Transcription – Complexity of RNA Structure

by Kevin Ahern, PhD

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    00:01 Now I have drawn this figure on the screen here to give you an idea of the transcriptional activation of a eukaryotic gene.

    00:10 Now it illustrates a couple of different terms that I wanna say something about.

    00:16 So there are three main things that I wanna communicate in this image and of course we are keeping in mind that the complexity of eukaryotic transcription is considerable more than it's shown in the slide. The first of this is the enhancer sequences that you can see here.

    00:29 Now enhancers are sequences in DNA and the sequences in DNA are located within usually a few thousand base pairs of a target gene that the cell will ultimately want to express.

    00:44 In some cases enhancer sequences are known to be as far as a million base pairs away but usually they are within a few thousand.

    00:52 The enhancer sequences are targets for binding by proteins called activator proteins.

    00:59 And as the name is suggest the activator proteins are activating something and these activator proteins are there to help activate the process of transcription.

    01:09 Well transcription doesn't happen at the site of the enhancer, as you can see.

    01:15 Instead transcription is happening a long way away. I said it could be few thousands base pairs for example.

    01:20 So how does an enhancer sequence activate transcription that is a long ways away and how those activator proteins accomplish this? Well they accomplish it, as you can see, on the screen by a bending of the DNA to bring the activator proteins and the enhancer close to the promoter. Now the promoter for the gene of interest here is on the bottom strands and it's where that handful of individual proteins are found.

    01:48 These are called transcription factor proteins.

    01:51 And these transcription factor proteins form a complex at the site of the promoter that is the place close to where the RNA polymerase is going to start transcription.

    02:03 Now in eukaryotic cells the RNA polymerase that catalyzes transcription is called RNA polymerase II.

    02:11 And the proteins that are the transcription factors that you see in the box have designation of TF as in transcription factor the roman numeral 2 (II) and the variety of letters corresponding to each of the individual transcription factors.

    02:26 So for example TFIID is one of the first proteins that binds to the promoter; because, it recognizes the AT rich sequence that we saw earlier in promoters of prokaryotic cells.

    02:42 This complex of proteins is helped to form by the activators. That's part of the function what the activators are doing.

    02:51 This large complex that you see here and they can actually be quite complicated is necessary for the RNA polymerase II to bind.

    03:00 The RNA polymerase II will not bind to bare DNA. It will not bind to DNA by itself. Now that's in contrast to what we saw in E-Coli in another presentation; because, in E-Coli all that it takes for RNA polymerase to bind in many cases is the sigma factor helping it to recognize the promoter.

    03:19 Eukaryotes are a lot different and the number and complexity of proteins allows for either activation or inactivation of transcription for a variety of reasons as might be needed by eukaryotic cells.

    03:32 Well there is a third factor that's involved in helping to control the transcription here.

    03:38 And this third factor is another sequence that can be adjacent to the promoter and adjacent to the enhancer and it's called an insulator sequence.

    03:48 An insulator sequence works opposite to an enhancer sequence.

    03:53 It works probably through a protein called CTCF.

    03:58 So what CTCF and the insulator sequence are thought to do, is to alter the 3D configuration of this entire complex that you see here.

    04:07 And that alteration doesn't allow for the looping back which is what I described earlier, the looping back of the enhancer to help form the transcriptional complex.

    04:18 In this way CTF is thought to stop the transcription of individual genes.

    04:24 Now factor affecting the binding of CTF to the insulator sequence may well be the modification chemically of the DNA.

    04:34 So we are starting get pretty complex here in terms of what all is happening.

    04:37 So the modification of the DNA may affect the insulator, the insulator may affect the enhancer and the enhancer may not be able to affect the promoter.

    04:47 It's complicated but eukaryotic transcription is very complicated.

    04:52 This schematically shows what I have described to you on the last figure.

    04:56 We have an enhancer and when the insulator is not active, the enhancer can help to activate individual genes by the looping I have described here.

    05:08 The insulator can block the sequences if CTCF binds and changes the 3D configuration that I described.

    05:17 Blocking the insulator, as I said, allows the enhancer to work but letting the insulator function stops transcription.

    About the Lecture

    The lecture Transcription – Complexity of RNA Structure by Kevin Ahern, PhD is from the course RNA and the Genetic Code.

    Included Quiz Questions

    1. RNA polymerase binds independently of everything else
    2. Activator proteins bind to enhancer sequences
    3. Enhancer sequences can function thousands of bases away from a promoter
    4. Bending of the DNA brings activator proteins into close proximity of a promoter
    1. They are bound by a protein called CTCF
    2. They keep protein enhancers from being inhibited in the transcription process
    3. They stimulate transcription
    4. They are activated by methylation of cytosine
    1. AT-rich sequences
    2. GC-rich sequences
    3. GT-rich sequences
    4. AC-rich sequences
    5. AG-rich sequences

    Author of lecture Transcription – Complexity of RNA Structure

     Kevin Ahern, PhD

    Kevin Ahern, PhD

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