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15. Genomes and Genomics

Genomics and Human Medicine

15. Genomes and Genomics

Genomics and Human Medicine

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Human Genome Composition

6m

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Hi in this video, we're gonna be talking about the human genome and medicine. So the human genome project was the first major sort of scientific undertaking to sequence the first human genome. And this is super important because without this sequence we have really no idea how many genes we have and therefore we can't you know, we can't do anything to determine whether gene mutations are causing disease. So sequencing the human genome was really the very foundation for a lot of the gene therapies and the personalized medicine that you're hearing about today. And so the human genome project is the main function was to identify what was in the human genome. So what were the major components in the human genome and what they found was actually extremely surprising. And so they were expecting the majority of the genome to be made up of protein coding regions, regions that created that had genes that had proteins. But instead, what they found is that those regions actually only composed of 2% of the genome, meaning 98%. So the overwhelming majority of the human genome does not encode genes. And that was really surprising to the scientists who were doing it Now. That doesn't mean that there are, you know, a small number of genes. Instead there's about 20,000, 25,000 depending on the text book you're using. Um we'll say either number, but it's about 20 let me write that down, whoops 20 to 25 K genes. Now, each gene though can produce more than one protein. Right? So we have protein Aissa forms that are made through alternative splicing. And so this number, although it's 20 to 25 different genes can produce a lot more proteins than 20 to 25 K. But still the overarching concept I want you to grasp here is that the majority of our genome is not composed of genes but is instead composed of other things. And we'll talk a little bit about those things in a second. Now, that means now is the next question was well are the genes equally distributed or the clusters of genes found throughout the genome? And they actually found that there's gene rich regions which are concentrated areas of genes and then gene deserts which are reasons regions without any jeans. And so that was another interesting finding. And then finally comparing individuals. Um there's about a 99% similarity between individuals. And we know our genomes aren't perfectly identical because if they were we would look all exactly the same and we don't. So there are two major concepts that allow for the genome to be different between individuals. So the first one is copy number variations. So these are variation and number of gene copies. So either the gene has been deleted or it's actually been inserted. And copy number variants is actually a big source of variation between identical twins because these copy number variations can occur very very early in development. And so even though identical twins have mostly identical genomes, they actually can have differences in a major differences, copy number variation. And so if it differs in between identical twins, then you can imagine how much it differs between me and you. It's a lot. Then the second type is single nucleotide polymorphisms, short snip. And these are single nucleotide variations between individuals between me and you. And there's actually thousands of these that exist if not even more than that that exists between me and you. There's a major sort of variation in the human genome. Now if we look at the human genome composition, you can see that approaching coding regions here are this dark green area. So proteins and you can see that it's very small and that the overwhelming majority of the entire human genome is made up of other things. And so these are things like um we disappear here. So you can see you have different types of transpose sins which uh we've either seen a video about or we'll see a video about the future depending on the order of your textbook. But these are kind of jumping genes that jump around the genome. We have n tron which make up a huge portion. So these are non coding regions in between the exxons of the protein coding genes. Um These are again transpose sins as well. Um We have duplications hetero chrome button here. So these are places these would be gene deserts. Right? Because hetero chromatic is not going to be expressed. These genes are gonna be expressed and then um this whole 12% unique sequences. And that can it's an interesting category that can include a lot of different things, some of which is still unknown to this day. And so um obviously the human genome is this diverse selection of art of of different molecules that do things other than just couldn't code for proteins. Now the important part of the human genome that the human genome project really discovered and that was a shock at the time was that these non coding regions of the genome are just as important as the coding regions. So the coding regions are only 2%. Right. So 98% are these non coding regions and that therefore they are extremely important. And so there have been a few different projects that have attempted to classify these um since the human genome project, one of these is called the encode project. It's the stands for the encyclopedia in of DNA elements. So I E N C E O D is how that stands for encode. And the encode project is looking for enhancers promoters and pretty much anything that would be a regulatory region in the genome. And so this is a huge undertaking because if we can understand how the genes are regulated, then we may be able to understand what's going wrong in diseased cases. And then another thing is that there are actually a big component of the genome is pseudo genes. So these are sequences that were jeans, they were jeans at some time. They resemble genes in a lot of different ways, but they're nonfunctional or inactive now. And that could be due to some type of mutation or inside insertion or transpose on. There's a lot of different ways that these genes may be an active now or a viral genome insertion. Like I said, lots of different ways, but essentially they were genes. And when you look at this genome, they're like, oh, that looks like a gene, but it's not quite because it's not functional anymore. So with that, let's now turn the page.

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Transgenic Organisms and Gene Therapy

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Okay. So now let's talk about transgenic organisms. And then we'll turn the page and go to gene therapy. So first these transgenic organisms and transgenic organisms are used to study human genes. So transgenic organisms used to study human genes. So what is a transgenic organism? Well a transgenic organism is some organism that contains foreign D. N. A. And so uh typically this is done in a laboratory setting right? Um Where scientists are taking a gene from one organism and putting it into another organism. And we're somewhat familiar with these um They're constantly in the news. Um And in reference to crops like ross, ross, like rice and wheat, these genetically modified organisms that create a lot of controversy. But it's really that's all they are is they're just a plant that contains a gene from another organism. So there's a couple different ways they can be created. Um We have a gene edition which is when some type of gene is added. And then we have a gene knockin um which is where the gene is added but it's added to a specific site. So gene addition is actually fairly simple. There's a lot of very easy ways to get a gene into a genome. But gene knockin is actually much harder because you want it in a specific site. Gene edition doesn't necessarily mean that gene will be expressed. But gene knockin, you're putting it in a specific situation with a specific promoter and it's gonna be in there. Um So examples of these are those wonderfully colored fish you can buy at the supermarket or at a pet store, those glow fish that glow well, these fish are just normal fish. But what they contain is they contain a gene from a jellyfish that allows them to glow those bright colors that you see in the grocery herbs that you see in these pet stores. So that's jean edition. But you can also create a different transgenic organisms by knocking out genes because they don't contain the correct number of genes. So you have gene knockout where the gene is entirely removed or silent, but you can also do gene replacement where you are removing one gene, but then you're adding a gene back in. And so this is an example of how gene replacement or removal of a gene can result in a transgenic organism. And so like I said before, these methods create these genetically modified organisms that we hear are the GMOs that we hear about so often in the news and see those anti GMO labels on certain organic foods. But essentially that's all it is. Is there are just um plants or animals that contain a gene that wouldn't normally be there otherwise. And so um some examples of this is that scientists can create mice um that have a specific disease because they now have that gene that mutated gene, for instance, that's creating that disease. And that way we can use mice to study that disease instead of having to study it in humans. Um but then probably the way we're most familiar with this is through crops or through food. And so one way that agriculture uses this is providing different crops with genes that make them resistant to pests. And so um transgenic organism. So here's an example of a mouse of the transgenic organism. The so these are otherwise genetically identical mice. But with the exception of the brown mouse is a knockout mouse and it's missing the gene for hair growth. And therefore it looks like this little brown mouse where the black mouse that's very genetically similar. Almost identical looks very different from it. Now gene therapy. So human gene therapy uses these trans genes. So these this foreign D. N. A. To treat or potentially if possible cure a disease. And so the buzzword that we hear all the time in the news is going to be personalized genomics or personalized medicine. And essentially what this is is when you have a disease and the doctors are unsure about what's causing it. What they can do is they actually can sequence the diseased individuals D. N. A. And what they're looking for is they're looking for a gene that's mutated. And when they find that mutant gene, what they wanna do is they want to use gene therapy to see if they can correct it or overcome that mutation in a certain way. So generally what this involves it involves um so you have some type of mutated gene right? And it's not working properly. Well gene therapy wants to give the diseased individual the correct version of that gene the un mutated version of that gene or that protein so that the body can create it and it can destroy the mutated version and use that good version that's been added through some type of medicine or shot or something. And so there's two major ways that this is currently done. The first actually uses viruses and it could even use viruses like HIV. Um Which sounds a little scary. But essentially these viruses have been stripped of their normal D. N. A. So all they are is this protein caps it and that protein caps it is what gets them into cells. So what the scientists do is they take something like HIV they take out the D. N. A. And that D. N. A. Is what makes it HIV right? It's what makes it do all the things it needs to do. So if it takes out that D. N. A. And all you're left with is the protein caps. It then pretty much all you have is this like robot essentially robot virus that can get into cells and it will infect but it will inject whatever you want it to. So scientists take that protein caps it and then they put in their own genes. And so this means that this virus can't replicate. It can't make more HIV. So it's not dangerous but what it can do is it can carry a correct version of a gene into a cell. And so when it gets there and it affects it gives the cell that good gene and then the cell has that good gene. It incorporates it into its own genome and then can produce it. And so then it will make the mutated version and the correct version and the cell can use the correct version. And so I'll show you an image of what that looks like in a second. But there are also non viral methods. And these include using these things called liposomes. But essentially they're just like vesicles little tiny vesicles compartments encapsulated by lipids. And they also just contain the gene of interest inside of them right in the middle. And so you can give these disease patients they'll go into for instance the lungs. Which is an example of how this is used and give that D. N. A. To the lung cells and lung cells will create that protein and hopefully will attenuate some of the disease symptoms or potentially even treat or cure the disease. So like I said I used the example lungs I did that for a reason because gene therapy is used for diseases like cystic fibrosis which have a lot of symptoms with a lot of lung symptoms. And so if they can sort of inhale that virus or inhale those liposomes they get into the lungs and they give those lung cells the correct gene which is CFTR that's the mutated gene and cystic fibrosis, you don't need to necessarily know this but I'm just giving it to you in case you're interested. So they normally have a mutated one and that virus can get in there and give them the healthy one. Then the cells can make that healthy protein and overcome at least for a little while some of the symptoms of cystic fibrosis. So here's an example of gene therapy using in this case adenovirus as um an example. So here we have um D. N. A. So this is the viral DNA that allows it to get in and this is the new gene that we're putting in here. So this would be the gene that would treat the disease. And we create these viruses where we have adenovirus here and inside is this. So it contains our new gene. Then we say, okay your virus do what you do best infect cells. And so that's what they do. They encounter cells they infect. They get in, keep going in and eventually they make their way to the nucleus where they just deposit the that gene of interest into the nucleus and then that gene will be transcribed translated produced into a protein which will hopefully treat the disease that you wanted to treat. So in some way this is an example of creating this like transgenic organism. With the exception of the fact that normally these genes that are put in there aren't foreign DNA, but instead just sort of the correct version of the mutated gene itself. So that's gene therapy. It's the coolest thing in the world, I think, that we can just give humans these jeans, um and hope that that will solve some of their disease problems. So with that, let's now move on.

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Problem

Problem

The human genome project discovered that protein coding regions make up what percent of the human genome?

A

1%

B

2%

C

10%

D

90%

4

Problem

Problem

Transgenic organisms are organisms that contain what?

A

DNA from another organism

B

RNA from another organism

C

Protein from another organism

5

Problem

Problem

The purpose of human gene therapy is to what?

A

Remove a mutated gene

B

Remove a mutated RNA

C

Remove a mutated protein

D

Add a normal-functioning gene into the organism

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