Wednesday, April 10, 2013

The human machine: setting the dials




The previous post in this series can be found here.

It may seem sometimes that nature is a cruel mistress. We are all dealt our hand from the moment of  liaison between our lucky gold-medalist sperm and its egg companion. We are short or tall, broad or skinny, strong or weak because of the haphazard combination of genes that we wind up with, and that should be the end of the matter. Yet, as any seasoned card player will tell you, it is not the hand that matters, but how you play it! This, it turns out, also holds true when it comes to our genetic makeup - we can only play the cards we're dealt, but we don't have to play them all and can rely on some more heavily than others. In this post I'm going to discuss the ways in which DNA is organised and its activity regulated, and how this regulation is a dynamic, ever-changing process with cards moving in and out of play all the time. What's more, we'll explore the ways in which we can all consciously take control of our own DNA to help promote good health and long life!

Esoteric instructions laid bare

Most people are familiar with the concept of DNA - the instruction manual for every component that makes you you - but most are perhaps unaware of how DNA is actually organised within your cells. The importance of DNA has led to it achieving a somewhat mystical image in the public perception: a magical substance that sits inside you with omnipotent influence over every aspect of your construction. This perhaps might lead a layperson to think that we don't really understand how genes work, a perception that is encouraged by the abstract way in which the link between genetics and diseases is reported in the mainstream media. However, this impression is entirely false; we understand very well how genes work: DNA acts as a template for the generation of information-encoding molecules called RNA, which are in turn used as templates to make proteins, which then make everything else. This is called the 'central dogma' of molecular biology, which I'm not going to go into in detail now but have touched upon more thoroughly in a previous post: here.

The mystification of genetics in the mainstream perception can encourage people to forget that DNA is just a molecule, with as much physical presence and chemical potential as any other molecule in your body. As such, its supreme influence over you is dependent on pure chemistry and physics. The most obvious consequence of its being a physical entity is that it needs, in some way, to be arranged and organised. DNA exists within the nuclei of your cells, but it doesn't just float around randomly and aimlessly - its organisation is tightly regulated. First of all, DNA exists as a number of different strands, each its own molecule. These are chromosomes, humans have 46 in each cell nucleus, 23 of which you inherit from your mother, and 23 from your father. The classic image of a chromosome is the tightly packed 'X' shape like those in the image below, but actually this is a comparatively rare structure in the life of DNA as this only forms as the cell is dividing.

Chromosomes seen under an electron microscope. Image is from http://trynerdy.com/?p=145.
In non-dividing cells, DNA does not exist in the cosily familiar 'X' shapes, but instead spreads out to fill the whole nucleus. This is out of physical necessity - the DNA in compact chromosomes like those above is simply too tightly packed to do anything! Proteins and other molecules that need to interact with the DNA in order for its influence to be felt just can't get to it because there's no space. If the DNA spreads out to fill the nucleus, however, there's plenty of room for manoeuvre. Nonetheless, this organisation is not random and is still highly organised. DNA never exists on its own in a live cell - it is always bound to proteins called histones, which act as a scaffold around which DNA is able to wind, like a string around a ball. There is about 1.8m of DNA in each cell of your body, but once wound around histones it has a length of only around 0.09mm - a pretty significant space saving measure! Each little ball of DNA and histone is called a nucleosome; it is held together by attraction between the negatively charged backbone of the DNA and the positively charged side chains of the amino acids making up the histone proteins. 

DNA wrapped around histone proteins to form nucleosomes. Adapted from Muthurajan et al. (2004) EMBO J. 2004; 23(2):260-71
Going up another level of scale now: these nucleosomes can be organised in different ways depending on the intended activity of the DNA therein. These complex organisations of nucleosomes are collectively known as chromatin, which can broadly be split into two forms: heterochromatin and euchromatin. The difference between hetero- and euchromatin is basically how tightly they are packaged. In euchromatin the nucleosomes are arranged much as in the image above - loosely packed and with short free segments of DNA in between. This is known as the 'beads on a string' form of DNA for hopefully obvious reasons. Heterochromatin, on the other hand, is far more tightly packed - nucleosomes are very closely associated and there is very little DNA between individual nucleosomes. This is called the '30nm fibre' because it is 30nm in diameter, and is quite similar to the kind of fibres that pack together the form the X-shaped chromosomes mentioned earlier.
DNA's many forms. Euchromatin corresponds to the 'beads on a string', whilst heterochromatin is the fibre of packed nucleosomes. Image from http://dellairelab.medicine.dal.ca/research.html.

These two types of DNA packing mean that all genes are not created equally! Heterochromatin and euchromatin have very different levels of activity - euchromatin's loose structure allows easy access to the machinery that relay DNA's instructions and so genes in this region are fairly active; whereas the inaccessible structure of heterochromatin means genes in these areas are pretty silent. Segregating areas of the genome into more and less active areas is important in the regulation of gene expression, as some genes simply need to be more or less active than others in order for the cell to function properly. 

A classic example of this is X-inactivation. As you may be aware, 2 out of our 46 chromosomes are the sex chromosomes: women have XX and men have XY. The Y chromosome is entirely distinct from the X chromosome, which means that for every gene that exists on the X chromosome women will have twice as many copies per cell. This presents a problem because it just isn't feasible for male and female cells to have a two-fold difference in gene activity for the important genes on the X chromosome - it would require differences in the wiring of the cell that are just too extreme to exist between members of the same species. So, either males need to ramp up activity from their solitary X chromosome, or females need to halve activity from theirs. In the case of mammals (including us) each cell in a female randomly chooses one X to exist as euchromatin (and so have high activity) and one to become heterochromatin (and so have low activity), thereby redressing the balance between males and females. So, if you are a woman, half of the cells in your body are working off genes from the X chromosome you got from your mother, whereas the other half are working of those from your father. This is particularly apparent in certain types of cat known as tortoiseshell or calico cats, in which one of the genes responsible for coat colour is contained on the X chromosome. So, if a female cat inherited different copies of this gene from each parent, then the colour varies at different areas of the coat because in some it will be the colour from the father, and in others the colour from the mother, giving an attractive speckled effect. This is why the first cat to be cloned (called CC for 'Copy Cat'), which was a female calico, looked pretty much completely different to the cat from which she was cloned despite having 100% identical DNA. 

X-inactivation is responsible for the attractive coats of calico cats. Image from Wikipaedia.
Reading the genetic code in many ways

The example of CC the cat touches upon a vitally important concept of genetics, that activity from genes is not fixed and is in fact quite malleable. Importantly, this is not limited to lifelong inherited traits such as cat coat colour, but is actually able to be influenced during the lifetime of an organism. Basically speaking, your genes can be switched on or off, or their activity decreased or increased by factors that occur during your lifetime, such as lifestyle, drugs, or hormonal changes. It is difficult to overstate just how ground-breaking an idea this was when it was first discovered: for the first time it seemed that we weren't limited by our pre-written genetic fate - we could be masters of our own destiny as long as we understood how to influence the system. The idea of nature and nurture being mutually exclusive was dismissed - we now knew that nature could be influenced by nurture.

The concept of a system of gene regulation by non-genetic means is called epigenetics. Segregating DNA into hetero- and euchromatin is a fairly rigid epigenetic mechanism that doesn't alter much throughout your lifetime. Instead, it is the behaviour of the associated histone proteins that can influence the activity of your DNA in a manner that alters according to environmental factors. This is possible because histones are able to undergo at least 60 different modifications to their amino acid building blocks whilst they are still bound to DNA. These modifications involve the addition or removal of chemical groups from the histone proteins, which acts as a code for how active any associated genes will be. Moreover, this is combined with chemical modifications made directly to the DNA itself that can further influence gene activity. Broadly speaking, each modification either promotes or inhibits activity from the DNA bound to that histone. For example, a methyl group is a chemical group comprised of one carbon atom attached to three hydrogen atoms - addition of three methyl groups on the lysine 4 or lysine 36 amino acids on histone protein 3 causes an increase in gene activity in that area, whereas adding three methyl groups to lysines 3 or 29 on the same protein causes a decrease in gene activity. The overall activity from any individual gene depends on the balance between pro- and anti-activatory histone modifications.

Histone proteins and the potential modifications that can occur. Each type of modification (acetylation, methylation etc.) represents that addition of a specific chemical group to amino acids in the histone proteins.Figure adapted from http://www.integratedhealthcare.eu/1/en/histones_and_chromatin/1497/.
The ways in which these modifications influence gene activity are extremely complex but they all work by either increasing or decreasing interactions between the histones and either the DNA itself or the machinery involved in relaying its activity. The modifications themselves are made by histone-modifying enzymes that exist within the nucleus either chopping off or sticking on the modifications as required. It is the activity of these enzymes that is sensitive to external factors: for example, a cell may be under some form of stress that necessitates the activity of a specific repair gene, so signalling pathways within the cell cause the activation of histone modifiers and then target them to the target gene in order to turn it on and save the cell. The system is highly complex and highly dynamic, meaning that the instructions that make you you can be read in an infinite number of ways. This is why identical twins are never fully identical even though they are genetically equivalent.  Importantly, though, it also means that if you are genetically predisposed to a certain medical condition, heart failure, hypertension, hereditary cancers etc., there is a chance that epigenetic alterations to your DNA may either spare you or condemn you by influencing how significant your genetic predisposition becomes. So, if we can understand and influence the code governing histone modifications then we may be able to change all of our genetic fates for the better.

This is very well exemplified by the link between epigenetics and cancer. Many cancers have been observed to rewrite the epigenetic coding within their DNA and so influence their growth. For example, a number of cancers have been found to block the activity of histone modifying enzymes responsible for adding activity-promoting acetyl groups to histone protein 3 bound to genes involved in suppressing cell growth, with the effect that these genes are now less active and so the cancer is freer to grow and multiply. Indeed, the projected outcome of patients diagnosed with some cancers is intimately linked the to epigenetic changes that have been found to occur in their cancerous cells. It is by no means limited to cancer, though, several developmental and immunological disorders have also been linked to epigenetic changes in the DNA of the affected patients. The more we learn about the code of histone modification, the more chance we have of being able to influence it in a clinical setting, both for therapeutic means such as in the treatment of cancer, but also as a prophylactic method of reducing the risk of some diseases in at-risk individuals. This is a big topic in molecular biology at the moment, and a huge amount of resources are being poured into unravelling its secrets.
Number of papers published with the keywords 'disease' and 'epigenetics' in the last 30 years - the exponential growth reflects the increased importance of epigenetic understanding to disease treatment. Source: http://www.sciencedirect.com/science/article/pii/S1357272508003889#.
Being master of your own destiny

I promised you at the outset that I was going to explain how you could take control of your own genetic fate and so give yourself the best chance of a long and healthy life. It may seem, so far, that the advances that I've mentioned will help those suffering from a number of terrible diseases, but will do little for us healthy folks whose genes haven't turned against us. Well it's certainly true that the majority of data collected is on the role of epigenetics in disease for the simple reasons that people with diseases need the most help and attention, and that they are easily classifiable into different groups (bowel cancer, lung cancer etc.) whilst healthy individuals can't be classified according to presented symptoms. Nonetheless, evidence is slowly building that some lifestyle changes can be beneficial to long-term health in part due to the epigenetic changes that they bring about. Not only that, but there are some indications that these changes may not be limited to your own lifespan but may also extend to those of your children by altering the epigenetics in the very first cell that grows into your bouncing bundle of joy!

Perhaps unsurprisingly, the best lifestyle choices that you can make to help improve your genetic lot are broadly the same ones that you should be making to improve your health in general anyway: i.e. exercise regularly, eat well, don't smoke etc. It seems that the beneficial outcomes of these behavioural choices are not limited to physiological effects such as strengthening the heart, but also influence long-term gene expression that may help to make you a healthier person throughout your entire life, as well as helping to stave off conditions such as cancer. For example, a report in Cell Metabolism has revealed that acute exercise has epigenetic effects on the expression of several genes involved with sugar metabolism that may help to prevent diabetes or improve the prognosis of diabetic patients. Current thinking is that the transient changes in gene expression brought about by lifestyle factors such as exercise may over time cause a stable reorganisation of epigenetic regulation that affords long-term health benefits that may well outweigh any genetic disadvantage that an individual may have. So the next time you consider slacking off training, remember that the effects may stay with you for the rest of your life! 

As far as your children go, well it had been thought for some time that epigenetic markers were erased in primordial gene cells (which eventually develop into sperm and eggs) so that each individual would get a clean slate, and it is certainly true that this is the case for the majority of epigenetic modifications. However, recent research has indicated that about 1% of genes manage to hang onto their modifications in the form of methyl groups directly added to the DNA itself. It's not yet clear whether its always the same genes that get through unchanged or whether the process is just not fully successful, but the possibility is there that epigenetic changes that occur in your lifetime could influence the health of your future children.

Where next?

Most efforts at present are focussed on fully understanding the interplay between different epigenetic mechanisms and the effects that environmental factors have on them. Once that is further advanced there is the possibility to tailor treatments and lifestyle recommendations to individuals based on both their genetic and epigenetic profiles. This is a step beyond the current efforts to promote genomics-based medicine, in which patients are treated on the basis of their genetic profiles alone, most notably in cancer therapeutics. 

Aside from that, uncovering the mechanisms of epigenetics is a worthy goal in and of itself as we will be one step closer to understanding the human machine in full. This is why I got into biochemistry in the first place - a love of the beautiful complexity of nature - and I hope that this, and not just the translational potential, drives future research in this and all areas of medical science.

The next post in this series can be found here.

Citations:


Barrès, R., Yan, J., Egan, B., Treebak, J., Rasmussen, M., Fritz, T., Caidahl, K., Krook, A., O'Gorman, D., & Zierath, J. (2012). Acute Exercise Remodels Promoter Methylation in Human Skeletal Muscle Cell Metabolism, 15 (3), 405-411 DOI: 10.1016/j.cmet.2012.01.001
Hackett, J., Sengupta, R., Zylicz, J., Murakami, K., Lee, C., Down, T., & Surani, M. (2012). Germline DNA Demethylation Dynamics and Imprint Erasure Through 5-Hydroxymethylcytosine Science, 339 (6118), 448-452 DOI: 10.1126/science.1229277

5 comments:

  1. So Lamarck was ever-so-slightly-kind-of-maybe-a-bit right about inheritance?

    I think this is the first post at the blog with a picture of a cat. I expect it to also be the most viewed post by the end of the month.

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    1. Actually there's renewed interest in the evolution of acquired characteristics (i.e. 'Lamarckian' evolution) in light of what we now know about epigenetics. Obviously, adaptation and speciation follow Darwinian lines, but short-term responses to environmental changes may well be more Lamarckian. This seems to be most profound in metabolic regulation, which makes sense because food availability can change quite rapidly and so the need to adapt is vital. Our bodies adapt over time to, say, a high fat or high protein diet, and perhaps giving our offspring some semblance of those adaptations might well be advantageous to their survival. This has been observed to occur in both rats and chickens so may well happen in humans too.

      I also think poor Lamarck gets a bit of a rough deal from history - he was actually a very significant early advocate of the concept of biological evolution, even though he didn't come up with the right mechanism.

      I'm counting on the cat to rope in a few extra hits - I should probably have picked a picture of one playing a piano or something.

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    2. I read a science fiction book once about a planet that had two suns. The orbit around one sun (the weaker one) took ~300 days, but the other orbit took centuries. Therefore the planet would have incredibly long hot periods and cold periods (thousands of years).

      Civilisations would rise and fall between the two dominant species. One was human and dominated the summers and one, not human, that had fur and thus dominated the winters. By the time spring would roll round (the beginning of the books) the humans were basically just hunter gatherers and by autumn they had cities, nations, etc.

      One part of the story involved a virus. This virus would only be active in the long term Autumn or Spring. A person who became infected would get very sick, but would also as a result gain a lot of weight or lose a lot of weight. I accepted that, but the thing was this trait then got passed on to the survivor's children. I thought that was too far.

      The thing was, this part of the story was actually really cool, because it was the other species that were the carriers of this virus for the centuries when it was dormant. And, the humans needed to get infected or they wouldn't survive the severe changes in temperature. This mean that their mortal enemies were actually necessary for their survival. They spent so much time trying to wipe this species out, but unknowingly needed them.

      Anyway, I'm glad that epigenetic research has determined that such a storyline is actually feasible.

      (The books were the Helliconia Trilogy)

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    3. 300 years, not 300 days (oops).

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    4. Aso, the other orbit took millennia, not centuries.

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