Okay, so now we're going to go into more specific detail about histone methylation and histone acetylation. And the consequences it has on the expression and how these different histone marks are actually read by the cell. So histone acetylation is universally associated with gene activity, so an active gene that's being transcribed. This is easy to explain in an electrostatic way because when we add an acetyl group to a lysine of the histone tail, this neutralizes part of the positive charge of the histones. And so the histones are not as strongly attracted to the negatively charged DNA and therefore it's going to be more open and more accessible to the transcriptional machinery. But the second mechanism by which acetylation can be associated with transcriptional activity is more of a general mechanism that's true for other modifications as well. And that is that this acetyl group can be bound by a bromodomain. So a bromodomain is found in many different types of proteins. And it's this bromodomain which themselves recognize the acetylation group. And one of two things can happen, either the bromodomain itself has other components within that particular protein which bring about changes. Say for example, their chromatin remodellers, which we will deal with in another lecture, so they actually move the nucleosomes around. Or the bromodomain might recruit another protein that can do that. This is a little bit similar to when we spoke about the MECP2, a methyl binding domain proteins. By themselves, may have the functionality to cause transcriptional change or they'll bring in a friend that does. So histone acetylation is the example of the epigenetic mark that I spoke about which may or may not be, which probably isn't, mitotically heritable. But even considering that that might be the case and we'd like to think about it a little bit further. We know that histones are acetylated by the histone acetyltransferases and these tend to be called HATs or because it's the lysine that gets acetylated, they are sometimes called KATs. And there are 18 different versions of HATs or KATs in the mouse, and about the same number in humans. The histone acetylation can also be removed by histone deacetylases or HDACs, of which there, again, 18 in the mouse. So, there are many ways to lay down or remove particular histone acetylation marks. As I mentioned, histone acetylation is arguably not an epigenetic modification, in which case, we would just call it a chromatin modification. It's a modification to the chromatin that isn't mitotically heritable. And this is because there's a very rapid dynamics of histone acetylation and deacetylation. So much so that it can occur within the one cell cycle, and therefore, isn't passed over from the parent's cell to the progeny. In fact, we know that if you look at histone acetylation during a circadian rhythm, so that sound day and night cycle. Histone acetylation changes with this circadian rhythm rather than we've, rather than necessarily being much directly inheritable. We also don't know of any mechanism by which acetylation would be copied from the parent to the daughter strand, so from the parent nucleosome to the daughter nucleosome. Histone methylation is slightly more complicated and that's because it doesn't simply change the charge of the histone. So instead, histone methylation can be associated either with gene activity or gene inactivity, so an active or silent gene, and it depends really on context. So, we know that methylation, as I mentioned earlier, can come in mono, di, or tri-methylation, so three different states. But here, we're just going to think about methylation in general rather than going through the specifics. What I'd like you to think about are these three particular histone methylation marks. H3K4 methylation, so that's methylation of lysine 4 on histone H3, methylation of lysine 9 on histone H3, and finally, the methylation of lysine 27 on histone H3. These are three of the best characterized histone methylation marks. And therefore, we're going through these in many of the examples that we talk about in later lectures, for example, X inactivation. So we know that H3K4 methylation is associated with gene activity, which is shown here by this active promoter. So, if you consider here these gray octagons are the nucleosome and we have the internal tails of the histones protruding out, and the DNA is wrapping around as this black string, yeah. H3K4 is found here, are these blue residues I'm showing you here. And they are found right out on the tips of those tails of histone H3 because the residues number through from the outside working their way in. And this active methyl group mark is found around the promoter of active genes. So just in that region that's immediately neighboring the transcriptional starts that. By contrast, H3K9 methylation is an inactive mark. Here, it's shown on here again. There are these methyl group marks here, slightly further in, because it is the lysine 9 residue, and it's associated with inactivity. In this case, H3K9 methylation is mostly associated with constitutive heterochromatin. That heterochromatin that's found at the centromeres or the telomeres. It doesn't change from one cell type to the other. But H3K9 methylation, unlike H3K4 methylation, isn't restricted to one region of the gene, but instead is spread over the entire locus. So the promoter, throughout the gene body, and over the axons, and even down at the untranslated region past that. H3K27 methylation is similar to H3K9 methylation in that it's also an inactive mark and it's also spread over the entire gene. But in this case, it's more associated with facultative heterochromatin, the sort that varies between cell types. So it's associated with tissue specific gene silencing and is also associated with the inactive X chromosome. So for histone H3K9 methylation, we know that it's laid down by a specific class of lysine methyltransferase. Not the same ones that lay down in the H3K27 methylation or H3K4 methylation. And these specific lysine methyltransferases recognize H3K9 rather than these other residues. Histone methylation can also be removed and this happens by lysine demethylases which are otherwise known as KDMs for short, and they have specific activity for the methylated version of H3K9. H3K27, as I said, has a different class of these lysine methyltransferases and similarly the lysine demethylases that are specific for its own H3K27 mark. The one that we're going to talk about in other examples is the methyltransferases known as Ezh2. Ezh2 doesn't exist alone but has several other molecules, at least two other molecules that make up the polycomb repressive complex 2, or PRC2. This is one of the best studied epigenetic complexes at the moment in mammals and also into softer or other organisms. So this is the one that's worth remembering, and it's the primary histone methyltransferase for histone H3 lysine 27. And because this is found in facultative heterochromatin, Ezh2 and the PRC2 complex has a very important role in silencing genes that need to be silenced for tissue specific silencing. So, how is it that these histone modifications actually influence chromatin structure? Well, as a general rule, just like I showed you for those bromodomain, these modified histone tails are read by other chromatin protein. So they act as docking sites for other chromatin proteins. And either that particular protein itself, with that bromodomain for example, has a functionality to alter the chromatin packaging or it can bring in a friend that does so. So I mentioned earlier that the acetyl lysine is bound by a bromodomain. But the methylated lysine can be bound by several different domain types, Chromodomains, MBT domains, PHD domains, or Tudor domains. And phosporylated serines, which we weren't really talked about, can be bound by a different class, again a different domain, the 14-3-3 domain. I'm going to go through one example now of how different chromodomain containing proteins have different functional consequences depending on the methylated lysine they bind. So here we have H3K4 methylation, H3K9 methylation, and H3K27 methylation. So these are three proteins that all have a chromodomain, but they have specificity for particular residues. So CHD1's chromodomain likes to bind H3K4 methylation, HP1's chromodomain likes to bind H3K9 methylation, and CBX2's chromodomain likes to bind H3K27 methylation. So for CHD1, which binds this active epigenetic mark, CHD1 is actually an ATP dependent chromatin remodeller, which we'll talk about in the next few lectures later on. But this means that this CHD1 actually moves the nucleosomes around so it could open the nucleosomes up and make the nucleosomes more broadly spaced or condense them down. HP1 is actually called heterochromatin protein one so, it's certainly quite associated with heterochromatin and it's one of the earliest heterochromatin proteins to be discovered. HP1 can actually bring in DNA methyltransferase one which then methylates the neighboring CpG, dinucleotides. CBX2 on the other hand is part of another polycomb repressive complex, PRC1, rather than PCR2 and it has it's own enzymatic activity which will lay down another epigenetic mark. Histone H2A lysine 119, ubiquitination shown here is ub. And so you can see, that the different chromodomains, although they all have the same domain to recognize a methylated lysine. They recognize them in different context, and have different functional outcomes. So, to go through one example, this isn't by any means a completely understood example, but an example of how this all works. We have these nucleosomes, which are shown again as these octagons, the gray octagons. And so HP1, which is shown here as the blue protein, combined to H3K9 methylation. We know HP1 can then recruit DNMT1, shown here as the orange, so DNMT1 can then methylate these CPT dinucleotides in the DNA. But HP1 can also recruit in a histone methyltransferase and it can then enable spreading of the H3K9 methylation mark to other neighboring nucleosomes. We also know that DNA methyltransferase, in orange here, can recruit a histone deacetylase and so it will then go and remove the lysine marks here and here. And if we are removing, sorry, removing the lysines, the acetylated lysines, this will result in a tighter compaction of the chromatin and again we'll lock in the silent epigenetic state. So while we don't understand all of the features of epigenetic control, and in particular, we don't understand the hierarchy, we don't understand which comes first. This shows you that it's not a matter of just a single epigenetic mark being bound by a single protein. But rather the epigenetic mark is being recognized by a protein which then results in the assembly of large, complexes of proteins on top of this nucleusome chromatin. So in summary for this section, we know that euchromatin is associated with histone acetylation, and particular histone H3K4 methylation, and is found with in around active genes. And we know heterochromatin is associated with the different type of histone methylation, tends to be H3K9 or H3K27 methylation. And this is also associated with DNA methylation, and heterochromatin is found in regions with inactive genes.
