In this lecture, we're going to think about how DNA is packaged into higher orders of chromatin. So, what what have we talked about in the last lecture was that the DNA is wrapped around the histone optima, and this is known as the nucleosome. And so here, you'll see on the bottom of the slide, a different way to see that. So we have the DNA here, this is wrapped around the histones, and this is a broader view to see the beads-on-a-string structure which we talked about last time. This beads-on-a-string structure, though, can also be condense into a higher order structure called the 30 nanometre of fibre, which is shown here in this central panel and this is because histone H1 can interact with other histone H1 molecules and this results in this very higher order chromatin packaging. So you can then see that this particular solenoidal type of fibre is much more densely packaged down where each of the blue dots that are found in here are singular nucleosomes. If on top of this you then add in scaffolding proteins which are shown in green in this central panel through here, this further condenses the chromosome down again. So, now we have the 30 nanometre fibre attached to scaffolding proteins. So this general structure where we have the 30 nanometer fibre then attached to different scaffolding proteins is generally how you find the DNA and the histones during interphase, that is when the cell isn't dividing, but it needs to be condensed at a fairly high rate. So if we look then at another movie to be able to see what this looks like in comparison to the open chromatin that we looked at in the last lecture. What you can see is that now when we start movie, you'll see that there's less motion. So there are less of those other yellow molecules that can be able to enter into this highly condensed chromatin. And you can see each of the nucleosomes again have got the blue, and now zoomed in, have got the blue histones with the purple DNA wrapped around. But the whole structure is much more densely compacted than it was in the beads-on-a-string sort of structure that we saw before. There's one final level of packaging on top of this interphase chromosome. And that's to get it to a metaphase chromosome. So a chromosome that would be found in a dividing cell. So here in this panel is kind of how we imagine chromosomes always look. Because this is how they tend to be depicted whenever they're drawn in images. However, this is only what they look like when the cell is dividing. And that's because all of the chromosomes need to be heavily condensed down as tight as they can be So that they can be pulled apart into the two daughter cells. If you had any open chromatin at this point, you can imagine, you've got in a drawer, if you had in a drawer two balls of string that were open a little bit, they'd be hard to pull apart from one another. They need to be tightly wrapped so that you can properly pull them apart, and each daughter cell can receive one ball of string each. So, this happens by the addition of additional scaffold proteins, which are shown in this panel here with these yellow proteins, and this allows for this final metaphase chromosome to be produced. So the summary then of how this DNA is packaged is that we start out with the DNA. The DNA is then wrapped around the histone proteins to make a nucleosome and this forming the beads-in-a-string structure. The beads-in-a-string via histone H1 interaction can then have the interaction in the 30 nanometre fibre. If you add scaffolding proteins on top of this 30 nanometre fibre we then have a an interface chromosome and finally if it needs to be compacted down more again for example at metaphase, then we add add a final layer of scaffolding proteins, that are shown here in yellow, to make what we often think of as the chromosome, and how we think of it as that X-shaped chromosome. So now, in this lecture, we're going to think about open chromatin, like the beads-in-the-string that is shown on the right, versus closed chromatin. And these various different forms that are shown on the left. So we have different names for open chromatin and closed chromatin. And these names came about because of when DNA was first being looked at in the nucleus and when they were staining with particular dyes. So open chromatin is generally known as Euchromatin because it was pale in its stain. So it wasn't densely stained. It was pale in its staining. And because it was fairly open, there was, there were less molecules to absorb the DNA stain. In comparison, heterochromatin is closed chromatin. And this is because it's densely staining. And so that's what the term, heterochromatin really means, where it stems from originally. While Euchromatin or open chromatin, where you would tend to find active genes, just comes in the one flavour, just Euchromatin. Heterochromatin comes in a couple of flavours. Both Facultative Heterochromatin and Constitutive Heterochromatin. So we are going to go through and explain what each of these mean. So Facultative Heterochromatin, as its name implies, suggests that it can differ by cell type. We've been talking about how tissue specific things can be expressed in one cell type and not another, so when these genes are epigenetically inactivated and densely packed down into heterochromatin. Say for example, the haemoglobin gene might be densely packed down in a neuron, but open in a red blood cell precursor. Then these genes would be called facultative heterochromatin. This also, the second example which we will deal with in later lectures which is the inactive X chromosome which I mentioned is this epigenetic silencing of one of the two X chromosomes in females. By contrast, then, we have constitutive heterochromatin. So again, according to its name, it suggests that the constitutive of heterochromatin is the same in every cell that you look at. It's unchanging, and that's in because constitutive heterochromatin performs a structural role. So you remember that I mentioned that there are epigenetic marks that are found at the beginnings or the ends of the chromosomes and even at the centre, called the centromere. So they found, constitutive heterochromatin is found at the telomeres, there are the ends of the chromosomes. At the centromeres, which are the centre of the chromosomes, but also in portions of the sex chromosomes and in this case it tends to be mostly the Y chromosome but also can be parts of the X chromosome. So in the next slide here, we can see an image, of chromosomes. These six different panels, are chromosomes from different species. And they're staining the dense, constitutive heterochromatin. These are metaphase chromosomes so they're those that are found in a dividing cell, and that is why they do in fact look like there's little X’s. that we imagine chromosomes look like. In Part A and Part B, so these two panels up here, you can see this dense, blacker part of the chromosomes are actually marking the centromeres. So they're marking the centre. And a great example is just this one here. The centre of the chromosome. In parts c and d, so here and here, what you can see is that the ends of the chromosomes particularly in this right hand panel, the ends of the chromosome, say for example, if you would look at that chromosome are more darkly and more densely staining and this is constitutive heterochromatin shown at the telomeres. You can also see on this particular one here there's also a densely stained end. So, there can be particular autosomes. So, non-sex chromosomes that also have very densely stained heterochromatin. And again, this can be seen here. For example, this whole chromosome arm, this whole upper arm of this chromosome is more densely staining than the lower arm. And finally in e and f we see that the sex chromosomes are densely stained. So here in panel f, you can see the X and Y chromosomes are densely stained and there's only half an X chromosome that is not. And here in panel e, you can see most of the Y chromosome is densely stained. And this is actually true throughout most mammals. The Y chromosome is generally constitutive heterochromatin and only a couple of genes like the testis-determining gene are really expressed. So heterochromatin then has a couple of functions that we've mentioned earlier and we'll talk about again. The first is for gene silencing and this tends to be more for facultative heterochromatin. And the second is to help maintain the structural integrity of the genome. And to help to mock the ends of the chromosomes in the centre of the chromosomes. And this tends to be constitutive heterochromatin. What we know is that each of these different types of chromatin, euchromatin and heterochromatin have a different set of epigenetic marks. So there are different punctuation marks if you like that are associated with each. So here I'll show you a movie that just summarises these points. That we can see again compare and contrast between the open open chromatin, the euchromatin and the closed chromatin or the heterochromatin. So here it's given for the X chromosomes but the same is true throughout the genome. So if we watch on the left you'll see the active chromatin, the euchromatin, where genes are active. And on the right, the inactive heterochromatin where genes are silenced or off. And if you look at the movies we'll then see that there are a particular set of epigenetic marks that are made on each. So there are active histone tail modifications on those internal tails that protrude out of the nuclear zone in the active heterochromatin. And a different set of those in the heterochromatin. So they differently coloured. In addition, there's DNA methylation found on the heterochromatin. So it's in the next lectures that we'll go through these histone tail modifications in addition to the DNA methylation.
