Junk DNA: A Journey Through the Dark Matter of the Genome (22 page)

We depend on our invaders

It’s even odder to think that each one of us has been colonised by organisms that probably developed around the same time our ancestors were diverging from the forebears of modern bacteria. ‘Colonised’ is really an understatement. Our entire survival and that of every other multicellular organism on this planet from grass to zebras and from whales to worms relies on this colonisation. It’s even true of the yeast we depend on for bread and beer.

Billions of years ago the cells of our earliest ancestors were invaded by tiny organisms. At this stage there probably weren’t any organisms more than four cells in size and the four cells would have been pretty non-specialist. Instead of warring against each other, these cells and their tiny invaders reached a compromise. Each benefitted from the compromise and so a beautiful friendship, lasting billions of years, was born.

These tiny organisms evolved into critical components of our cells called mitochondria. The mitochondria reside in the cytoplasm and are little power generators. They are the sub-cellular organelles that produce the energy we need to power all of our standard functions. It’s the mitochondria that have allowed us to make use of oxygen to create useful energy from food sources. Without them, we would be smelly little four-celled nobodies with hardly enough energy to do anything useful.

One of the reasons we are confident that mitochondria are the descendants of these once free-living organisms is that they have their own genome. It’s much smaller than the ‘proper’ human genome that is found in the nucleus. It is just over 16,500 base pairs in length compared with the 3 billion base pairs of the nuclear genome, and unlike our chromosomes it is circular.
The mitochondrial genome only codes for 37 genes. Remarkably, well over half of these don’t code for proteins. Twenty-two of them encode mitochondrial tRNA molecules
¹⁰
and two encode mitochondrial rRNA molecules. This allows the mitochondria to produce ribosomes, and to use these to create proteins from the other genes in its DNA.
^c
,
11

This seems a very risky strategy in evolutionary terms. Mitochondrial function is critical for life and ribosomal function is absolutely critical to mitochondrial function. So why have such an important process with no safety net of extra copies of the ribosomal genes in our power generators?

We can get away with this because mitochondrial DNA isn’t inherited in the same way as nuclear DNA. In the nucleus we inherit one set of chromosomes from each parent. But mitochondrial inheritance is different. We only inherit our mitochondria from our mother. This would seem to make for an even riskier scenario because it means if we inherit a mutant mitochondrial gene from our mother, there is no chance of a back-up normal gene from dad.

But there is (of course) a complication. We don’t just inherit one mitochondrion from our mother, we inherit hundreds of thousands, maybe even a million. And they aren’t all the same genetically, because they haven’t all originated from one mitochondrion in a previous cell. Every time a cell divides, the mitochondria also divide and are passed on to daughter cells. Even if some of these mitochondria have developed mutations, there will be plenty of other mitochondria in the cell that are fine.

That’s not to say that problems never develop, and many of those that do have been reported to be in the tRNA genes on the mitochondrial DNA. These include conditions with muscle weakness and wasting;
¹²
hearing loss;
¹³
hypertension
¹⁴
and cardiac problems.
¹⁵
But the symptoms may vary a lot from patient to patient, even within the same family. The most likely reason for this is because symptoms may not develop until the percentage of mutant mitochondria in a tissue reaches a threshold. This may not be until relatively late in life, as a consequence of random unequal distribution of ‘good’ and ‘bad’ mitochondria when a cell divides.

If all of this hasn’t been enough to demonstrate that RNA is not just some poor relation of DNA or an inferior species compared with proteins, consider this. Despite DNA being the poster child for biology, all life on earth may have originated not with DNA but with RNA.

In the beginning was the RNA (possibly)

DNA is a great molecule. It stores a lot of information, and because of its double-stranded nature it’s easy to copy and to maintain the sequence stably. But if we try to think back billions of years, to when life began to develop, it’s hard to see how it could happen based on a DNA genome.

That’s because although DNA is fantastic at storing information, it’s no use in terms of creating something from that information, not even another copy of itself. DNA can never function as an enzyme. Because of this, it can’t make copies of itself so how could it have been the starting genetic material? It is always reliant on proteins to do its bidding.

But if we look at rRNA, a molecule which has received very little by way of the spotlight even among most scientists, there’s a bit of a eureka moment. rRNA contains sequence information
but it is also an enzyme. This raises the possibility that RNA could have had a range of enzymatic activities in the past, and this could have led to the evolutionary development of self-sustaining and self-propagating genetic information.

In 2009 researchers published extraordinary work in which they generated such a system. They genetically created two RNA molecules both of which could act as enzymes. When they mixed these molecules in the lab, and gave them the raw materials they needed, including single RNA bases, the two molecules made copies of each other. They used the existing RNA sequences as the templates for the new molecules, creating perfect copies. As long as they were supplied with the necessary raw materials, they made more and more copies. The system became self-sustaining. The researchers went even further by mixing higher numbers of different RNA molecules, each of which had enzymatic activity. When they activated the experiment, they found that two sequences would rapidly outnumber all the others. Essentially, the system was not only self-sustaining, it was also self-selecting because the most efficient pairs of RNA molecules would recreate each other far more rapidly than any of the other pairings.
¹⁶
Very recently, scientists have even succeeded in creating a type of enzymatic RNA that will generate copies of itself.
¹⁷

An expression that is still heard in the UK is ‘Where there’s muck, there’s brass’, meaning that where there is dirt or rubbish, there’s money. Maybe where there’s junk, there’s life.

Footnotes

^a
The ones involved in the process described here are from a specific class called snoRNA C/D box.

^b
The methyltransferase enzyme required for this process is called fibrillarin, which works in a complex with three other proteins and the snoRNA.

^c
Mitochondria use lots of other proteins for their biochemical processes, but most of them they import from the cell cytoplasm. The ones that are uniquely encoded in the mitochondria are all involved in a process called the electron transport chain, which takes place within mitochondria themselves. This process is essential for life, as it is how we generate storable usable energy to power our cells.

12. Switching It On, Turning It Up

With a mere $1,700,000 price tag, the Bugatti Veyron is the world’s most expensive production road car. It’s hard to be sure what the cheapest car is, although the Dacia Sandero probably has a good claim to this honour, at about 1 per cent of the cost of the Veyron. But both cars have a number of things in common, and one of these is that each needs to be switched on before you can go anywhere. If you don’t activate the engine systems, nothing will happen.

Our protein-coding genes are the same. Unless they are activated and copied into messenger RNA, they do nothing. They are simply inert stretches of DNA, just as a Veyron is a stationary hunk of metal and accessories until you hit the ignition. Switching on a gene is dependent on a region of junk DNA called the promoter. There is a promoter at the beginning of every protein-coding gene.

If we think in terms of a traditional car, the promoter is the slot for the ignition key. The key is represented by a complex of proteins that bind to a promoter. These are known as transcription factors. These transcription factors in turn bind the enzyme that creates the messenger RNA copies of the gene. This sequence of events drives the expression of the gene.

It’s relatively easy to identify promoters by analysing DNA sequences. Promoters always occur just in front of the protein-coding regions. They also tend to contain particular DNA sequence motifs. This is because transcription factors are a special type of protein that can identify and bind to specific DNA sequences. If we analyse the epigenetic modifications at promoters, we also find
consistent patterns emerging. Promoters have particular sets of epigenetic modifications, depending on whether or not the gene is active in a cell. The epigenetic modifications are important regulators of transcription factor binding. Some modifications attract transcription factors and associated enzymes and this results in gene expression. Others prevent the factors from binding and make it really difficult to switch a gene on.

Researchers can copy a promoter and reinsert it elsewhere in the genome, or even into another organism. These kinds of experiments confirmed that promoters usually function immediately in front of a gene. They also showed that the promoter needs to be ‘pointing’ in the right direction. If you insert a promoter sequence in front of a gene, but the wrong way round, it doesn’t work. It would be like inserting a key the wrong way round into the ignition. Promoters are orientation-dependent in their activity.

Promoters can’t really tell which gene they are controlling. They switch on the nearest gene, if they are close enough and pointing in the correct direction. This allows researchers to use promoters to drive expression of any gene in which they are interested. That can be very handy experimentally but it can also have a sinister side. In some cancers, the basic molecular problem is that the DNA in the chromosomes becomes mixed up and a promoter starts driving expression of the wrong gene. In the case of cancer, the gene is one that pushes forward the rate at which cells proliferate. The first to be discovered, and probably still the most famous example of this, occurs in the blood cancer known as Burkitt’s lymphoma. This is a cancer type we already met briefly, in our discussion of good genes in bad neighbourhoods (
see page 48
). In this condition, a strong promoter on chromosome 14 gets placed upstream of a gene on chromosome 8 that codes for a protein that can really push cell proliferation forwards.
^a
1
The consequences
are potentially catastrophic. The white blood cells carrying this rearrangement grow and divide really rapidly, and start to predominate in the blood stream. If detected early in the disease’s progression, over half of the patients with this cancer can be cured, although this requires aggressive chemotherapy.
²
For patients with a late diagnosis, decline and death may be appallingly rapid and measured in weeks.

In healthy tissues, different promoters may only be active in certain cell types, usually because they rely on transcription factors that are expressed in some cell types and not others. Promoters also have different strengths. By this we mean that strong promoters switch on genes very aggressively, resulting in lots of copies of messenger RNA from the protein-coding gene. This is what happens in Burkitt’s lymphoma. Weak promoters drive much less dramatic levels of gene expression. The strength of the promoter is dependent on multiple factors in mammalian cells, including the DNA sequence but also the transcription factors available, the epigenetic modifications and probably a host of other variables that we haven’t yet identified.

Driving a graduated response

Any given promoter in any given cell type drives a relatively constant level of gene expression, at least in experimental systems. Yet gene expression under normal circumstances is not a binary phenomenon. Genes may be expressed to varying degrees. It’s analogous to being able to drive a car at any rate from one mile per hour up to its top speed of over 250mph for the Veyron, or rather less than half of that for the Sandero. In cells, this flexibility is dependent on a number of interacting processes including epigenetics. But it is also influenced by another region of junk DNA. This region is known as the enhancer.

Compared with promoters, enhancers are very fuzzy. They are
usually a few hundred base pairs in length but it’s almost impossible to identify them simply by analysing the DNA sequence.
³
They are just too variable. The identification of enhancer regions is also made more complex because they aren’t necessarily functional all the time. For example, a set of latent enhancers has been identified which only start to regulate gene expression once they themselves have been somehow activated by a stimulus. This showed that enhancers may not be pre-determined in the genome sequence.

An inflammatory response is the first line of defence to an assault on the body, such as a bacterial infection. The cells near the invasion site release chemicals and signalling molecules that create a really hostile environment for the invaders. It’s as if triggering a burglar alarm in a house initiated a downpouring of hot, foul-smelling liquid into the room that had been breached.