Regulation of transcription
Voiceover: So what makes a cell that's located inside of your nose responsible for smelling, say, a slice of pizza look and act differently from a cell that lines your gut and is responsible for absorbing the nutrients from that pizza? They have the exact same DNA so the differences can't be attributed to that fact alone. The answer actually lies in the expression of that DNA, which genes are actively transcribed and which ones aren't and there are several ways in which gene regulation occurs at the level of transcription and so we're going to be talking about the main ones here. Now let's draw out a hypothetical gene here and associated with this gene is a sequence upstream so towards the three prime region of the antisense strand, also called the template strand. And this sequence is called the promoter and there is another sequence in between the promoter and the gene called the operator. The operator is the sequence of DNA to which a transcription factor protein combined and the promoter is the sequence of DNA to which the RNA polymerase binds to start transcription. Now first off in prokaryotes we have what are called general transcription factors, which are a class of proteins that bind to specific sites on DNA to activate transcription. General transcription factors plus RNA polymerase and another protein complex called the mediator multiple protein complex constitute the basic transcriptional apparatus, which positions RNA polymerase right at the start of a protein coding sequence or a gene and then releases the polymerase to transcribe the messenger RNA from that DNA template. Now there's another type of DNA binding protein called activators and these enhance the interaction between RNA polymerase and a particular promoter, encouraging the expression of the gene and activators can do this by increasing the attraction of RNA polymerase for the promoter through interactions with sub units of the RNA polymerase or indirectly by changing the structure of the DNA. An example of an activator is the catabolite activator protein or CAP and this protein activates transcription of the lac operon in E. coli. In the case of the lac operaon and E. coli, cyclic adenosine monophosphate or cAMP is produced during glucose starvation and so this cAMP actually binds to the catabolite activator protein or CAP which causes a confirmational change that allows the CAP protein to bind to a DNA site located adjacent to the promoter and then this activator, the CAP, then makes a direct protein to protein interaction with RNA polymerase that recruits the RNA polymerase to the promoter. Now enhancers are sites on the DNA that are bound to by activators in order to loop the DNA in a certain way that brings a specific promoter to the initiation complex and as the name implies this enhances transcription of the genes in a particular gene cluster. And while enhancers are usually what are called cis-acting, cis meaning the same or acting on the same chromosome, an enhancer doesn't necessarily need to be particularly close to the gene that it acts on and sometimes it's not even located on the same chromosome. Enhancers don't act on the promoter region itself, but are actually bound by activator proteins and these activator proteins can interact with that mediator complex I mentioned earlier which recruits RNA polymerase and the general transcription factors which then can lead to transcription of the genes. So here I've drawn a little schematic of what it might look like to have the enhancer actually change the structure of the DNA so that the DNA is now looping around. Here you still have your promoter sequence, the operator sequence, the gene sequence, and the enhancer sequence, and having the DNA looped in such a way so that you could then recruit RNA polymerase, the transcription factors, the mediator protein complex, and then you have transcription begin of this gene here. Now let's talk about repressors. Repressors are proteins that bind to the operator, impending RNA polymerase progress on the strand and thus impeding the expression of the gene. Now if an inducer, which is a molecule that initiates gene expression, is present, then it can actually interact with the repressor protein in such a way that causes it to detach from the operator and then this frees up RNA polymerase to then transcribe the gene further down on the DNA strand. One example of a repressor protein is the repressor protein associated again with the lac operon operator, which prevents the transcription of genes used in lactose metabolism unless lactose, which is the inducer molecule, is present as an alternative energy source. Now silencers are regions of DNA that are bound by repressor proteins in order to silence gene expression and this mechanism is very similar to that of the enhancer sequences that I just talked about. And similarly, silencers can be located several bases upstream or downstream from the actual promoter of the gene and when a repressor protein binds to the silencer region of the DNA, RNA polymerase is prevented from binding to the promoter region. Now a few notes about the differences between prokaryotes and eukaryotes when it comes to transcriptional regulation. In prokaryotes, the regulation of transcription is really needed for the cell to be able to quickly adapt to the ever-changing outer environment that it is sitting in. The presence, the quantity, the type of nutrients actually determines which genes are expressed and in order to do that, genes must be regulated in some sort of fashion so a combination of activators, repressors, and rarely enhancers, at least in the case of prokaryotes, determines whether a gene is transcribed. In eukaryotes, transcriptional regulation tends to involve a combination of interactions between several transcription factors which allows for a more sophisticated response to multiple conditions in the environment. And another major difference between eukaryotes and prokaryotes is the fact that eukaryotes have a nuclear envelope which prevents the simultaneous transcription and translation of a particular gene and this adds an extra spacial and temporal control of gene expression.