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  • My name is Sue Wessler. I'm a professor of Genetics at the University of California, Riverside,

  • and my lab studies what is the subject of the talks today: and those are transposable elements.

  • The title of the general lecture is The Dynamic Genome and the title

  • of this first presentation is Introduction to Transposable Elements. Here I will talk about the discovery

  • of transposable elements, and how this seemingly trivial discovery

  • led to what is now recognized as a revolution in biology. So I start showing pictures

  • that are integral to the talk. The first is a picture of Barbara McClintock who

  • is the discoverer of transposable elements, and I'll tell you more about her as the talk

  • goes on, and the other is the corn kernels which are also integral to the discovery.

  • So I've divided the talk into three parts. The first is a description of the discovery

  • of transposable elements by Barbara McClintock. The second is a little more detailed

  • on how transposable elements actually move and increase their copy number

  • in the genome. And the third is just how abundant transposable elements are in genomes,

  • and this is really the part that made transposable elements more than just a trivial

  • discovery and that has led to transposable elements being viewed as the major

  • component of the genomes of higher organisms. Here's a picture of Barbara McClintock

  • when she was a graduate student. It's a picture of the lab of R.A. Emerson

  • who is the father of maize genetics. This picture was taken at Cornell

  • University in 1929 and in the next talk actually we will come back and revisit

  • this particular area of Cornell. Here's a picture of McClintock and you can see

  • that she wasn't wearing what women normally wore back then - that's a skirt - she wore knickers.

  • I had the good fortune to know her later in her life and I will talk about that a little later.

  • The focus of their lab was corn and corn genetics, and one of the reasons

  • it was such a wonderful organism to study genetics is it had an abundance

  • of interesting visible characteristics - traits. As we found out years later,

  • one of the reasons for this diversity is that it has a remarkably diverse genome. So McClintock

  • asked a very simple question, and this question is really at the heart of this talk

  • and the next talk. And that is "why are these corn kernels spotted?" Now many of you may recognize

  • this corn although it doesn't look like the corn you eat as the corn

  • that you see during Thanksgiving. It's usually hanging up in supermarkets.

  • It's Indian corn. It's known as Indian corn and unlike the corn we eat which is yellow, this corn is highly pigmented.

  • But what's unusual about this particular corn cob here are the spotted

  • corn kernels. McClintock was interested in what is the genetic mechanism responsible

  • for this spotted kernel phenotype. Here's a picture. A lot of McClintock's

  • work because she went on to be world famous is available online and you can actually

  • access her notebooks. This is a picture of her notebook with her typing

  • at the bottom describing these kernels and the genetic basis for their unusual phenotypes.

  • The one thing you'll notice is that the kernels are incredibly detailed.

  • That is one of the reasons that she was able to figure out so much about the behavior

  • of the transposable elements that I'll talk to you about because of the wonderful resolution

  • of the phenotypes in the kernels. I'm going to cut to the chase

  • and tell you McClintock's solution to the spotted corn kernel question and that is that

  • she discovered that spotted corn kernels were caused by a new type of genetic

  • element - a new mutation - and I've diagrammed it here. If we start with the gene,

  • the gene is mutant but not due to a basepair change or deletion, it's due to actually an insertion

  • of a piece of DNA into the gene and this insertion inactivates

  • the gene. But unlike other mutations such as, as I said before, basepair changes or deletions this mutation

  • is reversible. The way it's reversible is that the piece of DNA - the TE or transposable

  • element and you'll see this abbreviation throughout "TE". The TE can insert into the gene

  • and it can then excise from the gene. When it inserts we have a mutant phenotype.

  • When it excises we revert to a wildtype phenotype or normal phenotype.

  • What I've drawn here is a spotted corn kernel.

  • And I've tried to explain how the different sectors in the kernel arise.

  • What you see at the top is a mutant

  • gene and so we can imagine that this gene is a gene responsible for pigment biosynthesis

  • so that if the gene is mutant there's no pigment - the kernel is yellow.

  • If the gene is wildtype, normal, the kernel is purple. To explain a spotted kernel

  • we have to have a reversible phenotype, a reversible mechanism.

  • So what you see is that the colorless areas are due to the gene at the top.

  • That is cells that have the gene at the top that is a gene that is disrupted by a transposable element

  • so it cannot produce the products necessary for pigment biosynthesis

  • and so we end up with the yellow unpigmented areas. However, during kernel development

  • the transposable element can excise from the gene and when it does that it restores expression of the gene

  • and we end up with the spotted kernels and so because kernel development is very regular

  • - that is that unlike in animal systems

  • plant cells when they divide they don't move around they divide and they're literally cemented in place

  • - we end up with these sectors. A large sector is due to a cell

  • in which the transposable element has excised from the gene and all of the mitotic progeny

  • then can express the gene so we end up with a sector much like a clone on a Petri dish of bacteria.

  • As I said before, the rest of the kernel are from cells

  • that still have the transposable element in the gene.

  • McClintock was able to use the behavior of transposable elements and the detailed resolution

  • that the corn kernels facilitated to understand something about the behavior of the element

  • and that's shown in this slide.

  • What we have here at the top is a gene that's pigmented

  • and it's pigmented because the color gene is wildtype.

  • That's one allele: a wildtype gene. We have another allele where we have what I call an 'NTE'.

  • It stands for non-autonomous TE and I'll explain that in a second.

  • What you're going to see here is that there's two different types of transposable elements.

  • One is autonomous, one is non-autonomous and these slides will hopefully clarify what I mean by that.

  • In this case we have a transposable element sitting in a gene,

  • but the transposable element, which is non-autonomous, is not able to move on its own.

  • However, that transposable element can move if there's a second transposable element in the genome

  • and that's shown here as the 'TE' and this is elsewhere in the genome.

  • It could be on a different chromosome. It is not near this color gene,

  • but that transposable element activates the non-autonomous element

  • and causes it to excise from the gene and we end up with a spotted kernel.

  • In the absence of that autonomous element as you see above it,

  • the colorless kernel, the transposable element cannot move.

  • That's why we call it non-autonomous.

  • And finally the last situation is we can have autonomous elements inserting into genes and that's shown here.

  • We have the autonomous element inserting into a gene and because the autonomous element

  • makes everything that is needed for transposition that kernel will be spotted.

  • To review: McClintock not only discovered transposable elements

  • but she also discovered that there are different types of transposable elements

  • and in this case we have the autonomous element and that's defined as an element

  • that provides everything needed for transposition

  • and non-autonomous elements which can only move or transpose in the presence

  • of the autonomous element that is if the autonomous element is in the genome simultaneously.

  • McClintock made her discoveries initially in the 1940s - a very long time ago

  • - but it took a long time for the scientific world to catch up with her.

  • That's why I say here that she was well ahead of her time. In the 40 or 50 years after their discovery,

  • transposable elements which were initially only recognized to be present in maize

  • were found in many organisms in fact in virtually all eukaryotes.

  • In the 1950s transposable elements were discovered in Drosophila fruit fly.

  • In the 1960s, they were discovered in bacteria, in E. coli.

  • And in the 1970s they were discovered in the human genome

  • as a cause of some mutations in the human genome, and we'll talk a lot about that, more about that later.

  • So here is one of my favorite pictures.

  • It is a picture of a transposable element in action in a rose in the Napa Valley.

  • And another picture from my colleague Tom Gerats is a picture of a petunia flower.

  • And the reason that I show you this is that if you look in gardens, rose gardens or other gardens,

  • you will notice these phenotypes.

  • They are not just patterns, which you see with a lot of flowers.

  • They are actually sectors and in case these sectors are completely analogous

  • to the spots on the corn kernels that I showed you before.

  • So McClintock as I said, it took 40 years really for the world, the scientific world,

  • to recognize that her discovery in corn, in maize, was true for most eukaryotes.

  • And in fact what McClintock discovered was that there was more in the genome than just genes.

  • She discovered a new component of the genome.

  • And I've drawn that here as a chromosome before McClintock.

  • showing these rectangular boxes, and those are representations of genes.

  • So before McClintock, people thought, when they thought about it at all,

  • that the genome, that the chromosomes, were essentially genes sort of lined up like beads on a string.

  • After McClintock, it was recognized that there was another component in the genome.

  • And that component as I have drawn as black ellipses here were the transposable elements.

  • So McClintock recognized that these transposable elements were moving around were not coming from

  • the environment. They are not viruses that are infecting the organism.

  • They actually are residents of the genome, and these we now know are residents of most eukaryotic genomes.

  • So for this discovery McClintock was awarded the Nobel Prize in Medicine or Physiology in 1983.

  • Now Nobel Prizes are frequently awarded many years after the discovery.

  • 40 years is a very long time, even for Nobel Prizes.

  • In this really is for the reason I said before. She was really ahead of her time.

  • The other thing is that Nobel Prizes are frequently awarded for up to three people.

  • She was awarded the Nobel Prize by herself,

  • and this really recognizes that this was her discovery.

  • So here is a picture of her. She lived from 1902 to 1992.

  • I had the wonderful fortune of knowing her for the last 10 years of her life,

  • and continuing on with some of her discoveries, and I will be talking about that in the next talk.

  • She also commented on how her life really encompassed the entire history of genetics.

  • So Mendel's laws were rediscovered in 1902, the early part of the 1900s, which was the year of her birth.

  • And she lived long enough first of all to be recognized for her great discoveries, but second of all,

  • to actually see the world enter the genomics age.

  • So the age of DNA sequencing, and that is what we will talk about in a minute.

  • So what I am going to do now is tell you a little bit about how transposable elements move.

  • So we are going to move from the genetics to the molecular biology.

  • So here is a diagram of what a generic transposable element looks like.

  • And so they are very simple genetic systems.

  • This is a piece of DNA. It varies from a couple of hundred nucleotides to several thousand basepairs.

  • Transposable elements are.... this is an autonomous element,

  • so remember this is the element that can move on its own.

  • It encodes everything needed to move itself and to move a non-autonomous element.

  • So when it says everything needed, that is a single protein that it encodes, and that is called transposase.

  • And I will tell you in a minute a little bit more about what transposase does.

  • The element is flanked by special sequences which are called terminal inverted repeats.

  • These are sequences that are the same sequence forward and then flipped over backwards.

  • And I will show you in a minute why, what the functional significance of that is.

  • And the whole element is flanked by a target site duplication. A 'TSD'.

  • And I will show you in a minute how that is derived.

  • So I mentioned that there are autonomous elements and non-autonomous elements.

  • Non-autonomous elements which cannot move on its own.

  • They cannot move on their own.

  • And they require an autonomous element to provide the stuff needed to move them,

  • and you can see here that what we have is a non-autonomous element is sometimes,

  • but not always, a defective version of an autonomous element.

  • So what I have drawn here is a deletion that has been sustained which prevents the non-autonomous element

  • from making transposase.

  • The transposase that is made by the autonomous element, as we will see in a second,

  • can influence both the movement of the autonomous element and the non-autonomous element.

  • So that is shown in this slide.

  • So what I've shown here is the transposase, I am sorry, the autonomous element, which is at the top,

  • encodes a single protein, and that protein is a transposase. And what that transposase does initially

  • is it binds to the ends, to the terminal inverted repeats,

  • of both the autonomous element and the non-autonomous element.

  • So one of the functions that the transposase has is as a DNA binding protein.

  • Ok, so this cartoon sort of will take you through the steps in the transposition

  • of a transposable element.

  • So I've shown here that this is what we saw in the previous slide, but in a more abbreviated form.

  • We have the transposase proteins bound to the ends of a transposable element

  • Those transposase molecules come together and form a dimer.

  • They then cleave the transposable element out of what is called the donor DNA,

  • out of the rest of the DNA, and that entire complex as you see here then can insert somewhere else.

  • So what we end up with is a transposable element in a new location in the genome.

  • So I want to define another term and that is a transposable element family.

  • And this we will see a lot more in the next talk.

  • So a transposable element family, as you saw before, has autonomous elements and non-autonomous elements,

  • and there can be lots and lots of members of the family.

  • So we can have one ore more autonomous elements,

  • one or more... many, many non-autonomous elements in the genome.

  • And as you see here the structure of the non-autonomous element can vary.

  • Sometimes it will be a simple deletion of the transposase region.

  • Sometimes it will be more extensive, and sometimes there may be none of the...

  • the only thing it may share with the autonomous element

  • are the terminal inverted repeats and the length of the target site duplication.

  • So what I am going to do in this slide is to show you how the target site duplication arises.

  • So what you see at the top is going to be a new insertion site of a transposable element.

  • So this is a piece of DNA where the transposase is going to bind.

  • It is going to... we talked before about the transposase binding to the ends of the transposon.

  • Now that is not... this is different from that. This is the target site.

  • This is where the transposable element is going to insert.

  • The transposase has a lot of different functions built into this single protein.

  • One of the functions is to cleave the target site.

  • And it cleaves it in a way that is much like restriction endonucleases.

  • It makes a staggered cut, so you see that here.

  • It cuts on the two strands of the DNA, at essentially the same sequence, and when those strands come apart

  • you see that we are left with these overhangs.

  • These sequence overhangs.

  • It is into this region that the transposable element inserts.

  • Then we are left with these gaps on the side. Those gaps are filled in by host enzymes.

  • And because of this reaction, the transposable element, which is shown in green,

  • is then flanked by a repeat, a target site duplication,

  • which is a... and the length of that duplication in this case,

  • we show that the transposable element is cleaving 5 basepairs. It is a staggered cut of 5 basepairs.

  • The repeat sequence will be 5 basepairs.

  • Different transposases have characteristic staggered cuts.

  • So some transposases will cut three basepairs apart. Some will cut 8 basepairs apart.

  • And the resulting transposable element will then have a target site duplication

  • that is the length of the staggered cut.

  • So again here to remind you, here is our transposable element family.

  • And this is to show you that the families, like all families, like human families,

  • can be different, can look different.

  • What we see here is that there could be multiple autonomous elements in the genome.

  • There could be many, many, many non-autonomous elements in the genome.

  • And we will see more in the second talk.

  • The other thing that differs is that genomes can and do have multiple families of transposable elements.

  • So I've shown you here at the top the family we've been working with