So eukaryotic transcription is more complex than prokaryotic transcription, and I don't think anyone's probably surprised about that. Of course, it is. And the first way that it's different is through RNA polymerases because there are a lot of different ones that transcribe RNA in eukaryotic transcription that don't exist in prokaryotic transcription. So you have RNA polymerase 1, 2, and 3. There are a couple others, such as 45, which I'm not going to mention, but 1, 2, and 3 are the main ones. RNA polymerase 1 does ribosomal RNA. RNA polymerase 2 is messenger RNA, and so this is the one we're going to be talking about for the most part. And RNA polymerase 3 does tRNA. Now they also do other RNAs. There are various non-coding RNAs that I'm not mentioning here. But just in general, this is the main RNA that's transcribed by each one. So because I think RNA polymerase 3 does certain types of rRNA. They usually all do some kind of non-coding RNA as well, but they're very specific with what they do, and they don't transcribe the RNAs they shouldn't.
And so the first thing you start with is transcription initiation, and transcription initiation requires many different factors. In requires many different factors, and these are generally proteins. And, the first set of factors that it requires are called general transcription factors, and they're given fancy names. TFIID (TF2D), TFIIB2 (TF2B). They're given these fancy names. We're going to talk about this one in a second, but they're general transcription factors. And so anytime transcription is occurring for mRNA, which is what we're talking about messenger RNA, they have to be there to initiate transcription. They are there every single time mRNA is being transcribed, And what happens to them is there's a bunch of different ones, but essentially what they do is they bind to the eukaryotic promoter. And this promoter exactly the same as the prokaryotic promoter. It's a DNA sequence that initiate the initiation vectors bind to its present upstream of the gene that's being transcribed. Now the eukaryotic promoter has different sequences than the prokaryotic, promoter. So eukaryotic promoter, a very common one is called the TATA box. This is a sequence of TATA around 30 base pairs upstream of where the transcription starts. And so the protein that stream of where the transcription starts. And so the protein that binds this is the general transcription factor. You see it depending on your book, you may see it as TFIID, or you may see it as the TATA binding protein. It's the same thing. And essentially, it binds this sequence and recruits all the other general transcription factors that are necessary for transcription to be initiated. And so, when all those factors are present, the general transcription factors, bind to this promoter, and, eventually, when they're all there and transcription's ready to start, they recruit RNA polymerase 2. And so, this is called the pre-initiation complex with all of the general transcription factors and RNA polymerase 2.
So here's an example. So here's a bunch of different factors, but because the general transcription factors, and RNA polymerase are present, this would be the pre-initiation complex of that I mentioned before. And then transcription will go and, eventually, it'll be released. Now, after initiation begins, transcription elongation begins. And how this happens is because the RNA polymerase 2 that controls, that is transcribing the mRNA has a special protruding region on its protein. It has a tail on it, and this tail is called the carboxy terminal domain (CTD). And so RNA polymerase has this little protein tail hanging off of it, and we call it the CTD. And this is what controls its ability to elongate the transcript. So what happens is that the region on this tail can be phosphorylated, meaning that it gets phosphates. So when a phosphate is added to this tail that will activate the RNA polymerase and release it from the pre-initiation complex, and then it's free to go. So what happens is you kind of think of it as like a wind-up car or toy. Right? So the RNA polymerase is there and the GTS, so the transcription factors wind that toy up. And they do that by adding phosphates. But when that phosphate's added, it gets it winds at once. You know, phosphates get added and it gets wound up. And then eventually, it gets so wound up, so phosphorylated, it's released. And so it's released from the transcription initiation complex and, it then goes and it elongates that transcript. So once it's released, once it's been wound up and phosphorylated, it will elongate the transcript. Now, it keeps going, it keeps going, it keeps going, and it'll keep going indefinitely until transcription termination starts. Now for eukaryotic cells, there's not really a specific sequence that triggers termination. Right? I said in prokaryotic transcription, there were specific sequences called terminators that did it. But in eukaryotic transcription, it doesn't really work like that. And often, the RNA polymerase 2 will transcribe 100 or even 1000 nucleotides past where it should have stopped, past the coding sequence. And eventually, it will fall off. Right? It eventually sometimes there are sequences way downstream, but essentially, the RNA polymerase will eventually fall off. Off. It'll receive some type of signal, phosphorylation will get weak, it will fall off. And this RNA processing has to occur after it's fallen off, after the termination, because now you have potentially thousands of nucleotides that shouldn't be there. So the RNA has to undergo processing after it's transcribed. We'll talk about this in its whole separate video. So here we have the RNA polymerase, and now it has a phosphate on it, and this will release the RNA polymerase from this complex, and it will go and transcribe until it falls off.
Now, a number of factors control transcription. So we've talked about promoters, we've talked about the generalized transcription factors, but there's a lot of other factors that also control transcription. One of them is called an enhancer, and this is going to help activate and enhance or speed up transcription. There's also silencers, which do exactly what you think they would do, they repress it. And then, we talked about generalized transcription factors, but there are actually some genes have specific transcription factors. And these at work to activate or repress only specific genes. So if these specific transcription factors aren't there with the generalized ones, it won't work correctly. So there are all these different factors and all these different levels of regulation that control the transcription. Now these factors, we've always just sort of assume that they're, you know, directly next to the gene, but that's actually not the case. And they can be located near or far based on where transcription starts. So there are things called cis-acting elements, and they're called cis-acting elements as long as they're found on the same chromosome. So these could be right next to the gene or they could be located almost the entire chromosome away, but as long as they're on the same chromosome, they're cis-acting elements. And then there are trans-acting elements that are so far away from the gene trans the transcription start site that they're actually found in other chromosomes. And you may say, how does that even work? And the reason is because we often think of chromosomes in this form, because that's how we see them when cells are dividing. But actually, most of the time, chromosomes don't look like this. They look like this in the cell. There are all chromosomes, and they're all, like, rounded up together, and they're not in this form. And when it looks like this, you can very easily imagine how a portion of a gene on another chromosome to a transacting element may be close enough to the gene to initiate transcription, to control transcription. And so this is an example of a cis-acting element. So here we have an enhancer. It's pretty far away. Here's the promoter, and here's the gene of interest. So you can see here it's not labeled here, but this is RNA polymerase. Right? RNA polymerase is being recruited. Here's some other factors, some transcription factors, some enhancers, potentially some suppressors that are coming on, and this will actually can fold over and initiate transcription on the chromosome. So that is eukaryotic transcription, so with that, let's now move on.
