I read today that what can only be described as a group of geniuses in Illinois has been quietly making amazing discoveries about the molecular processes involved in DNA, including the fascinating field of epigenetics.
The DNA contains four different nucleic acid bases, called Adenosine, Cytosine, Guanine and Thymine, or ACG and T. C and G bond together, as do A and T, making the rungs of a long and beautifully coiled ladder of data.
This vast two-dimensional storage system only a few atoms wide (if an atom were a grain of sand, the smallest visible object would need to be at least 4 metres wide) is twisted, coiled and supercoiled repeatedly to such an extent that the collections it forms, the chromosones, become visible through a microscope.
The field of epigenetics deals with a newly discovered layer of meaning superimposed on the DNA itself. Epigenetic processes seem to be influenced by the experiences and lifestyle of an individual, and leave markers which can survive for many generations – the effects are so long lasting in successive generations of laboratory animals that some researchers believe the markers laid down can’t be turned off.
These processes don’t change the arrangement of the letters, but instead, they can change one of the base molecules – usually cytosine, sometimes adenosine – by swapping one of its hydrogen ions to a more complex methyl group. It’s as if they swap a capital letter instead of the same letter in lower case. The 4-character information remains the same, but the changed letter is read differently by the other equipment in the cell. Therefore while the DNA remains intact, the proteins which it is supposed to make can be switched on or off. Up until recently, it was thought that this was the main extent of changes caused by “methylation”.
Above you can see the little molecular machine grabbing the DNA, finding the right sequence and adding a methyl group to the cytosine. Now, you may well ask, from where do those little machines come from, that is, where are their designs stored and how are they assembled? How should I know? I’m only a programmer!
This process is almost always carried out to cytosine bases lying in the sequence:
So as both DNA strands have a cytosine, both strands will be converted with a methyl group. When the DNA is replicated, each of the new DNA double helices will have one old strand, complete with methyl groups, and one new strand, which is not methylated. But all the machinery has to do is find such a group, and apply the modification to the cystine on the other strand. Impressive though, for a machine which can’t see and doesn’t seem to have any kind of a memory in which to store its instructions. What makes it act the way it does?
Well, who knows – or to be more precise: it’s a hotly debated topic at present. But now to the real story: the catchily-named Theoretical and Computational Biophysics Group did a rather clever thing. By trying to break apart strands of DNA before and after methylation, they proved:
..a role of methylated DNA physical properties needs to be reconsidered as a direct epigenetic control factor. We found through novel and extremely extensive force measurements comparing non-methylated and various methylated DNAs that methylation affects the propensity for mechanical DNA strand separation to a significant degree.
This means that methylation doesn’t just accent the language of DNA, it makes the DNA itself stronger – tougher to break apart – which is important because your DNA, much like your wealth or your beautiful girlfriend, is subject to constant break-ins or attempts to rip it off altogether.
Yes, even on the molecular level there are crooks and predators on the make. What a neighborhood! Some attacking machinery from bacteria tries to splice in their own, alien, DNA into ours to mess up the activity of our cells. So any process which makes the DNA stronger is a boost to our immune systems.
It may well be that the resistance some people have to disease is a direct result of epigenetics. Perhaps the susceptibility to addictions in materialist societies is a result from weakened genetics. It is striking that in the last days of the Raj, virtually all the male children became alcoholics, something hardly seen before.
Perhaps the races which have had to cope with slavery and oppression by raising their spiritual values in non-violent protests have also increased the resilience of their DNA. It is true that African Americans led the way in practically all sports, once freed from the chains of slavery. Perhaps the well researched but otherwise inexplicable tendency of families with strong moral backgrounds to produce men of genius is because of beneficial changes to the DNA by virtue of, well, of virtues – if so, perhaps virtues and vices, far from being arbitrary and meaningless concepts, have biological reflections of their own.
Anyway, it is already known that positive attitudes can defeat the onset of infections or improve the recovery time from illnesses. From this, and in the light of The TCBG’s work, it’s not much of a leap to suppose the epigenetic system to be closely tied to our emotional state, and an important part of the biology reflecting our strength of spirit. And to all, a good night.
Next week! How to make this amazing bit of machinery for uncoiling knots:
DNA Gyrase from E.Coli is an enzyme which helps untangle, un-knot and relax supercoils in its DNA. It does so by binding to a strand of DNA, cutting both strands and then, while keeping hold of both cut ends, passing another piece of double stranded DNA through the gap. It then reseals the double stranded break.
Essentially it allows portions of the large circular bacterial genome to pass through itself, to prevent knotting and entanglement. A number of antibiotics (e.g. Simocyclinone D8) target this enzyme, since it is essential to the organism’s survival. Humans also have a form of this enzyme but its construction is different and we are thus not affected by the antibiotics.