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Epigenetics 8: some terms

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Histone, with DNA wrapping, rendered by the Protein Data Bank (PDB)
Histone, with DNA wrapping, rendered by the Protein Data Bank (PDB)

 

The gene is not more ‘basic’ than the organism, or closer to ‘the essence of life’, whatever that means. Organisms have DNA codes, and they maintain external forms and behaviours. Both are equal and fundamental components of being. DNA does not even build an organism directly, but must work through complex internal environments of embryological development, and external environments of surrounding conditions. We will not know the core and essence of humanity when we complete the human genome project. 

Stephen Jay Gould, ‘Magnolias from Moscow’, in Dinosaur in a Haystack, 1996

I remember ages ago promising that I’d start every blog piece with a quote, then I more or less immediately forgot about it. Anyway the above quote kind of refers to epigenetics, and anticipates, in a way, the disappointment that many have felt about the human genome project and its not-quite-revelatory nature. As we learn more about the complexities of epigenetics, more about the relationships between genotype and phenotype will be revealed, but the process will surely be very gradual, though relentless. But I can’t talk, knowing so little. In this post, I’ll look at a very few key terms to help orient myself in this vast field. Not all will be specifically related to epigenetics, but to the whole field of DNA and genetics. 

nucleosome: described as ‘the basic structural form of DNA packaging in eukaryotes’, it’s a segment of DNA wound round a histone ‘octamer’, a set of eight histones in a cubical structure. All of this is for fitting DNA into nuclei. Nucleosomes are believed to carry epigenetic info which modifies their core histones, and their positions in the genome are not random. Each nucleosome core particle consists of approximately 146 base pairs. 

chromatin: a complex of DNA and protein, which packages DNA protectively, condensing the whole into a tight structure. Histones are essential components of chromatin. Chromatin structure is affected by methylation and acetylation of particular proteins, which in turn affects gene expression. 

nucleotides: the basic building blocks of DNA and RNA, they consist of a nucleoside and a phosphate group. A nucleoside itself is a nitrogenous base (also known as a nucleobase) and a five-carbon sugar ribose (a ribose – these explanations always need more explaining – is a simple sugar, the natural form of which is D-ribose, and which comes in various structural forms). DNA and RNA are nucleic acid polymers made up of nucleotide monomers. 

nucleobase: a nitrogenous base (e.g. adenine, cytosine, thymine, guanine, and uracil which replaces thymine in RNA), the fundamental units of our genetic code. Also simply known as a base. 

base pairs: a base pair, in DNA, is one of the pairings adenine-thymine (A-T) or cytosine-guanine (C-G). They are pyrimidine-purine pairings. Adenine and guanine are purines, the other two pyrimidines. Due to their structure pyrimidines always pair with purines. 

CpG islands: regions of DNA with a high frequency of CpG (C-G) sites, i.e. sites where a cytosine nucleotide is followed by a guanine nucleotide in linear sequence in a particular direction. 

histones: highly alkaline proteins, the chief proteins of chromatin, and the means of ordering DNA into nucleosomes. There are four core histones, H2A, H2B, H3 and H4. These form an octamer structure, around which approximately 146 base pairs are wound. 

Obviously, I’m very much a beginner at comprehending all this stuff, but I note that the number of videos on epigenetics seems to increase almost daily, which is raising my skepticism more than anything. I try to be selective in checking out these videos and other info on the topic, as there’s always this human tendency to claim super-solutions to our problems, as in super-foods and super-fitness regimes and the like. I’m more interested in the how of things, which is always a more complicated matter. Other information sources tend to assume knowledge or to skate over obvious complexities in a facile manner, and then of course there’s the ‘problem’ of being a dilettante, who wants to learn more about areas of scientific and historical knowledge often far removed from each other, and time’s running out, and we keep forgetting…

So anyway, I’ll keep plodding along, because it’s all quite interesting.  

Written by stewart henderson

February 23, 2020 at 12:20 pm

epigenetics and imprinting 7: more problems, and ICRs

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This image has an empty alt attribute; its file name is screen-shot-2020-02-02-at-10.11.35-pm-1.pngthe only image I can find that I really understand

 

In the previous post in this series I wrote about the connection between two serious disorders, Angelman syndrome and Prader-Willi syndrome, their connection to a missing small section of chromosome 15, and how they’re related to parental inheritance. These syndromes can sometimes also be traced back to uniparental disomy, in which the section of chromosome 15 is intact, but both copies are inherited from the mother (resulting in PWS) or the father (resulting in AS).

So the key here is that this small section of chromosome 15 needs to be inherited in the correct way because of the imprinting that comes with it. To take it to the genetic level, UBE3A is a gene which is only expressed from the maternal copy of chromosome 15. If that gene is missing in the maternal copy, or if, due to uniparental disomy, both copies of the chromosome are inherited from the father, UBE3A protein won’t be produced and symptoms of Angelman syndrome will appear. Similarly, PWS will develop if a certain imprinted gene or genes aren’t inherited from the father. Other imprinting disorders have been found, for example, one that leads to Beckwith-Wiedemann syndrome, though the mechanism of action is different, in that both copies of a gene on chromosome 11 are switched on when only the paternal copy should be expressed. This results in abnormal growth (too much growth) in the foetus. It too has an ‘opposite’ syndrome, Silver-Russell syndrome, in which the relevant protein expression is reduced, resulting in retarded growth and dwarfism. 

But now to the question of exactly how genes are switched on and off, or expressed and repressed. DNA methylation, briefly explained in my first post on this topic, is essential to this. Methyl groups are carbon-hydrogen compounds which can be bound to a gene to switch it off, but here’s where I start to get confused. I’ll quote Carey and try to make sense of it:

… it may be surprising to learn that it is often not the gene body that is methylated. The part of the gene that codes for protein is epigenetically broadly the same when we compare the maternal and paternal copies of the chromosome. It’s the region of the chromosome that controls the expression of the gene that is differently methylated between the two genomes.

N Carey, The epigenetics revolution, 2011 p140

The idea, I now realise, is that there’s a section of the chromosome that controls the part of the gene that codes for the protein and it’s this region that’s differently methylated. Such regions are called imprinting control regions (ICRs). Sometimes this is straightforward, but it can get extremely complicated, with whole clusters of imprinted genes on a stretch of chromosome, being expressed from the maternally or paternally derived chromosomes, and not simply through methylation. An ICR may operate over a large region, creating ‘roadblocks’, keeping different sets of genes apart, and affecting thousands of base-pairs, not always in the same way. Repressed genes may come together in a ‘chromatin knot’, while other, activated genes from the same region form separate bundles.

Imprinting is a feature of brain cells – something which, as of the writing of Carey’s book (2011), is a bit of a mystery. Not so surprising is the number of expressed imprinted genes in the placenta, a place where competing paternal-maternal demands are played out. As to what is going on in the brain, Carey writes this:

Professor Gudrun Moore of University College London has made an intriguing suggestion. She has proposed that the high levels of imprinting in the brain represents a post-natal continuation of the war of the sexes. She has speculated that some brain imprints are an attempt by the paternal genome to promote behaviour in young offspring that will stimulate the mother to continue to drain her own resources, for example by prolonged breastfeeding.

N Carey, The epigenetics revolution, 2011. pp141-2

This sounds pretty amazing, but it’s a new epigenetic world we’re exploring. I’ll explore more of it next time.

References

The epigenetics revolution, by Nessa Carey, 2011

Epigenetics, video: SciShow

Written by stewart henderson

February 2, 2020 at 10:33 pm

a DNA dialogue 4: purines, mostly

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Canto: So what’s a pyrimidine, molecularly speaking, and why does it differ from a purine, and why does it matter?

Jacinta: They’re two different types of nitrogenous bases, dummy, which are a subset, maybe, of nucleotide bases. All of which is largely gobbledygook at present.

Canto: Ok, we know there are four different nitrogenous bases in DNA.  Two of them, A & G, adenine and guanine, are purines, which structurally are two-carbon nitrogen ring bases. The other two, thymine and cytosine, T & C, are pyrimidines, which are one-carbon nitrogen ring bases. Uracil, in RNA, is also a pyrimidine. It replaces the thymine used in DNA.

Jacinta: That’s right, now we know that in DNA these nitrogenous bases are connected across the double helix, in pairs, in a particular way. A (a purine) always connects with T (a pyrimidine), and similarly C is always bonded to G. So why is this?

Canto: Why is it so? Well, put simply, the molecular structure of purines, which you’ll note have a two-carbon ring structure and so are larger than pyrimidines, doesn’t allow them to bond within the group, that’s to say with other purines, and the same goes with pyrimidines. It’s essentially due to the difference between hydrogen bond donors and acceptors for these groups.

Jacinta: So, looking at purines first, considering that they’re one of the building blocks of life, it’s not surprising that we find them in lots of the food we eat, especially in meat, mostly in organs like kidneys or liver. Structurally they’re heterocyclic aromatic organic compounds – as are pyrimidines. Heterocyclic simply means they have a ring structure composed of more than one element – in this case carbon and nitrogen. An aromatic compound isn’t quite what you think – structurally it means that it’s strong and stable, due to resonance bonds, which we won’t go into here. Below is a model of a purine molecule, which has the chemical formula C5H4N4 – the black globes are carbon atoms, the nitrogens are blue and the hydrogens white.

Purines and pyrimidines are both self-inhibiting and activating, so they actively bond with each other but inhibit self-bonding, so that they maintain a more or less equal amount as each other within the cell.

Canto: So that’s purines in general, but in DNA there are two purines, adenine and guanine, which must differ structurally – and are there any others?

Jacinta: Oh yes, caffeine is a purine, as well as uric acid…

Canto: Definitely aromatic.

Jacinta: And there are many others. Purines are very important molecules, used throughout the body for a variety of purposes, as components of ATP, cyclic AMP, NADH and coenzyme A, for example.

Canto: I’ve heard of some of those…

Jacinta: As to the difference between adenine and guanine, here’s how it’s described in this Research Gate article, which I’m sure is reliable:

The main difference between adenine and guanine is that adenine contains an amine group on C-6, and an additional double bond between N-1 and C-6 in its pyrimidine ring, whereas guanine contains an amine group on C-2 and a carbonyl group on C-6 in its pyrimidine ring

Canto: Shit, that explanation needs to be explained, please.

Jacinta: Haha well let’s look at more diagrammatic structures, but first – an amine group, also called an amino group, is a derivative of  NH3 (ammonia), consisting of a nitrogen atom bonded to hydrogen atoms, at its simplest. This gives adenine the formula ‎C5H5N5. Guanine has, in addition to the amine group, a carbonyl group, which is a carbon double bonded to an oxygen, C=O. This gives guanine the formula C5H5N5O. Anyway, it’ll all become clear over the next dozen or so years…

adenine
guanine


References

https://www.researchgate.net/publication/316984935_Difference_Between_Adenine_and_Guanine

https://en.wikipedia.org/wiki/Purine

https://en.wikipedia.org/wiki/Adenine

https://pubchem.ncbi.nlm.nih.gov/compound/Adenine

https://en.wikipedia.org/wiki/Guanine

Written by stewart henderson

January 26, 2020 at 5:26 pm

epigenetics and imprinting 6: when things go wrong

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some visible signs of Angelman syndrome

So imprinting involves parent-of-origin effects of which we find evidence in certain segments of certain chromosomes, in which genes are switched on or off, depending on inheritance. It often seems that these parent-of-origin effects counter-balance each other, as both parents have their own mutually exclusive way of trying to ensure the continuation of their genetic line.

It’ll be tough (for me) to take this down to a molecular level, but I’ll rely heavily on Nessa Carey’s book. It describes work on chromosome 7 in mice. I should first mention that there’s a convention in naming genes using italics, and the proteins they code for without italics. So there’s a gene in chromosome 7 called insulin-like growth factor 2 (Igf2) which promotes embryonic growth, and is usually expressed from the paternal copy. When researchers introduced a mutation which prevented the gene from effectively coding for the Igf2 protein, the offspring of this mutation were unaffected when the mutated gene was inherited from the mother, but the litter of offspring were much smaller when the gene was mutated in the father, showing that it was the paternal copy of the Igf2 gene that was required for foetal growth.

Fascinatingly for this ‘battle of the sexes’, there’s a gene in mouse chromosome 17 – Igf2r – which acts against the Igf2 protein, stopping it from promoting growth. This gene is also imprinted, from the maternal side. And so it goes.

According to Wikipedia, we now know of at least 80 imprinted genes in humans, mostly related to embryonic and placental growth and development. This is almost twice the amount Carey reported on less than a decade ago, so discoveries in this area are moving fast. As Carey writes, it’s uncertain whether there’s less imprinting in humans than in other mammals (we know of about 150 imprinted genes in mice) or whether they’re just harder to detect. Imprinting evolved about 150 million years ago (how do they know that? – as the much-treasured Bill Bryson would say), and is particularly prevalent amongst placental mammals.

This post was supposed to be about the mechanisms involved in imprinting, but my vast readership will have to wait awhile. I’m going to follow Carey, because I’m learning a lot from her, into the next area she writes about – ‘when imprinting goes bad’. She describes two very different conditions from birth, Angelman syndrome (AS) and Prader-Willi syndrome (PWS). Researchers separately studying these conditions found that the parents of the sufferers were usually healthy, yet everything pointed to something genetic going on, presumably during the production of eggs or sperm.

The separate work on the origins of these two permanently debilitating but very different conditions eventually converged, when it was found that in both AS and PWS, the patients were missing a small, identical stretch of chromosome 15. What caused the two entirely different results of this defect was whether it was inherited from the mother (resulting in AS) or the father (resulting in PWS). So the disorder is epigenetically inherited, a further example of a parent-of-origin effect.

Yet some children inherit these disorders without any deletions to chromosome 15. They have two normal copies of chromosome 15 but not from each parent. Instead they have two copies from the mother and none from the father – called uniparental disomy. In another variation on the theme it was later discovered that AS was in some cases caused by the opposite form of uniparental disomy, in which two normal copies of the chromosome were inherited from the father. So, because the particular region of the chromosome is normally imprinted, it’s essential, for healthy offspring, that the region is inherited in the ‘correct’ way, from each parent.

I’ll be looking at more examples of problematic inheritance and imprinted genes next time.

References

https://en.wikipedia.org/wiki/Genomic_imprinting

Nessa Carey, The epigenetics revolution, 2011

Written by stewart henderson

January 23, 2020 at 12:49 pm

a DNA dialogue 3: two anti-parallel strands

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but why the twist? – we don’t know yet

Jacinta: Ok so these two strands of DNA are described as anti-parallel. Is this just intended to confuse us?

Canto: Apparently not, in fact it’s quite essential. The useful q&a site Quora has good info on this, and understanding it in all its complexity should help us to understand DNA general – it’s one of a thousand useful entry points.

Jacinta: Yes, and I’ll try to explain. It became clear to us last time that the strands or ribbons twisted round in a double helix, called the backbone of the molecule, are made from phosphate and deoxyribose sugar, covalently bonded together. That means tightly bonded. Between the two strands, connecting them like ladder rungs, are nitrogenous bases (this is new to us). That’s adenine, thymine, guanine and cytosine, bonded together – A always to T, and C to G – with weak hydrogen bonds. We’ll have to look at why they must be paired in this way later.

Canto: It’s called Chargaff’s base pairing rule, which doesn’t tell us much.

Jacinta: And, according to a respondent from Quora, ‘the two strands of DNA are anti-parallel to each other. One of them is called leading strand, the other is lagging strand’. But I don’t quite get this. How are there two strands of DNA? I thought there was one strand with two sugar-phosphate backbones, and a rung made up of two – nitrogenous nucleobases? – weakly connected by hydrogen bonds.

Canto: I think the idea is there are two strands, with the attached bases, one next to another on the strand, and weakly attached to another base, or set of bases each attached to another phosphate-sugar backbone. As to why the whole thing twists, rather than just being a straight up-and-down ladder thing, I’ve no idea. Clearly we’re a couple of dopey beginners.

Jacinta: Well, many of the Quora respondents have been teaching molecular biology for years or are working in the field, and just skimming through, there’s a lot be learned. For now, being anti-parallel is essential for DNA replication – which makes it essential to DNA’s whole purpose if I can call it that. I’ll also just say that the sugars in the backbone have directionality, so that the way everything is structured, one strand has to go in the opposite direction for the replication to work. If for example the strands were facing in the same direction, then the base on one side would connect to a hydrophobic sugar (a good thing) but the base on the other side would be facing a hydrophilic phosphate (a bad thing). Each base needs to bond with a sugar – that’s to say a carbon atom, sugar being carbon-based – so one strand needs to be an inversion of the other. That’s part of the explanation.

Canto: Yes, I find many of the explanations are more like descriptions – they assume a lot of knowledge. For example one respondent says that the base pairs follow Chargaff’s rule and that means purines always pair up with pyrmidines. Not very helpful, unless maybe you’re rote-learning for a test. It certainly doesn’t explain anti-parallelism.

Jacinta: Well, although we don’t fully understand it yet, it’s a bit clearer. Anti-parallelism is an awkward term because it might imply, to the unwary, something very different from being parallel. The strands are actually parallel but facing in the opposite direction, and when you think about the structure, the reason for that becomes clearer. And imagining those backbone strands facing in the same direction immediately shows you the problem, I think.

Canto: Yes and for more insight into all that, we’ll need to look more closely at pyrmidines and purines and the molecular structure of the backbone, and those bases, and maybe this fellow Chargaff.

References

https://www.quora.com/Why-are-DNA-strands-anti-parallel

https://slideplayer.com/slide/13304243/

Written by stewart henderson

January 21, 2020 at 2:38 pm

A DNA dialogue 2: the double helix

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Canto: Ok we talked about base pairs at the end of dialogue 1. A (nucleo)base pair is, duh, a pairing of nucleobases. There are four types of base in DNA – adenine and thymine, which always pair together, and the other pairing, cytosine and guanine.

Jacinta: Please explain – what’s a nucleobase, what do they do, and why do they come in pairs?

Canto: Well, let’s see, how do we begin… DNA stands for deoxyribonucleic acid…

Jacinta: So it’s an acid. But bases are like the opposite of acids aren’t they? So how can an acid be constructed of its opposite?

Canto: Look, I can’t answer that right now – I haven’t a clue – but let’s keep investigating the structure and function, and the answers might come. So, you’ll know that there was a battle in the 1950s to elucidate the structure of DNA, and it was found to form a double helix two strands of – I don’t know what – connected to each other in a twisted sort of way by, I think, those base pairs connected by hydrogen bonds. Anyway, here’s a fairly typical explanation, from Nature Education, which we’ll try to make sense of:

The double helix describes the appearance of double-stranded DNA, which is composed of two linear strands that run opposite to each other, or anti-parallel, and twist together. Each DNA strand within the double helix is a long, linear molecule made of smaller units called nucleotides that form a chain. The chemical backbones of the double helix are made up of sugar and phosphate molecules that are connected by chemical bonds, known as sugar-phosphate backbones. The two helical strands are connected through interactions between pairs of nucleotides, also called base pairs. Two types of base pairing occur: nucleotide A pairs with T, and nucleotide C pairs with G.

Jacinta: So I think I have a problem with this description. I think I need a picture, fully labelled. So the two strands themselves are made up of nucleotides, and the connections between them are made up of bonded sugar and phosphate molecules? But the strands are connected, via sugar and phosphate, in particular ways – ‘through interactions’ – which only allow A to pair with T, and C to pair with G?.

Canto: I think that’s right. Maybe we can find a picture.

Jacinta: Ok, so we got it completely wrong. The backbone, of sugar-phosphate, is the outer, twisted strand, or two of them, like the vertical bars of a twisted ladder, or the toprails of a spiral staircase, and the base pairs are like the stairs themselves, made of two separate parts, the bases, bonded together by hydrogen…

Canto: Forget the description, the picture above is worth all our words. It also tells us that the DNA molecule is around 2 nanometres wide. That’s two billionths of a metre. And 3.4 nanometres long for a full twist of the double helix, I think.

Jacinta: Whateva. There’s also this claim that the two strands are ‘anti-parallel’. It looks to me as if they’re simply parallel, but twisted. What does this mean? Is it significant?

Canto: I don’t know – maybe we’ll find out next time. I’m already exhausted.

Jacinta: …….

Written by stewart henderson

January 16, 2020 at 5:13 pm

Posted in biochemistry, DNA, science

Tagged with , ,

A DNA dialogue 1: the human genome

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what genomics tells us

Canto: I’m often confused when I try to get my head around all the stuff about genes and DNA, and genomes and alleles and chromosomes, and XX and XY, and mitosis and meiosis, and dominant and recessive and so on. I’d like to get clear, if only I could.

Jacinta: That’s a big ask, and of course we’re both in the same boat. So let’s use the magical powers of the internet to find answers. For example, here’s something that confuses me. The Human Genome project, which ended around the year 2000, involved a mapping of the whole human genome, and that includes coding and non-coding genes, and I think it was found to contain 26,000 or so – what? Letters? Genes? Coding genes? Anyway there’s a number of questions there, but they’re not the questions that confuse me. I don’t get that we now, apparently, have worked out the genetic code for all humans, but each of us has different DNA. How, exactly, does our own individual DNA relate to the genome that determines the whole species? Presumably it’s some kind of subset?

Canto: Hmmm. This article from the Smithsonian tells us that the genetic difference between human individuals is very tiny, at around 0.1%. We humans differ from bonobos and chimps, two lineages of apes that separated much more recently, by about 1.2%….

Jacinta: Yes, yes, but how, with this tiny difference between us, are we able to use DNA forensically to identify individuals from a DNA sample?

Canto: Well, perhaps this Smithsonian article provides a clue. It says that the 1.2% difference between us and chimps reflects a particular way of counting. I won’t go into the details here but apparently another way of counting shows a 4-5% difference.

Jacinta: We probably do need to go into the details in the end, but clearly this tiny .1% difference between humans is enough for us to determine the DNA as coming from one individual rather than 7 to 8 billion others. Strangely enough, I can well believe that, given that we can detect gravitational waves and such – obviously using very different technology.

Canto: Yeah the magic of science. So the Human Genome Project was officially completed in April 2003. And here’s an interesting quote from Wikipedia:

The “genome” of any given individual is unique; mapping the “human genome” involved sequencing a small number of individuals and then assembling these together to get a complete sequence for each chromosome. Therefore, the finished human genome is a mosaic, not representing any one individual.

Of course it would have to be a mosaic, but how can it represent the whole human genome when it’s only drawn from a small number? And who were these individuals, how many, and where from?

Jacinta: The Wikipedia article does give more info on this. It tells us that the project isn’t really finished, as we’ve developed techniques and processes for faster and deeper analyses. As to your questions, when the ‘finished’ sequencing was announced, the mosaic was drawn from a small number of anonymous donors, all of European origin.

Canto: But we all originated from Africa anyway, so…

Jacinta: So maybe recent ‘origin’ isn’t so important. Anyway, that first sequencing is now known as the ‘reference genome’, but after that they did sequence the genomes of ‘multiple distinct ethnic groups’, so they’ve been busy. But here are some key findings, to finish off this first post. They found some 22,300 protein-coding genes, as well as a lot of what they used to call junk DNA – now known as non-coding DNA. That number is within the mammalian range for DNA, which no doubt surprised many. Another blow for human specialness? And they also found that there were many more segmental duplications than expected. That’s to say, sections of DNA that are almost identically repeated.We’ll have to explore the significance of this as we go along.

Canto: Yes, that’s enough for starters. Apparently our genome has over 3 billion nucleobase pairs, about which more later no doubt.

References

http://humanorigins.si.edu/evidence/genetics

https://en.wikipedia.org/wiki/Human_Genome_Project

Written by stewart henderson

January 13, 2020 at 11:48 pm