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.