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.[31],{230} 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.{231} 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.
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.{232} 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.
Scientists studying the inflammatory response were among the first to show that DNA sequences can be co-opted to become enhancers when necessary. In this study, the researchers found that once the inflammatory stimulus was removed, the enhancers didn’t revert to being inert. Instead they continued to be enhancers, ready to up-regulate expression of the relevant genes again, if the cells re-encountered the inflammatory stimulus.{233} It’s probably not a coincidence that these enhancers are regulating genes involved in the response to foreign invaders. This memory in terms of gene expression can be very advantageous for fighting off an infection as efficiently and swiftly as possible.
One way in which genetic regions can maintain a memory even after a stimulus has gone away is via epigenetics. Epigenetic modifications can make a region easier to switch on again, by keeping the region in a fairly de-repressed state. In human terms, it’s like a doctor being on call rather than on holiday. In the example above, the researchers demonstrated that certain histone modifications remained at the ‘new’ enhancers after the inflammatory stimulus was removed, keeping them in a state of readiness.
We are generally starting to make a bit more progress at identifying enhancers by looking at epigenetic modifications, which are independent of the underlying DNA sequences. The modifications can be used as functional markers to show how a specific cell type uses a stretch of DNA. Researchers have also shown that these modifications can change in cancer, creating different patterns of gene expression that may contribute to the cellular alterations that lead to cancer.{234}
But even if we can find an epigenetic signature that indicates we may be looking at an enhancer, we still have another problem. We don’t know which protein-coding gene is influenced by a putative enhancer. The only way we can establish this is by disrupting an enhancer using genetic manipulations, and then assessing which genes are directly influenced by this change. This is because enhancer function is different from that of the promoter. Enhancers are not orientation-dependent — they act as enhancers no matter which way they are pointing. The other difference is even more dramatic — enhancers can be a very long way from the protein-coding gene whose expression they are influencing.
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The gene codes for a protein called MYC. MYC is also involved in a range of other cancers.