Functional Genomics

Hi in this video, we're gonna be talking about functional genomics. So functional genomics. This is the type of genomics that studies the function expression and interactions of genes and proteins. Now there are many different subdivisions, a functional genomics that focus on different parts of gene expression. And so there's going to be the transcript dough mix that studies the expression, the sequence and expression of transcripts. You have proteomics which is going to be the expression of proteins. Um And you may ask why are these different, well sometimes things get transcribed but then they get suppressed before they're translated and can actually be very different between the what transcripts are produced and what proteins are produced. And then finally there's interact comics and this is going to be various interactions between DNA. RNA and proteins. How are proteins interacting with each other? How are proteins interacting with DNA and how are proteins interacting with RNA. So these are the three main subdivisions that make up functional genomics. Now there are many different types of techniques that study function that scientists who are studying functional genomics use. So at first we're going to go through each one individually. So the first that your book talks about our D. N. A micro rays and micro rays are used to determine which genes are active in a particular cell under certain circumstances. So this is very specific and can change from minute to minute and different environmental conditions. Right? Because gene expression changes is dynamic is not constant. So it's different between cells. It's different between environmental conditions. It's different between age and development and so DNA microwaves, microwaves looked at the active genes in a particular cell at a particular time in particular circumstances. So you want to know more, you have to do different cells in different times in different circumstances. So this particular experiment is looking at cancer cells and normal cells under certain conditions. So how this happens is you grow the cells and these plates you take are in a um you take the M. R. N. A. Right? This is the messenger RNA. So this is what's being expressed or trying to be expressed. You reverse transcribe it that produces C. D. N. A. You then label it differently. So we made the cancer cells red and the non cancer cells green we put this onto a microwave which has different probes for pretty much every gene in the cell. And so the probes that are binding well then we'll have this release of color. So if the green binds that means that that gene is being expressed in normal cells. And if the red binds that means that genes being expressed in cancer cells. And you compare the relative levels of green and red. And you may find that in cancer cells there's one gene that's just really expressed but not expressed very much in normal cells and vice versa. You may find a gene that's expressed very highly in normal cells and suppressed and cancer cells and DNA micro roads are looking at expression of these genes. these RNA transcripts in different cells. Second test is going to be a two hybrid test. This is performed in east and this study protein interactions. So how this is done is done using a system called the gal the gal system. But I didn't put it here because I feel like we've talked about the gal genes before and I didn't want to necessarily confuse you. But essentially what this is is there's a promoter region here. This is usually the U. A. S. Region from the galle region. If you are familiar with it you don't necessarily need to know it. And what happens is that in order for transcription to be activated um these two pro you need to come together because how this has been designed is that normally this gal system requires one protein to be activated. So what the scientists have done is they chopped this protein in half and they have attached a bait protein onto it onto one side and a prey protein onto the other side. And so for activation, these two regions need to come together again. And the only way that they'll come together is if the bait and the prey are interacting. So what you see is in this case the bait and the prey are two proteins that normally interact in the self so they come together then these two regions will come together and that will activate transcription if the bait and the prey do not normally interact then they won't come together and transcription will be halted and you say okay well how do you measure transcription? Will you measure transcription through some type of gene called a reporter gene? Usually this is something like uh you may say G. F. P. Which stands for green fluorescent protein. Not super important but know that this protein when it's transcribed and produced produces a green color and you can see it. And so if these two proteins come together and bind transcription of G. F. P will be activated and then you'll see green in the cell. If these two proteins do not bind together, this transcription will not be activated and therefore the cell will not be green. So that's how the two hybrid test works. Another test that's important is chip or chroma tin, immuno precipitation and this looks at protein D. N. A interactions. So how you do this is you have genomic D. N. A. There's protein binding onto it at various regions whether to activate transcription, suppress it. You know, buying two enhancers whatever they're doing, they're buying nature genomic D. N. A. So what you do is you actually um introduce chemicals that cross link it and what crosslink means it means to just sort of bind it tightly together. So it just sort of it's like kind of super glue that really sticks it on there. So those proteins in D. N. A. Will be stuck to each other Like really really difficult to remove. Then you cut the D. N. A. Into pieces. You take antibodies against these proteins you're interested in seeing are they buying D. N. A. And where are they binding? Then you can actually take the D. N. A. You introduce more chemicals. Right. And you separate the D. N. A. From this protein that you've particularly isolated. And so then when you have the D. N. A. You know, you can then sequence it and figure out what sequence this particular protein is binding to. Now. The important part here is specificity. Right? Because the purpose of this is to look at which DNA sequence is this protein binding to. So the specificity comes into the fact that the antibodies that you use are specific only for the one protein that you're investigating. Right. And so you're saying does this P. O. I. Protein bind to D. N. A. And where does it behind? So you use an antibody that specific only for P. 01 P. O. I. Then you can sequence it and figure out is it binding yes or no. Right. If you get no sequences is not binding to D. N. A. And then when you have the sequence the normal sequencing reactions, you can say, okay, well this P. O. I protein is binding to this sequence which is located on chromosome three, you know right here. And that allows you to figure out which proteins are binding to which DNA sequences and what potentially that's doing in relation to nearby genes. And then finally, the last one I'm going to talk about is reverse genetics, which is what is mentioned in your book. But there's actually kind of two sides of reverse genetics. There's um forward genetics and reverse genetics which are very tightly related. So I do want to introduce both of them. But reverse genetics works because you have a gene sequence and you know what's normal. So you've erupt, you disrupt it somehow. You introduce mutations and then you see what happens when you have a mutation. So reverse genetics, say you you know the genotype, you mess it up, you cause a mutation and you say, okay, I'm gonna look at the phenotype. Forward genetics is the opposite of that where you don't know the genotype, but you say you have a weird phenotype, say that a fly only has three legs instead of four. So you take all the three legged flies that you have and you figure out what the genotype is. And so your book only mentions reverse genetics, but it is important to understand the reverse of this, the forward genetics part. Um So that you understand how those two play in together that reverse genetics, those genotype to phenotype, whereas forward genetics go phenotype to genotype. Um So those are some methods with that. Let's now move on

Which of the following terms describes the study of physical interactions between DNA, RNA, and Protein?

• A. Proteomics
• B. Transcriptomics
• C. Metagenomics
• D. Interactomics

Which of the following methods is used to study protein interactions in live cells?

• A. DNA microarrays
• B. Two-hybrid test
• C. ChIP
• D. Reverse genetics

Which of the following methods is used to study protein-DNA interactions?

• A. DNA microarrays
• B. Two-hybrid test
• C. ChIP
• D. Reverse genetics