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  • My name is Sue Wessler. I am a Professor of Genetics at the University of California, Riverside.

  • And my lab studies transposable elements.

  • The title of these two presentations are The Dynamic Genome.

  • In the first talk I introduced transposable elements by describing their discovery by Barbara McClintock,

  • how they move, and how that discovery over the years was recognized as a major revolution in biology

  • as it became appreciated that transposable elements

  • are the major component of most of the genomes of higher eukaryotes.

  • In this talk I am going to go into detail about how my lab

  • studies the evolutionary impact of transposable elements on genomes.

  • And how we develop strategies to identify elements

  • that have an impact on transposable elements.

  • I have divided this talk into three parts.

  • In the first part I talk about the transition from genetic approaches to genomic approaches

  • in order to identify elements that in fact impact genome evolution.

  • The elements that were discovered in my lab are called MITEs,

  • and I will tell you about that discovery in the second part of this talk.

  • And in the final part of the talk I will tell you about how MITEs

  • are able to increase their copy number in the genome without harming the host significantly.

  • So to review the first part, we talked about the genetic analysis of transposable elements,

  • how genetic analysis led to the discovery of transposable elements,

  • and I used this spotted corn kernel as an example to tell you really how powerful the genetic analysis was.

  • So when you see a spotted corn kernel like this,

  • we know, the geneticist knows, that the reason that kernel is spotted

  • is because there are active transposable elements.

  • There are... that is the spots reflect the movement of transposable elements.

  • The other thing the genetics tells us is exactly where in the genome that active transposable element is.

  • So for example, here when we are looking at spotted corn kernels,

  • we know that there is an active transposable element, in other words, one that is capable of moving

  • in a gene responsible for kernel pigmentation.

  • The other thing that the genetics tells us is the type of element that's there.

  • And I described at the beginning of the first talk the difference between autonomous elements,

  • that is, ones that encode transposase, and non-autonomous elements.

  • Those are the elements that don't make transposase

  • but are able to move if there is an autonomous element in the genome.

  • McClintock and others were able to deduce this just by looking at the behavior

  • of transposable elements in crosses.

  • Now that is the good news about the genetic analysis.

  • Unfortunately the genetic analysis is limited in its scope.

  • And that is that by its very nature genetics depends on the analysis of mutant alleles,

  • and so the transposable elements that were being studied were the ones causing mutations.

  • They were mutagenic elements.

  • Now because these elements cause mutations, there aren't many copies of them in the genome.

  • So, I mentioned in the first talk that genomes are up to 50-80%

  • of the genome sequence is derived from transposable elements.

  • However, the elements that cause mutations are not those elements.

  • And you can understand that an element that causes mutation is eventually,

  • if its copy number increases too high, will kill the host.

  • So these are.... these are a special class of transposable elements that cause mutations.

  • And as such these elements really have a minimal impact on genome evolution.

  • They're bad. They are really bad.

  • So McClintock as I also described in the first talk,

  • not only discovered transposable elements,

  • but she hypothesized that they were also tools that diversify organisms.

  • And to review, she hypothesized that transposable elements that are in the genome

  • do not move around frequently,

  • that there are conditions, such as changes in climate for example,

  • that could activate transposable elements.

  • that this activation would generate genetic diversity in the population

  • by increasing the frequency of mutation,

  • and that some of these transposable element mutations may be adaptive.

  • I will come back to this scenario at the end of the talk

  • when I show you how the elements that we have identified

  • in plant genomes fit this scenario very, very nicely.

  • So to review, I described in the last talk the two general classes of transposable elements in the genome.

  • The first class, which is called Class 2,

  • are DNA transposons. These are the elements that were discovered by McClintock genetically.

  • We know these elements have a typical structure of terminal inverted repeats,

  • that they encode a single protein necessary for the movement of the element, and that is transposase.

  • The other class of elements which I am not going to go into extensively in this talk,

  • and nor did I in the last talk, are called retrotransposons.

  • These are elements that encode reverse transcriptase,

  • and they move through an RNA intermediate, again by mechanisms that were described in the last talk.

  • I also want to re-introduce you to transposable elements families

  • because we are going to revisit families in this talk.

  • That transposable element families contain autonomous elements.

  • That is the elements that encode transposase.

  • And non-autonomous elements these are elements that don't encode transposase,

  • but are able to move utilizing the transposase that's encoded by the autonomous element.

  • Something else that I discussed in the first talk is just how prevalent transposable elements are in genomes.

  • So this was a human gene where I showed you the exons that are in the gene,

  • and this is really a pretty typical gene. And what we find is that

  • in the non-coding regions, there are many, many, many transposable elements,

  • that some human genes have over a hundred transposable elements in their introns.

  • Now the element that I am referring to, most of the elements in the human genome are called Alu.

  • They are a class 2 retrotransposon which are present at an astonishing copy number of over a million copies.

  • It's almost ten percent of the human genome.

  • Now one of the things, if we are interested in the evolutionary impact of a particular transposable element,

  • one question we could ask is, so for example, if we picked out one of these elements,

  • we could ask what happened when it inserted?

  • Did it change the expression of the gene?

  • These are the questions, if we are interested in the evolutionary impact,

  • these are the questions that we would like to be able to address.

  • Unfortunately we can't do that with the human elements, most of the humans elements.

  • And that is that the insertions may have changed gene expression,

  • but we have no way to address that now. And the reason is

  • first of all in the human population, virtually all of us, 99.99% of us, have these insertions,

  • have exactly these insertions. That's because these elements moved millions of years ago.

  • So what that means is that if we want to know how did the insertion

  • of a particular element change the expression of a gene, if at all, we are too late.

  • So what we want to do is identify a group of organisms

  • where these high copy number elements are actively transposing.

  • And I am going to talk about that strategy- that's exactly what this talk is about.

  • So here is our strategy for analyzing the impact of transposable elements on genome evolution.

  • And this is a figure from the previous talk which is sort of a typical region of a genome, a grass genome,

  • and this is from the barley genome,

  • and the blue boxes are genes and the triangles are transposable elements.

  • So in barley about 85% of the genome is derived from transposable elements.

  • So the strategy that we would like to do to identify evolutionarily relevant transposons

  • is to find a species that is in the midst of genome expansion.

  • So where these high copy number elements are moving, are increasing their copy number.

  • And we would then go ahead and identify and isolate an active element.

  • So this is not one of the mutagens that was identified by the geneticists,

  • but in fact these are the high copy number elements that are now increasing in copy number.

  • Ok, so we would then ask the question,

  • how is this element able to increase its copy number so extensively without harming the host?

  • What are its strategies for success? And success in this case is defined by being able to increase

  • your copy number without killing or harming the host, and possibly even by benefiting the host in some way.

  • And we are going to address all of those issues in this talk.

  • So in the first talk we talked about the discovery of transposable elements in maize.

  • Well, maize is a member of a larger group of organisms. It's a grass.

  • These are the most important organisms for human health, for the human diet.

  • More calories come from members of the grass clade than any other group of organisms on this planet.

  • We are familiar with maize. The other members of the grass clade is: rice,

  • which actually is the most important source of human calories,

  • sorghum, which is also a very important crop plant especially in Africa,

  • and finally barley. Another member of this family, which I am not showing is wheat.

  • So what you would notice here, those numbers are the size of the genome.

  • The maize genome is about the same size as the human genome, at 2500 megabasepairs.

  • The rice genome is much, much smaller. It is almost ten-fold smaller.

  • And what is remarkable is that here are these plants that are so incredibly similar,

  • yet their genomes size differs dramatically, by more than ten-fold.

  • So these organisms diverged from a common ancestor only about 70 million years ago.

  • And the main reason for this difference in genome size is this dramatic amplification,

  • expansion of transposable elements.

  • And this slide helps explain in part how that can happen.

  • These organisms, the grasses, in fact have about the same gene number.

  • They have about 30,000 genes, give or take a few 1000.

  • And so the genomes of these organisms are largely syntenous. The genes are mostly in the same order.

  • So in rice you could see, with smallest genome, I've shown three genes there in pink, yellow and blue

  • that are pretty close together. In maize those genes are further apart.

  • And in rice those genes, I'm sorry, in barley those genes are even further apart.

  • So what's happening here is transposable elements,

  • which are the squares and circles and ellipses in between,

  • transposable elements are inserting massively between the genes and expanding the genome.

  • So this is largely responsible for the difference in genome size.

  • And it's the safe havens that transposable elements can go without harming the host.

  • So I want to show you a little bit at a higher resolution

  • to show you what elements are involved.

  • So I introduced to you before that there were two types of transposable elements.

  • There were Class 1 elements which are retrotransposons,

  • and then Class 2 elements which are DNA transposons.

  • The retrotransposons which are generally these big elements that make RNA copies.

  • That RNA copy is then made into double stranded DNA.

  • The double stranded DNA can insert back into the genome.

  • It almost make copies like a printing press, like an old fashioned mimeograph machine,

  • which most of you probably never experienced.

  • So what you see here is that the huge blocks could be hundreds of kb

  • that separate some genes in the grass genome

  • are largely retrotransposons that are inserted into each other,` literally driving the genes apart.

  • So as we say it's almost like genes sitting in a sea of transposable elements.

  • Now these are not the elements that we are going to talk about today.

  • Instead we are going to talk about elements that I think are probably more involved in diversifying the genome.