Regulation of Gene Expression Part 2

Let's begin by continuing part 1 of regulation of gene expression. In this page, we will be discussing DNA bending, transcription factories, and alternative splicing.

First, let's talk about DNA bending. What is it and why do our cells do it? DNA bending happens when proteins gather together and literally bend DNA in order to make it more accessible to RNA polymerase. To understand this complex process, let's go over transcription factors again in more detail. General transcription factors are transcription factors that are used for transcription of all protein-coding genes. But while general transcription factors give RNA polymerase access to the gene, RNA polymerase doesn't really interact with the gene. That leads to low levels of transcription. If you need a gene to really be transcripted at higher levels, you need control elements called specific transcription factors that utilize another set of proteins. However, there are far more intricacies involved than just two types of proteins. There are also two other kinds of control elements - proximal and distal control elements - that are DNA sequences either close to (proximal) or further away from (distal) the promoter sequence of DNA. Groups of distal control elements are called enhancers. Genes can have multiple enhancers that interact at different times, but enhancers themselves are usually only used to control that specific gene. Transcription of genes can be monitered by the proteins that bind to the enhancers. Now, you still need to know a few more things before we can finally start getting into the process. There are two types of structural domains in activator proteins that also are useful in transcription. DNA-binding domains bind to the DNA itself and activation domains bind to other protein transcription factors or necessary means in transcription. The protein-protein interaction created by this domain helps amplify transcription. These activators can have more of either type of domain.

Here are some pictures below to help you understand all these different kinds of proteins, since this is quite complicated and difficult to visualize:

Now that we've gone over the types of proteins involved, let's finally move on to the actual process of DNA bending! Sorry for yapping for so long, but you need the context before we can look at the real deal. This time, I'll put a picture first so you can connect the concepts in your tiny brain. I'm trying to keep this easy to understand, since I was literally flabbergasted when I first read this in my textbook.  

At first, as we can see in the picture, the DNA strand is just kind of lying there when activator proteins then bind to its enhancers. In order to bring the activator-enhancer protein thingy closer to the promoter, a DNA-bending protein binds to the DNA and starts bending the DNA. General transcription factors and a group of something called mediator proteins (proteins that mediate or communicate with the promoter and enhancers) then arrive at the scene, and RNA polymerase also makes its way over. The mediators and general transcription factors bind along with the RNA polymerase, which can then transcript. This makes the gene much more accessible to RNA polymerase.

Whoo, that took all day to write. But we're still not done yet. We still need to go over transcription factories and alternative splicing. Don't worry though, I will just brush over these so you know the general definition.

In the nucleus, each chromosome (unraveled) has a specific area that it stays in. However, there are some areas where DNA loops from different chromosomes congregate. These areas are filled with RNA polymerase and transcription factors, and they are called transcription factories.

Alternative splicing is also a cool thing on its own - we believe it is how humans are able to survive with about the same amount of genes as a nematode (roundworm). Do you remember RNA splicing? Remember how we have to cut out the introns from the DNA strand? Alternative splicing occurs when you consider different parts introns and different parts exons, allowing you to create many similar proteins from just one gene! Cool, isn't it?

Unfortunately though, this is all I have for you today. This section will be continued next weekend, when I will finally finish the Regulation of Gene Expression series. I hope you enjoyed this page as much as I enjoy it! Email me at twisha.sharma30@gmail.com if you have any questions. Thanks so much for reading and I'll see you in the next one!