rare form of the illness factor VII is at fault.

  Factor VIII is a protein of two thousand two hundred and thirty-two amino acids, with a gene larger than most — about 186,000 DNA bases long, which, on the scale from Land's End to John o'Groat's, makes it about a hundred yards long. Just a twentieth of its DNA codes for protein. The gene is divided into dozens of different functional sections separated by segments of uninformative sequence. Much of this extraneous material consists of multiple copies of the same two-letter message, a 'CA repeat'. There is even a lgene-within-a-gene' (which produces something quite different) in the factor VIII machinery.

  The haemophilia A mutation, which once appeared to be a simple change, is in fact complicated. All kinds of mistakes can happen. Nearly a thousand different errors have been found. Their virulence depends on what has gone wrong. Sometimes, just one important letter in the functional part of the structure has changed; usually a different letter in different haemophiliacs. The hits of the machinery which join the working pieces ot the product together are very susceptible to accidents of this kind. In more than a third of all patients part, or even the whole, of the factor VIII region has disappeared. A few haemophiliacs have suffered from the insertion of an extra length of DNA into the machinery which has hopped in from elsewhere.

  Once, the only way to measure the rate of new mutations to haemophilia (or any other inherited illness) was to count the sufferers, estimate the damage done to their chances of passing on the error and work out from this how often it must happen. Technology has changed everything. Now it is possible to compare the genes of haemophiliac boys with those of parents and grandparents to see when the mutation took place.

  If the mother of such a boy already has the haemophilia mutation on one of her two X chromosomes, then she must herself have inherited it and the damage must have occurred at some time in the past. If she has not, then her son's new genetic accident happened when the egg from which he developed was formed within her own body. In a survey of a British families with sons with haemophilia B (whose gene, that for Factor IX, is 33,000 bases long) many different mutations were found, most unique to one family. Eighty per cent of the mothers of affected boys had themselves inherited a mutation. However, in most cases the damaged gene was not present in their own father (the grandfather of the patient). In other words, the error in the DNA must have taken place when his grandparental sperm was being formed.

  A quick calculation of the number of new mutations against the size of the British population gives a rare for the haemophilia B gene of about eight in a million. The difference in the incidence of changes between grandfathers and their daughters suggest that the rate is nine rimes higher in males than in females. The sex difference is easy to explain. There are many more chances for things to go wrong in men (who — unlike women — produce their sex cells throughout life, rather than making a store of them early on, and hence have many more DNA replications in the germ line than do females). For some genes the rate of mutation among males is fifty times higher than in the opposite sex. Men, it seems, are the source of most of evolution's raw material.

  Most people with severe forms of haemophilia have each suffered a different genetic error. Such mistakes happen in a parent's sex cells and disappear at once because the child dies young. Those with milder disease often share the same change in their DNA; an error that took place long ago and has spread to many people. The shared mutation is a clue that these individuals descend from a common ancestor. The non-functional DNA in and around the haemophilia gene is full of changes which appear to have no effect at all and have passed down through hundreds of generations. Near the gene itself is a region with many repeats of the same message. The number of copies often goes up and down, but its high error rate seems to do no damage.

  All this hints that mutation is an active process, with plenty of churning round within the DNA. This new fluidity once alarmed geneticists as it violates the idea of gene as particle (admittedly a particle which sometimes makes mistakes) which used to be central to their lives. So powerful is the legacy of Mendel that his followers have sometimes been reluctant to accept results which do not fit. This is very true of some of the new and bizarre aspects of mutation.

  Scientists, in general, despise doctors, loi in.my years, physicians reported a strange genetical effect called 'anticipation*. The malign effects of some inherited disi-.isi's seemed to show themselves at a younger age with mcli generation that passed. The effect was named eighty years ago by an enthusiastic eugenical doctor called Mott. He thought that it presaged the inevitable degeneration of society: 'The law of anticipation of the insane represents… rotten twigs continually dropping off the tree of life.' Later geneticists were resistant to the idea and it disappeared from view. In fact it represents a new kind of mutation, an inherited error which gets worse as the generations succeed and which is now known to be common.

  The process is seen in a disease called the fragile X syndrome, the most important single cause of inborn mental impairment, with symptoms that range from mild to crippling. Many children diagnosed as autistic have in fact a minor form of this illness. At first sight its inheritance is odd, as in some families it is found in just one person, whereas others have dozens of affected members. Boys tend to suffer more damage than do girls, with mental retardation and, sometimes, a characteristic face with large ears, and heart problems.

  Although both males and females are affected, the gene is sex-linked. Males never pass it on to their sons, but girls whose mothers have it are carriers, and some may be affected. Fragile-X is one of the few genetic diseases in which the damage can be seen down the microscope, for near the end of every affected X chromosome is a small constriction which looks as if it might be about to break. About one woman in two hundred and fifty has one or other X chromosome damaged in this way. Many show no symptoms at all and neither do their children. Others have signs of the disease, as do their offspring, while a fraction albeit themselves normal may have children with the illness.

  The mutation is a multiplication of a three-letter DNA repeat — C, G and G — within a gene. Its protein helps form the connections made as the young brain begins to respond to experiences from the outside world. The damage is not in the coding section of the gene, but in its on-off switch. The mutation is flexible. Most people have thirty or fewer repeats, and some have as few as half a dozen. When the number creeps above fifty or so, children are in danger and may find it hard to speak or to read and as it rises over two hundred (and severely affected individuals have more than a thousand repeats) the full symptoms set in.

  The stra
ngest aspect of fragile X — and, we now know, of many other mutations — is that the number of repeats (and the amount of damage) changes from generation to generation. The daughter of a mother who has fragile X is more likely to have an affected child than was her own parent although (or so it seems) she has passed on exactly the same gene. Each generation, the number of copies changes, going up when it is transmitted through a female, but staying the same or decreasing when a man passes on the damaged chromosome.

  One form of muscular dystrophy also shows more virulent effects as the generations succeed. Again, a repeated sequence is involved. The pedigrees of one group of the children with the disease shows that all shared an ancestor who b'ved in the seventeenth century. He was healthy; as were, for two hundred years, his descendants; but suddenly some, distant relatives though they now are, began to suffer from dystrophy. More copies of a DNA repeat within the crucial gene had been made each generation. Once a critical number was reached the symptoms appear. Each generation, more and more appear, and the effects of the damaged gene become more severe as it passes down the lineage. Huntington's Disease, too, is duo to a repeal of the three DNA letters CACi. Each triplet codes Inr.1 single amino acid, which shoulders itself into tin* inuklle ul tin1 hunt-ingtin molecule. Some people liavi- li-wcr than uti copies, some more than a hundred. Once more tluui.ihoui thirty-five copies are made, the symptoms of the disease emerge, and the more repeats, the earlier they do so. Those with fifty are in danger of illness while still in their twenties. Half a dozen other diseases of the nervous and muscular system are due to such three-letter intruders. Why nerves should be so prone to them is not certain, although the tendency of such augmented proteins to form great clumps in the cell may have something to do with it.

  If the rate of mutation to haemophilia is taken as the norm, there must be about one new DNA change in a functional gene per five generations. This means ten million changes in functional genes per generation in Britain. The actual incidence may be even higher. Hormonal changes in women who are attempting to become pregnant show that eight out of ten fertilised eggs are lost. Many may carry new lethal mutations. Often, they involve the loss of all or part of a chromosome, and the incidence of such errors in still-born children is ten times that among those born alive.

  Each gene has its own mutation rate. The frequency varies more than a thousand times from gene to gene. Larger genes with more interspersed pieces of DNA go wrong more often than smaller ones, and certain combinations of bases change more readily than others. The short segments of repeated DNA outside the functional genes (such as those involved in the 'genetic fingerprint') have a high rate of error. As many as one person in ten may pass on a change. The rate of mutation itself has evolved, too, and is controlled by enzymes which can repair injured DNA. When these are themselves damaged it shoots up.

  Many things increase the mutation rate. Radiation, for example, can have a powerful effect. Plenty of mutations do not arise from the natural instability of the genes, but from damage inflicted from outside (as many of the early workers on radium, many of whom died of cancer, soon found out). Up to two thirds of the sperm cells of cancer patients who have been given large X-ray doses carry chromosomal changes. Evidence from other animals makes lower doses of radiation a real cause for concern, given the link between agents that cause mutations in sperm and egg and those that cause cancer. The acceptable dose for humans is set in part by research on mice (which seem to be more susceptible than we ourselves are) and there have been calls to have the limits increased; but nobody denies that radiation damages our genes. Sunlight, too, is harmful to cells and even an increase in temperature can increase the rate of error.

  The biggest avoidable source of radiation in Britain is radon gas, which leaks from granite. People who live in granite houses in Cornwall may be exposed to more excess radiation than are those who work in nuclear power stations (although their equivalents in the granite city of Aberdeen may in part reverse the effect as they wear the kilt, with its cooling influence). In the United States, houses built with radioactive sands in their foundations have been demolished as their occupants faced twenty times the average dose. In the UK, those at risk are advised to install fans to stop the build-up of gas. Other sources of radiation include the cosmic rays experienced during air travel and medical X-rays, but for most people these involve very small doses.

  Chemicals are much more important agents of genetic damage. The number of chromosome errors in nuclear power-station workers is ************ that of the general public, but the number in those employed in coal-fired stations is even higher because ****** noxious byproducts of burning coal. Bacteria are used to test a huge number of likely, and some unlikely, substances. Some, such as those once used in hair dyes, had a powerful effect and have been banned. Others, those in black pepper, in Earl Grey tea and in some pesticides, also cause mutations. Some of the most potent are quite natural. Plants produce many toxic chemicals for defence against insects and even lettuce, the epitome of a healthy diet, contains substances that cause mutations in mice. Almost half of all cancers may be influenced by the food we eat; and the vast majority of the pesticides — perhaps more than 99.9 % — in the Western diet are perfectly natural. Cynics argue that organic foods are more dangerous than food which has been sprayed because of the noxious chemicals found in the moulds which grow on them. Fresh fruits and vegetables reduce the rate, and some plants, such as broccoli and tomatoes, are filled with anti-mutagens that may help protect those who eat them.

  Mutations are the raw material of evolution. Life progresses; it does not decay, but every individual is mortal. As we grow old our machinery corrodes until at last it breaks down.

  Parr of this erosion comes from genetic changes within the body and part from the delayed effects of genes advantageous when young but harmful when old. To build an adult from a fertilised egg involves making hundreds of millions of cells, each with its own copy of the original message. The copying process is imperfect, and there are plenty of chances for mistakes. Even in adulthood most cells continue to divide. Red blood cells, for example, are renewed every four months or so. Kvcry minute everyone makes thousands of miles of DNA. As a result, huge numbers of mutations build up in body cells. Each individual is an evolving system whose identity changes from day to day.

  Some of these changes can lead to disaster. Many cancers result from genetic accidents. Indeed, some cancers look more and more like genetic diseases. They represent a decay of the genetic message and a loss of control by DNA of the cells in which it lives. Age is a reflection of the same process. As our bodies are in a constant fever of replication, the older we are the more divisions there have been and the more chance for error. The cells of a new-born baby are separated by just a few hundred divisions from the egg; but mine, as a fifty-something-year-old are distanced from it by thousands. My genes have had more chances to mutate than have those of a baby. What is worse, they are less effective at repairing the damage. The cells of old people even contain altered genes which make inappropriate proteins. Thus, many aged Europeans have small amounts of sickle-cell haemoglobin in their blood. This gene is normally found in Africans but has, in their case, appeared as a new mutation within their elderly bodies.

  Ageing accelerates with age. The lowest risk of death is at about the age of twelve — just before puberty. After that, the rate doubles every eight years or so, giving a seventy-six-year old about a two hundred and fifty times greater chance of dying than a teenager. The power of accelerated decay is impressive. If the death rate stayed at that of a twelve-year-old, most people would live to a thousand and there would be a small but noticeable proportion of people around who were born in the last Ice Age. Unfortunately, our obsolescence is such that even centenarians are rare. All this helps to explain why cancer is a disease of the old; so much so that even if the disease were eliminated altogether lite expectancy would go up by only about four years. The biological identity crisis which we define as old age and which
is solved by deaih happens when the genetic message becomes so degenerate th.u its instructions no longer make sense. The rate ol ageing is programmed. Mouse cells in culture stop dividing after about four years, while human cells can carry on for almost a century.

  Parts of the message disappear with time. DNA is packaged into chromosomes. Each has a specialised length of DNA at its end that marks the point at which the DNA-duplication machinery stops and loops back on itself, rather like the crimp at the ends of shoelaces that stops them from fraying. This gets shorter with age. In a baby it is about twenty thousand letters long, while in a sixty year-old it is less than half that length. Cells from tumours have lost even more DNA from the chromosome ends. About forty letters are dropped from this section of the message each time a cell divides, so that an old body works from an imperfect instruction manual, full of typographic errors. The same happens to mitochondria! genes, which are shot full of holes as rhe years conrinue their inexorable progress.