Eukaryotic Gene Transcription

Good evening, all! After a long (hahahaha… ha…) night’s sleep and a fresh dose of caffeine and Japanese, I’m here to bring you more biochemistry! I know you’re super excited! (And by “super excited,” I mean, groaning and saying to yourself, “This girl is clogging up my Facebook feed again…?”)

As promised, today’s question is a fun one—we’re going to be talking about eukaryotic gene transcription. In a way, it’s more interesting, because, you know, we’re all eukaryotes. Still, I have to ask you, going into this: are you ready to have a bad time?

We eukaryotes pride ourselves in being more complicated and more interesting than prokaryotes, but that doesn’t mean we’re immune to the need to carry out simple processes like protein synthesis. However, it does mean that we’ve got new and complicated ways of doing it, because apparently we like to show off.

The differences in prokaryotic and eukaryotic transcription start with the polymerases; while prokaryotes only have one (RNA polymerase), eukaryotes have three (RNA polymerase I, RNA polymerase II, and RNA polymerase III). RNA polymerase I makes rRNA, while RNA polymerase III makes tRNA. However, today, we’re interested in RNA polymerase II, which makes mRNA.

Now, you’d think that our polymerase would carry out transcription pretty much the same way that RNA polymerase does in prokaryotes, but unfortunately, that’s not the case. In reality, our RNA polymerase II needs quite the kick in the pants to get moving, which means it needs the help of a lot of different regulatory sequences.

The core region, where Transcription Factors and Co. actually bind, contains consensus sequences like we’re used to seeing: the TATA (TATAAA) box, where the helix comes apart (A-Ts are “weaker,” remember), a CAAT box, and sometimes a GC box (common in “housekeeping genes,” genes that are expressed in a generally constant manner). We also have an initiaton site, which, in eukaryotes, consists of a two-pyrimidine-CA-five-pyrimidine sequence between -3 and +5 (where +1 is where transcription begins).

However, unlike prokaryotes, we also have more distant regulatory sequences (“regulatory elements”), which can either be enhancers or inhibitors. These can be thousands of base pairs away from the gene of interest, and either enhance its transcription or inhibit it. We also have response elements, which are elements found in the promoter that activate genes in response to specific environmental stresses, such as heat, steroids, or heavy metals. For example, the metallothionein gene, whose gene product protects cells from heavy metal poisoning, contains MREs (metal response elements) that increase its transcription in the presence of heavy metals.

(brb, fangirling…)

Okay, now, this is where things get complicated. In prokaryotes, all we needed to initiate transcription was the holoenzyme. Here, we need a fistful of proteins that make up the preinitiation complex, or PIC. The PIC contains RNA Polymerase II (shocker), but it also contains seven other kinds of proteins: TFIIA, B, D, E, F, H, and S.

TFIID specifically is of interest because it contains something called TBP, or TATA-binding protein, and TAFs, or TATA-associated factors. As you’ve guessed, TBP recognizes and binds to the TATA box, bending the DNA so that the parts ahead of and behind the TATA box come closer together.

The other proteins do other things, but I’m going to gloss over that now, because it’s kind of beside the point; what we’re worried about is what happens after TFIIB opens the promoter, turning our PIC into an initiation complex.

Surely, you think, we’re ready to start, right? Well, unfortunately, we’re not there yet. We still need the help of Mediator.

Mediator is a vaguely crescent-shaped protein that bridges the gap between enhancers/inhibitors and the initiation complex. In effect, this protein is responsible for the final outcome of gene transcription: that is, whether things get enhanced, or whether they get turned off. In fact, Mediator is even more involved in transcription than that—it has activity that lets it expose the promoter (promoting formation of the PIC), and it can phosphorylate RNA polymerase II (pushing it into the elongation phase).

Now, there’s a lot more to it than that (you know, elongation and termination), but getting it going seems to be the mind-bogglingly hard part. Once it starts, it seems to do things in a way that’s otherwise pretty familiar.

And besides, my book stops talking about it at initiation. (I, uh, just realized that… Whoopsie…)

That’s all right, though, because I’ve gotta get to physics lab. Don’t think you’re getting a break from me, though—when I get back, we’re going to talk about post-transcriptional modifications. Won’t that be fun…?

Questions? Comments? Put them below! Flames? Please forward to this address—it’s where I spend most of my time.



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