The Dynamic Genome and Transposable Elements
Transcript of Part 1: Introduction to Transposable Elements
00:00:00.06 My name is Sue Wessler. I'm a professor of Genetics at the University of California, Riverside, 00:00:04.14 and my lab studies what is the subject of the talks today: and those are transposable elements. 00:00:10.14 The title of the general lecture is The Dynamic Genome and the title 00:00:15.06 of this first presentation is Introduction to Transposable Elements. Here I will talk about the discovery 00:00:21.17 of transposable elements, and how this seemingly trivial discovery 00:00:25.23 led to what is now recognized as a revolution in biology. So I start showing pictures 00:00:33.11 that are integral to the talk. The first is a picture of Barbara McClintock who 00:00:40.12 is the discoverer of transposable elements, and I'll tell you more about her as the talk 00:00:44.04 goes on, and the other is the corn kernels which are also integral to the discovery. 00:00:51.07 So I've divided the talk into three parts. The first is a description of the discovery 00:00:58.29 of transposable elements by Barbara McClintock. The second is a little more detailed 00:01:04.12 on how transposable elements actually move and increase their copy number 00:01:09.17 in the genome. And the third is just how abundant transposable elements are in genomes, 00:01:15.01 and this is really the part that made transposable elements more than just a trivial 00:01:23.23 discovery and that has led to transposable elements being viewed as the major 00:01:29.24 component of the genomes of higher organisms. Here's a picture of Barbara McClintock 00:01:36.00 when she was a graduate student. It's a picture of the lab of R.A. Emerson 00:01:41.23 who is the father of maize genetics. This picture was taken at Cornell 00:01:47.23 University in 1929 and in the next talk actually we will come back and revisit 00:01:54.09 this particular area of Cornell. Here's a picture of McClintock and you can see 00:02:01.24 that she wasn't wearing what women normally wore back then - that's a skirt - she wore knickers. 00:02:07.14 I had the good fortune to know her later in her life and I will talk about that a little later. 00:02:13.06 The focus of their lab was corn and corn genetics, and one of the reasons 00:02:20.26 it was such a wonderful organism to study genetics is it had an abundance 00:02:24.24 of interesting visible characteristics - traits. As we found out years later, 00:02:31.29 one of the reasons for this diversity is that it has a remarkably diverse genome. So McClintock 00:02:40.28 asked a very simple question, and this question is really at the heart of this talk 00:02:46.20 and the next talk. And that is "why are these corn kernels spotted?" Now many of you may recognize 00:02:54.08 this corn although it doesn't look like the corn you eat as the corn 00:02:57.29 that you see during Thanksgiving. It's usually hanging up in supermarkets. 00:03:01.16 It's Indian corn. It's known as Indian corn and unlike the corn we eat which is yellow, this corn is highly pigmented. 00:03:08.22 But what's unusual about this particular corn cob here are the spotted 00:03:16.20 corn kernels. McClintock was interested in what is the genetic mechanism responsible 00:03:23.18 for this spotted kernel phenotype. Here's a picture. A lot of McClintock's 00:03:30.24 work because she went on to be world famous is available online and you can actually 00:03:36.20 access her notebooks. This is a picture of her notebook with her typing 00:03:41.09 at the bottom describing these kernels and the genetic basis for their unusual phenotypes. 00:03:46.11 The one thing you'll notice is that the kernels are incredibly detailed. 00:03:51.17 That is one of the reasons that she was able to figure out so much about the behavior 00:03:58.24 of the transposable elements that I'll talk to you about because of the wonderful resolution 00:04:03.24 of the phenotypes in the kernels. I'm going to cut to the chase 00:04:08.09 and tell you McClintock's solution to the spotted corn kernel question and that is that 00:04:15.26 she discovered that spotted corn kernels were caused by a new type of genetic 00:04:21.18 element - a new mutation - and I've diagrammed it here. If we start with the gene, 00:04:26.23 the gene is mutant but not due to a basepair change or deletion, it's due to actually an insertion 00:04:35.10 of a piece of DNA into the gene and this insertion inactivates 00:04:41.11 the gene. But unlike other mutations such as, as I said before, basepair changes or deletions this mutation 00:04:49.05 is reversible. The way it's reversible is that the piece of DNA - the TE or transposable 00:04:56.24 element and you'll see this abbreviation throughout "TE". The TE can insert into the gene 00:05:03.09 and it can then excise from the gene. When it inserts we have a mutant phenotype. 00:05:08.13 When it excises we revert to a wildtype phenotype or normal phenotype. 00:05:13.09 What I've drawn here is a spotted corn kernel. 00:05:17.00 And I've tried to explain how the different sectors in the kernel arise. 00:05:23.07 What you see at the top is a mutant 00:05:27.09 gene and so we can imagine that this gene is a gene responsible for pigment biosynthesis 00:05:33.10 so that if the gene is mutant there's no pigment - the kernel is yellow. 00:05:37.23 If the gene is wildtype, normal, the kernel is purple. To explain a spotted kernel 00:05:44.04 we have to have a reversible phenotype, a reversible mechanism. 00:05:48.16 So what you see is that the colorless areas are due to the gene at the top. 00:05:56.06 That is cells that have the gene at the top that is a gene that is disrupted by a transposable element 00:06:01.11 so it cannot produce the products necessary for pigment biosynthesis 00:06:06.21 and so we end up with the yellow unpigmented areas. However, during kernel development 00:06:12.05 the transposable element can excise from the gene and when it does that it restores expression of the gene 00:06:19.01 and we end up with the spotted kernels and so because kernel development is very regular 00:06:25.14 - that is that unlike in animal systems 00:06:28.03 plant cells when they divide they don't move around they divide and they're literally cemented in place 00:06:33.07 - we end up with these sectors. A large sector is due to a cell 00:06:40.18 in which the transposable element has excised from the gene and all of the mitotic progeny 00:06:46.22 then can express the gene so we end up with a sector much like a clone on a Petri dish of bacteria. 00:06:54.11 As I said before, the rest of the kernel are from cells 00:06:59.13 that still have the transposable element in the gene. 00:07:02.03 McClintock was able to use the behavior of transposable elements and the detailed resolution 00:07:15.01 that the corn kernels facilitated to understand something about the behavior of the element 00:07:23.11 and that's shown in this slide. 00:07:25.02 What we have here at the top is a gene that's pigmented 00:07:28.28 and it's pigmented because the color gene is wildtype. 00:07:32.15 That's one allele: a wildtype gene. We have another allele where we have what I call an 'NTE'. 00:07:40.04 It stands for non-autonomous TE and I'll explain that in a second. 00:07:44.07 What you're going to see here is that there's two different types of transposable elements. 00:07:47.26 One is autonomous, one is non-autonomous and these slides will hopefully clarify what I mean by that. 00:07:53.21 In this case we have a transposable element sitting in a gene, 00:07:57.28 but the transposable element, which is non-autonomous, is not able to move on its own. 00:08:02.01 However, that transposable element can move if there's a second transposable element in the genome 00:08:10.21 and that's shown here as the 'TE' and this is elsewhere in the genome. 00:08:14.02 It could be on a different chromosome. It is not near this color gene, 00:08:18.03 but that transposable element activates the non-autonomous element 00:08:23.07 and causes it to excise from the gene and we end up with a spotted kernel. 00:08:28.27 In the absence of that autonomous element as you see above it, 00:08:32.24 the colorless kernel, the transposable element cannot move. 00:08:35.19 That's why we call it non-autonomous. 00:08:37.29 And finally the last situation is we can have autonomous elements inserting into genes and that's shown here. 00:08:45.19 We have the autonomous element inserting into a gene and because the autonomous element 00:08:49.26 makes everything that is needed for transposition that kernel will be spotted. 00:08:55.11 To review: McClintock not only discovered transposable elements 00:09:00.23 but she also discovered that there are different types of transposable elements 00:09:06.02 and in this case we have the autonomous element and that's defined as an element 00:09:10.07 that provides everything needed for transposition 00:09:14.00 and non-autonomous elements which can only move or transpose in the presence 00:09:20.11 of the autonomous element that is if the autonomous element is in the genome simultaneously. 00:09:24.26 McClintock made her discoveries initially in the 1940s - a very long time ago 00:09:34.00 - but it took a long time for the scientific world to catch up with her. 00:09:38.27 That's why I say here that she was well ahead of her time. In the 40 or 50 years after their discovery, 00:09:45.08 transposable elements which were initially only recognized to be present in maize 00:09:51.00 were found in many organisms in fact in virtually all eukaryotes. 00:09:56.08 In the 1950s transposable elements were discovered in Drosophila fruit fly. 00:10:01.15 In the 1960s, they were discovered in bacteria, in E. coli. 00:10:05.11 And in the 1970s they were discovered in the human genome 00:10:10.01 as a cause of some mutations in the human genome, and we'll talk a lot about that, more about that later. 00:10:14.23 So here is one of my favorite pictures. 00:10:18.04 It is a picture of a transposable element in action in a rose in the Napa Valley. 00:10:25.04 And another picture from my colleague Tom Gerats is a picture of a petunia flower. 00:10:32.12 And the reason that I show you this is that if you look in gardens, rose gardens or other gardens, 00:10:38.11 you will notice these phenotypes. 00:10:40.06 They are not just patterns, which you see with a lot of flowers. 00:10:42.19 They are actually sectors and in case these sectors are completely analogous 00:10:47.21 to the spots on the corn kernels that I showed you before. 00:10:50.04 So McClintock as I said, it took 40 years really for the world, the scientific world, 00:10:58.12 to recognize that her discovery in corn, in maize, was true for most eukaryotes. 00:11:06.26 And in fact what McClintock discovered was that there was more in the genome than just genes. 00:11:16.21 She discovered a new component of the genome. 00:11:18.06 And I've drawn that here as a chromosome before McClintock. 00:11:24.00 showing these rectangular boxes, and those are representations of genes. 00:11:27.27 So before McClintock, people thought, when they thought about it at all, 00:11:32.03 that the genome, that the chromosomes, were essentially genes sort of lined up like beads on a string. 00:11:38.01 After McClintock, it was recognized that there was another component in the genome. 00:11:43.27 And that component as I have drawn as black ellipses here were the transposable elements. 00:11:48.14 So McClintock recognized that these transposable elements were moving around were not coming from 00:11:56.28 the environment. They are not viruses that are infecting the organism. 00:11:59.26 They actually are residents of the genome, and these we now know are residents of most eukaryotic genomes. 00:12:08.14 So for this discovery McClintock was awarded the Nobel Prize in Medicine or Physiology in 1983. 00:12:18.03 Now Nobel Prizes are frequently awarded many years after the discovery. 00:12:25.13 40 years is a very long time, even for Nobel Prizes. 00:12:31.01 In this really is for the reason I said before. She was really ahead of her time. 00:12:34.19 The other thing is that Nobel Prizes are frequently awarded for up to three people. 00:12:39.00 She was awarded the Nobel Prize by herself, 00:12:43.07 and this really recognizes that this was her discovery. 00:12:47.27 So here is a picture of her. She lived from 1902 to 1992. 00:12:53.19 I had the wonderful fortune of knowing her for the last 10 years of her life, 00:12:57.12 and continuing on with some of her discoveries, and I will be talking about that in the next talk. 00:13:04.07 She also commented on how her life really encompassed the entire history of genetics. 00:13:15.25 So Mendel's laws were rediscovered in 1902, the early part of the 1900s, which was the year of her birth. 00:13:23.05 And she lived long enough first of all to be recognized for her great discoveries, but second of all, 00:13:30.16 to actually see the world enter the genomics age. 00:13:33.13 So the age of DNA sequencing, and that is what we will talk about in a minute. 00:13:36.26 So what I am going to do now is tell you a little bit about how transposable elements move. 00:13:44.05 So we are going to move from the genetics to the molecular biology. 00:13:46.11 So here is a diagram of what a generic transposable element looks like. 00:13:57.17 And so they are very simple genetic systems. 00:14:00.23 This is a piece of DNA. It varies from a couple of hundred nucleotides to several thousand basepairs. 00:14:07.21 Transposable elements are.... this is an autonomous element, 00:14:10.27 so remember this is the element that can move on its own. 00:14:13.26 It encodes everything needed to move itself and to move a non-autonomous element. 00:14:18.19 So when it says everything needed, that is a single protein that it encodes, and that is called transposase. 00:14:24.24 And I will tell you in a minute a little bit more about what transposase does. 00:14:27.25 The element is flanked by special sequences which are called terminal inverted repeats. 00:14:35.08 These are sequences that are the same sequence forward and then flipped over backwards. 00:14:39.27 And I will show you in a minute why, what the functional significance of that is. 00:14:45.12 And the whole element is flanked by a target site duplication. A 'TSD'. 00:14:51.20 And I will show you in a minute how that is derived. 00:14:53.21 So I mentioned that there are autonomous elements and non-autonomous elements. 00:14:57.28 Non-autonomous elements which cannot move on its own. 00:15:01.13 They cannot move on their own. 00:15:03.09 And they require an autonomous element to provide the stuff needed to move them, 00:15:11.01 and you can see here that what we have is a non-autonomous element is sometimes, 00:15:15.15 but not always, a defective version of an autonomous element. 00:15:21.08 So what I have drawn here is a deletion that has been sustained which prevents the non-autonomous element 00:15:29.29 from making transposase. 00:15:33.05 The transposase that is made by the autonomous element, as we will see in a second, 00:15:36.29 can influence both the movement of the autonomous element and the non-autonomous element. 00:15:42.25 So that is shown in this slide. 00:15:45.11 So what I've shown here is the transposase, I am sorry, the autonomous element, which is at the top, 00:15:51.13 encodes a single protein, and that protein is a transposase. And what that transposase does initially 00:15:56.14 is it binds to the ends, to the terminal inverted repeats, 00:15:59.24 of both the autonomous element and the non-autonomous element. 00:16:04.23 So one of the functions that the transposase has is as a DNA binding protein. 00:16:09.29 Ok, so this cartoon sort of will take you through the steps in the transposition 00:16:17.18 of a transposable element. 00:16:20.05 So I've shown here that this is what we saw in the previous slide, but in a more abbreviated form. 00:16:25.01 We have the transposase proteins bound to the ends of a transposable element 00:16:32.16 Those transposase molecules come together and form a dimer. 00:16:38.05 They then cleave the transposable element out of what is called the donor DNA, 00:16:45.09 out of the rest of the DNA, and that entire complex as you see here then can insert somewhere else. 00:16:53.19 So what we end up with is a transposable element in a new location in the genome. 00:16:58.12 So I want to define another term and that is a transposable element family. 00:17:06.12 And this we will see a lot more in the next talk. 00:17:09.27 So a transposable element family, as you saw before, has autonomous elements and non-autonomous elements, 00:17:16.18 and there can be lots and lots of members of the family. 00:17:21.06 So we can have one ore more autonomous elements, 00:17:23.26 one or more... many, many non-autonomous elements in the genome. 00:17:28.15 And as you see here the structure of the non-autonomous element can vary. 00:17:31.14 Sometimes it will be a simple deletion of the transposase region. 00:17:36.18 Sometimes it will be more extensive, and sometimes there may be none of the... 00:17:39.22 the only thing it may share with the autonomous element 00:17:44.00 are the terminal inverted repeats and the length of the target site duplication. 00:17:49.28 So what I am going to do in this slide is to show you how the target site duplication arises. 00:17:56.11 So what you see at the top is going to be a new insertion site of a transposable element. 00:18:02.06 So this is a piece of DNA where the transposase is going to bind. 00:18:08.28 It is going to... we talked before about the transposase binding to the ends of the transposon. 00:18:14.01 Now that is not... this is different from that. This is the target site. 00:18:16.20 This is where the transposable element is going to insert. 00:18:20.06 The transposase has a lot of different functions built into this single protein. 00:18:26.05 One of the functions is to cleave the target site. 00:18:31.05 And it cleaves it in a way that is much like restriction endonucleases. 00:18:34.23 It makes a staggered cut, so you see that here. 00:18:37.08 It cuts on the two strands of the DNA, at essentially the same sequence, and when those strands come apart 00:18:43.27 you see that we are left with these overhangs. 00:18:48.28 These sequence overhangs. 00:18:50.18 It is into this region that the transposable element inserts. 00:18:54.02 Then we are left with these gaps on the side. Those gaps are filled in by host enzymes. 00:19:01.04 And because of this reaction, the transposable element, which is shown in green, 00:19:05.18 is then flanked by a repeat, a target site duplication, 00:19:11.08 which is a... and the length of that duplication in this case, 00:19:16.09 we show that the transposable element is cleaving 5 basepairs. It is a staggered cut of 5 basepairs. 00:19:22.10 The repeat sequence will be 5 basepairs. 00:19:25.03 Different transposases have characteristic staggered cuts. 00:19:30.29 So some transposases will cut three basepairs apart. Some will cut 8 basepairs apart. 00:19:36.08 And the resulting transposable element will then have a target site duplication 00:19:41.02 that is the length of the staggered cut. 00:19:44.26 So again here to remind you, here is our transposable element family. 00:19:53.00 And this is to show you that the families, like all families, like human families, 00:19:57.19 can be different, can look different. 00:20:00.12 What we see here is that there could be multiple autonomous elements in the genome. 00:20:04.17 There could be many, many, many non-autonomous elements in the genome. 00:20:07.27 And we will see more in the second talk. 00:20:10.29 The other thing that differs is that genomes can and do have multiple families of transposable elements. 00:20:21.08 So I've shown you here at the top the family we've been working with 00:20:25.17 with where the transposase, the blue family, 00:20:27.20 where the transposase is produced and binds to all the yellow terminal inverted repeats. 00:20:35.12 At the same time the genome could also have a different family. 00:20:39.07 And I've shown the green family at the bottom. 00:20:42.13 The transposase from this family binds specifically to the purple terminal inverted repeats. 00:20:48.13 So in this way there can be multiple families that co-exist in a genome 00:20:52.29 that have really nothing to do with each other. 00:20:55.26 What I want to do now is in a few slides take you through... What I haven't explained to you 00:21:03.04 is... I've told you that there are multiple copies of transposable elements in the genome. 00:21:07.18 But I haven't explained how a transposable element can increase its copy number. 00:21:11.29 Because in fact what I have told you is sort of the opposite. 00:21:14.11 What I have told you is that a transposable element at one place 00:21:17.00 excises and moves someplace else. And I am not really great at math, 00:21:22.01 but I can figure out that that won't increase the copy number. 00:21:25.10 You start with one. You move from one site; you move to another. 00:21:28.02 So I want to show you in the next couple of slides is, just very simply, 00:21:32.04 I'll show you a schematic on how by doing that a transposable element can actually increase its copy number. 00:21:37.21 Because the copy number of transposable elements will be a major part of the talk, the rest of this talk 00:21:43.20 and the talk that follows. 00:21:45.16 So what I have drawn here is at the top I have a transposable element at a particular site 00:21:51.05 in the genome. That region is now ... the DNA is being replicated. 00:21:56.06 And what we see is the familiar replication fork. So here are the sister chromatids. OK, 00:22:03.22 so what happens, this is the same thing at the top, we are replicating. 00:22:08.12 The transposable element is going to move from one of the sister chromatids after replication 00:22:14.11 to another site, to the other sister chromatid. 00:22:17.12 And that is shown at the bottom here. 00:22:20.00 So I've redrawn that at the top and what happens after this is kind of neat. 00:22:30.19 The site, the empty site here, sometimes it remains empty, 00:22:36.17 sometimes the host will use the transposable element on the sister chromatid 00:22:42.20 to copy it into that empty site, and that is what you see at the bottom here. 00:22:46.14 So when these chromosomes... when replication is finished, 00:22:50.22 and we end up with two double stranded daughter strands, 00:22:56.11 what we have is the top strand has one transposable element, 00:22:59.15 and the bottom strand has two transposable elements. 00:23:02.20 So we've gone from a situation where we had two transposable elements, 00:23:05.06 I am sorry, one transposable element, 00:23:06.25 to one that now we have two. 00:23:09.24 These chromatids will separate and they will go into separate cells. 00:23:13.12 So one cell will have two transposons, and one will have one. 00:23:16.06 And I think in the next slide what I have done is I have summarized all of the steps. 00:23:21.11 So we start out with a single transposable element. 00:23:24.00 There is replication. There is transposition that occurs from one sister chromatid to the other. 00:23:31.00 There's repair of the empty site using the transposon from the sister chromatid. 00:23:37.01 And there is separation of the chromatids, and we end up with an increase in one transposon in one of the cells. 00:23:43.08 That is one mechanism. There is another mechanism which I have just drawn as a shortcut here. 00:23:48.18 And that is you see at the top just what we started with before. We have a transposable element. 00:23:53.28 We have replication. We then have transposition not from a replicated site into another replicated site, 00:24:01.00 but instead from a replicated site into an unreplicated site ahead of the replication fork. 00:24:07.27 What happens then is again we will have the completion of replication, 00:24:15.09 and we end up with a separation of strands, 00:24:18.08 and we end up again with a gain in the number of transposable elements. 00:24:23.13 So I have told you so far I have focused on one... what is now known to be one 00:24:31.23 of two classes of transposable elements that are in the genome. 00:24:35.07 The elements that were discovered by McClintock and that are responsible for the unstable, 00:24:41.01 for the spotted kernels, the sectored flowers, 00:24:45.12 those are caused by the element type that I have shown you here 00:24:51.02 with a transposase with terminal inverted repeats, 00:24:54.00 but there in fact is another class of transposable elements that I am not really focusing on in this talk. 00:25:01.17 And I am only going to mention it briefly. 00:25:05.07 But these are in fact incredibly abundant transposable elements. 00:25:09.00 They are called retrotransposons. 00:25:13.03 And these are called now Class 1 transposons. 00:25:17.05 Whereas the DNA transposons that McClintock studied are called Class 2 transposons. 00:25:23.17 Now the retrotransposon is characterized by terminal inverted repeats, 00:25:31.07 long terminal inverted repeats, where the ends of the element are not inverted repeats like the DNA transposon, 00:25:38.02 they are direct repeats which are shown here. 00:25:41.04 They also have a target site duplication because 00:25:44.13 the insertion occurs in the same way as the insertion of DNA transposons. 00:25:48.10 And now I am calling them DNA transposons and RNA transposons 00:25:51.18 and the reason is they're named for the intermediate in transposition. 00:25:57.16 So a DNA transposon excises from one site as a DNA element and moves elsewhere. 00:26:03.20 In contrast, an RNA transposon or retrotransposon, the intermediate is RNA, 00:26:09.15 and I've summarized that in the next slide. 00:26:12.27 So here I have shown you a retrotransposon sitting inserted into a chromosome somewhere. 00:26:25.23 The element is transcribed much like a gene. 00:26:29.15 That RNA then is converted into... it is copied into DNA, into a DNA copy. 00:26:39.10 And this is copied by an enzyme called reverse transcriptase, 00:26:42.11 and it is encoded by the retrotransposon. 00:26:46.00 That is then converted into a double stranded DNA molecule. 00:26:51.13 And that double stranded DNA molecule inserts elsewhere in the genome. 00:26:57.05 So this is a lot easier than the DNA transposition mechanism that I showed you before. 00:27:01.06 In essence you could think of a retrotransposon as like a printing press. 00:27:05.21 It makes RNAs and each of those RNAs potentially could be converted 00:27:10.09 into a double stranded DNA, and that double stranded DNA can insert elsewhere in the genome. 00:27:16.13 So a single element because there can be many, many transcripts that come from a single element, 00:27:23.07 a single element could potentially lead to hundreds and hundreds of new 00:27:28.08 integrations, of new copies in the genome. 00:27:30.26 So I've told you about the discovery of transposable elements. 00:27:36.19 I've told you about, something about how elements move and increase their copy number 00:27:42.03 Now I want to sort of wow you with something that I think 00:27:45.13 has been one of the major findings of this era of genomics, 00:27:51.04 and that is just how many transposable elements there are in the genomes of higher organisms. 00:27:56.28 So, when we started sequencing genomes, 00:28:03.05 and when I say we I am using the general "we" of the scientific community. 00:28:06.12 It turns out that the largest component of genomes are derived from transposable elements. 00:28:13.03 50% of the human genome, of the chimp genome, of the mouse genome, 00:28:18.19 more or less fifty percent are derived from transposable element sequences. 00:28:23.24 Plants, especially flowering plants have even higher proportions of their genomes that are transposable elements. 00:28:31.19 The maize genome, over 75% of the genome is derived from transposable elements. 00:28:37.16 The barley genome, and we will be talking more about these creatures in the next talk. 00:28:45.29 The barley genome is almost 85% transposable elements. 00:28:49.17 And even more remarkable, the iris genome is 98% transposable elements. 00:28:53.29 And I don't know about you, but if I look at an iris plant, I mean they are beautiful, 00:28:57.14 there is nothing that would tell us that their genomes are just largely transposable elements. 00:29:06.13 I want to give you a feel for how many transposable elements there are in the human genome. 00:29:12.07 So our genome is comprised of 2.5 billion basepairs. 00:29:20.13 Let's call them A, G, C, of T. Let's say that's 2.5 billion letters, like A, B, C, and D. 00:29:26.16 So if they are letters, let's start filling up some books. 00:29:32.05 So this is equivalent to about a thousand textbooks of a thousand pages each. No pictures. 00:29:38.28 Only 20 to 40 of those 1,000 textbooks contain all of the genes necessary 00:29:52.13 to encode the proteins that make us up. 00:29:56.00 Five hundred of the 1000 textbooks contain sequences that are derived from transposable elements. 00:30:01.28 So it is pretty stunning. 00:30:04.00 To give you and idea of just how many transposable elements there are and where they are 00:30:11.23 I am showing you an example of a typical human gene. 00:30:14.26 And what you see are the green boxes which are the exons, 00:30:18.07 coding regions, and the blue areas which are the introns. 00:30:23.06 Let's look and see where there are transposable elements in this gene. 00:30:26.22 Because there are transposable elements in 70-80 percent of our genes contain transposable elements. 00:30:32.08 So this shows you all the different places that this genes has transposable elements. 00:30:38.14 What you'll notice, it is kind of hard to tell in this slide, but that mostly the non-coding regions, 00:30:44.26 the non-exonic regions contain some transposable elements. 00:30:49.14 In fact some human genes have almost a hundred transposable elements in their introns. 00:30:54.27 So transposable elements are really everywhere. 00:30:58.19 So what I want to show you in the next slide is how transposable elements 00:31:03.23 can diversify a group of very, very closely related organisms. 00:31:08.10 And for this I am going to go back to plants, and I am going to show you 00:31:13.20 a group of organisms that we are very familiar with - the cereal grasses. 00:31:17.00 You may not know I came from New York City, 00:31:19.13 so I didnâ€™t realize that all of these were in fact members of the grass clade. 00:31:24.08 They are rice, sorghum, maize, and barley are some of the most important organisms 00:31:32.03 on this planet for human calories. 00:31:35.09 And what you see here, we've talked about maize a lot. 00:31:39.26 Maize... the maize genome size is 2500 megabases. 00:31:43.09 That's about the same size as the human genome. 00:31:46.12 However, what you see is that relatively closely related organisms, 00:31:51.16 such as the rice genome has a genome size that is almost ten times smaller, 350 megabases. 00:31:58.05 Sorghum is twice the size of that, 700 megabases. Barley is 5000 megabases. 00:32:03.26 These genomes have gone through a remarkable expansion. 00:32:07.18 An explosion. 00:32:08.15 And what's responsible for that largely is the increase in the genome size due to transposable elements. 00:32:15.08 How do organisms function with that much stuff? 00:32:20.23 There is actually three major reasons for the success of organisms 00:32:26.06 despite being crowded with that many transposable elements. 00:32:29.13 The first thing is that most of the transposable elements in the genome 00:32:33.11 are dead. And when I say dead, I mean they can't move. 00:32:36.18 They don't move anymore. They probably haven't moved for a long time. 00:32:40.03 And they are dead because they are mutated. They contain mutations. 00:32:44.14 So every single generation mutations are introduced into our DNA. 00:32:49.11 Mutations that occur in genes will lead to problems for the organism, and they are selected against. 00:32:56.20 However, mutations that occur in transposable elements just accumulate. 00:32:59.24 It's not a problem to the organism at all. 00:33:02.01 So we end up with most of the transposons, the vast majority of the 50% of our genome 00:33:07.19 that are transposable elements are not able to move around anymore. 00:33:10.25 And will never move around. They will just sort of, as we say, senesce. 00:33:15.15 The sequences will mutate and mutate 00:33:17.13 until there is really no trace that they ever were derived from a transposable element. 00:33:20.20 The second way that organisms survive, it's really how transposable elements survive, 00:33:28.18 is that transposable elements have evolved mechanisms that allow them to insert into places in the genome 00:33:36.21 that won't harm the organism. 00:33:39.24 So for example, one safe haven might be into another transposable element. 00:33:44.22 So if a transposable element inserts there, it is not inserting... it is not causing 00:33:49.01 a mutation in any of the genes necessary for the organism to survive. 00:33:53.24 And we will talk a lot more about that in the second talk. 00:33:58.09 The final thing which I am just going to allude to briefly here 00:34:00.22 is that the host has a way to fight transposable elements, and it is a very sophisticated way. 00:34:06.10 The host silences transposable elements using epigenetic mechanisms and inactivates them. 00:34:14.15 And I've... I'll show you on the next slide. 00:34:18.10 So this is just an example of a region of the barley chromosome. 00:34:23.00 And what you see are... remember I said that 85% of the barley genome is derived from transposable elements. 00:34:30.12 And this is how a region of the genome might look. 00:34:33.25 So here we have a few genes, the little blue boxes over there. 00:34:36.14 And what you see stacked up here are all the transposable elements. 00:34:40.12 They are the vast majority of this particular region of the gene. 00:34:43.24 So, but if you look at a flat version of the DNA, 00:34:50.02 if you actually look at the three dimensional structure, the chromatin, 00:34:53.09 the way the genome exists, what you find is that the region where these transposable elements are clustered 00:35:02.25 in fact is a tightly compacted region of the genome. 00:35:06.24 It is what's called heterochromatin. 00:35:08.22 There's very little, nothing really... This is a host response. 00:35:16.11 It condenses the chromatin and prevents the transposons 00:35:20.28 from making the transcripts and proteins needed for it to move. 00:35:25.18 So they are said to be silenced. 00:35:28.01 This in addition to the fact that these transposable elements are accumulating mutations. 00:35:31.20 In contrast, the region where the host needs the genes to be expressed, 00:35:38.02 those are euchromatic regions. They are less condensed. 00:35:42.21 So the genome, the chromosome, is composed of regions that are very, very densely compacted, 00:35:49.26 and that is generally where the transposable elements are, 00:35:52.15 and regions that are much less compacted so that the host can access 00:35:56.08 those to make the gene products needed for its development in life. 00:36:00.26 So like many things with transposable elements, McClintock was ahead of her time. 00:36:07.05 She didn't only discover transposable elements, 00:36:09.24 but she proposed that they had a role in generating diversity. 00:36:15.16 And this scenario had the following components. 00:36:19.27 That transposable elements in the genome usually do not move around, 00:36:24.00 because if they did move around, they would cause mutations. 00:36:26.22 That "stress" conditions may activate transposable elements. 00:36:32.00 Now when I say stress conditions I am thinking more... I am not talking about like driving in rush hour traffic, 00:36:36.17 I am talking more about climate change, that might be one thing. 00:36:40.26 This is a scenario. This is not proven by any means. 00:36:44.12 This was her ideas 20 or 30 years ago. 00:36:48.05 So genomes have a stash of transposable elements. Most are inactive, some are active. 00:36:54.29 And the host is keeping them inactive by these epigenetic mechanisms, but if something happens to the host, 00:37:03.27 some of these, or the host population, some of these transposable elements can be activated to move around. 00:37:09.16 The significance of that is that the movement of transposable elements will generate genetic diversity. 00:37:17.03 And it will do this by increasing the frequency of mutation. 00:37:20.11 So what we end up with is a population that is now more diverse because of the movement of transposable elements. 00:37:26.10 There is new mutations in that population, and it is possible that some of those new mutations may be adaptive. 00:37:34.10 May help the population survive this dramatic change in climate, or whatever. 00:37:40.04 So I want to end by essentially saying to you that the way I think of transposable elements 00:37:49.01 is that they shake up the genome. And the genome is inherently conservative. 00:37:54.26 So they shake up an otherwise conservative genome in ways that we are jut beginning to understand 00:37:59.25 and ways that I will go into in the next talk.