Transposons

Barbara McClintock and the Discovery of Jumping Genes (Transposons)
By: Leslie Pray, Ph.D. & Kira Zhaurova (Nature Education) © 2008 Nature Education
Citation: Pray, L. & Zhaurova, K. (2008) Barbara McClintock and the discovery of jumping genes (transposons). Nature Education 1(1):169
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McClintock’s maize breeding experiments provided the first detailed descriptions of transposable elements. What exactly are these “jumping genes,” and why are they so important?
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Some of the most profound genetic discoveries have been made with the help of various model organisms that are favored by scientists for their widespread availability and ease of maintenance and proliferation. One such model is Zea mays (maize), particularly those plants that produce variably colored kernels. Because each kernel is an embryo produced from an individual fertilization, hundreds of offspring can be scored on a single ear, making maize an ideal organism for genetic analysis. Indeed, maize proved to be the perfect organism for the study of transposable elements (TEs), also known as "jumping genes," which were discovered during the middle part of the twentieth century by American scientist Barbara McClintock. McClintock's work was revolutionary in that it suggested that an organism's genome is not a stationary entity, but rather is subject to alteration and rearrangement-a concept that was met with criticism from the scientific community at the time. However, the role of transposons eventually became widely appreciated, and McClintock was awarded the Nobel Prize in 1983 in recognition of this and her many other contributions to the field of genetics.
McClintock and the Origins of Cytogenetics
Barbara McClintock began her scientific career at Cornell University, where she pioneered the study of cytogenetics-a new field in the 1930s-using maize as a model organism. Indeed, the marriage of cytology and genetics became official in 1931, when McClintock and graduate student Harriet Creighton provided the first experimental proof that genes were physically positioned on chromosomes by describing the crossing-over phenomenon and genetic recombination. Although Thomas Hunt Morgan was the first person to suggest the link between genetic traits and the exchange of genetic material by chromosomes, 20 years elapsed before his ideas were scientifically proven, largely due to limitations in cytological and experimental techniques (Coe & Kass, 2005). McClintock's own innovative cytogenetic techniques allowed her to confirm Morgan's ideas, and these techniques are numbered among her greatest contributions to science.

Discovering TEs Through Experimentation with Maize
A circular life cycle diagram shows the release of two diploid sporocytes from a flowering plant. The development of one sporocyte into a pollen grain and the second sporocyte into an egg cell is shown using a series of schematic illustrations connected by arrows. The five stages that compose the top half of the diagram are labeled as the diploid (2n) portion of the life cycle. The five stages that compose the lower half of the diagram are labeled as the haploid (n) portion of the life cycle. The double fertilization event appears in the middle of the drawing, at the transition from the haploid portion of the life cycle to the diploid portion of the life cycle, and is emphasized with a highlighted box.
View Full-Size ImageFigure 1
As previously mentioned, McClintock is best known for her discovery of transposable elements through experimentation with maize. However, in order to understand McClintock's observations and the logic that led to her discovery of TEs, it's first necessary to be aware that the phenotypic system McClintock studied-the variegated color pattern of maize kernels-involves three alleles rather than the usual two.
To better grasp this idea, consider every maize kernel as a single individual, originating as an ovule that has undergone double fertilization (Figure 1). During double fertilization, one sperm fuses with the egg cell's nucleus, producing a diploid zygote that will develop into the next generation. Meanwhile, the other sperm fuses with the two polar nuclei to form a triploid endosperm, which forms an outer protein layer known as the aleurone layer. As a result, the colored (or colorless, as the case may be) tissue that makes up the aleurone layer of the kernel is triploid, not diploid.

The Ac/Ds System of Transposable Elements
A photograph shows two horizontal rows of kernels on an ear of corn. The six kernels in the top row are a pale, beige color. One has dark brown speckles and splotches, while four have purple speckles and splotches, and one has red speckles and splotches. Four kernels in the bottom row are a pale, beige color with no speckles. A fifth kernel is speckled with red. A sixth kernel is a dark brown color.
View Full-Size ImageFigure 2: Variation in kernel phenotypes is used to study transposon behavior.
Kernels on a maize ear show unstable phenotypes due to the interplay between a transposable element (TE) and a pigment gene.
© 2002 Nature Publishing Group Feschotte, C. et al. Plant transposable elements: where genetics meets genomics. Nature Reviews Genetics 3, 330. All rights reserved. View Terms of Use
McClintock worked with what is known as the Ac/Ds system in maize, which she discovered by conducting standard genetic breeding experiments with an unusual phenotype. Through these experiments, McClintock recognized that breakage occurred at specific sites on maize chromosomes. Indeed, the first transposable element she discovered was a site of chromosome breakage, aptly named "dissociation" (Ds). Although McClintock eventually found that some TEs can "jump" autonomously, she initially noted that the movements of Ds are regulated by an autonomous element called "activator" (Ac), which can also promote its own transposition.

Of course, these discoveries were preceded by extensive breeding experimentation. It was known at the time from previous work by Rollins A. Emerson, another American maize geneticist and the "rediscoverer" of Mendel's laws of inheritance, that maize had genes encoding variegated, or multicolored, kernels; these kernels were described as colorless (although they were actually white or yellow), except for spots or streaks of purple or brown (Figure 2). Emerson had proposed that the variegated streaking was due to an "unstable mutation," or a mutation for the colorless phenotype that would sometimes revert back to its wild-type variant and result in an area of color. However, he couldn't explain why or how this occurred. As McClintock discovered, the unstable mutation Emerson puzzled over was actually a four-gene system, as outlined in Table 1.

Table 1: Maize Genes Studied by Barbara McClintock

Gene Description
C' Dominant allele on the short arm of chromosome 9 that prevents color from being expressed in the aleurone layer of the maize kernel, causing a so-called "colorless" phenotype (which is actually white or yellow in color). This is also known as the inhibitor allele.
C Recessive allele on the short arm of chromosome 9 that leads to color development.
Bz Dominant allele on the short arm of chromosome 9 that leads to a purple phenotype.
bz Recessive allele on the short arm of chromosome 9 that leads to a dark brown phenotype.
Ds Genetic location on the short arm of chromosome 9 at which chromosomal breakage occurs.
As A factor of unknown location (at least when McClintock was conducting her research) that impacts the expression of Ds.
Adapted from McClean, 1997

In her experiments, McClintock bred females that were homozygous for C and bz and that lacked Ds (denoted CCbzbz--, where the dashes indicate the absence of Ds alleles) with males that were homozygous for C', Bz, and Ds (denoted C'C'BzBzDsDs) to yield heterozygotes with an aleurone layer that had the genotype C'CCBzbzbz--Ds. (Remember, in double fertilization, the sperm provides one set of alleles, and the egg provides two.) Because of the presence of the dominant inhibitor allele C', the offspring kernels were expected to be colorless, no matter what their genetic makeup at the Bz/bz locus. In fact, upon crossbreeding, many of these kernels were indeed colorless. However, McClintock also observed many kernels with colorless backgrounds and varying amounts of dark brown spots or streaks, and she concluded that individual cells in those kernels had lost their C' and Bz alleles because of a chromosomal break at the Ds locus. Without either the C' allele (to prevent color expression) or the Bz (purple) allele, the cells that had experienced a breakage at the Ds locus ended up with some brown coloring.

Within the affected seeds, the amount of colored streaking or spotting depended upon when during seed development the somatic cell mutation at Ds occurred. If this mutation occurred early in development, then, as the one mutant cell continued to divide, more cells in the mature kernel would have the brownish phenotype, and the spot or streak of color on the kernel would be larger. On the other hand, if the mutation occurred later in development, the spotting would be smaller, because the kernel would undergo less cell division prior to maturity.

Expression of Ds in Maize
McClintock also performed additional experiments to demonstrate that the phenotypic effect of Ds depended upon the presence of another element, which she called Ac. McClintock had trouble mapping both the Ac and Ds elements, however, noting that they changed their positions on the chromosome in different maize plants. In fact, further experiments showed that Ds didn't just break chromosomes, but it could actually move from one chromosomal location to another. When Ds inserts itself into the Bz allele, for example, it causes a mutation in the Bz gene (but only when Ac is present), thereby destroying the ability of the Bz gene to produce any pigment at all. Ds can also excise from the Bz allele (again, only in the presence of Ac), causing Bz to revert back to its purple or brown phenotype. Again, the amount of purple or brown depends upon when during development Ds is inserted or excised. If excision happens prior to fertilization, then the affected kernel will be entirely purple or brown, depending upon the Bz/bz genotype.

Years after McClintock discovered the Ac/Ds system, scientists were finally able to study both TEs in much more molecular detail. Today, we know that Ac elements are about 4,500 base pairs long and are similar in structure to other DNA transposons.

McClintock and the Theory of Epigenetics
Beyond her discovery of TEs and her revolutionary cytogenetic research techniques, Barbara McClintock was also the first scientist to correctly speculate on the basic concept of epigenetics-or heritable changes in gene expression that are not caused by changes to DNA sequences. Mainly, she recognized that genes can be expressed and silenced during mitosis in genetically identical cells. McClintock proposed this theory before the molecular structure of DNA and more than 40 years before the concept of epigenetics was formally studied, thereby further cementing her reputation as an innovator in her field.
Summary
Barbara McClintock's discovery of transposable elements in Zea mays changed the way scientists think about genetic patterns of inheritance. Although not widely accepted at the time of its discovery, McClintock's observation of the behavior of kernel color alleles was revolutionary in its proposition that genomic replication does not always follow a consistent pattern. Indeed, as a result of both autonomous and activator-controlled transposition at different stages of seed development, the genes of maize kernels are capable of producing a variety of coloration patterns. Over time, McClintock's work with TEs became widely accepted, and McClintock eventually earned a Nobel Prize for her discoveries in this area. Today, McClintock is also recognized for her groundbreaking cytogenetic techniques, as well as her early speculations on the concept of epigenetics. Thanks to these and other valuable contributions to the field, Barbara McClintock is rightly viewed as one of the pioneering figures in modern genetics.
References and Recommended Reading
Coe, E., & Kass, L. B. Proof of physical exchange of genes on the chromosomes. Proceedings of the National Academy of Sciences 102, 6641–6646 (2005)

Creighton, H. B., & McClintock, B. A correlation of cytological and genetical crossing-over in Zea mays. Proceedings of the National Academy of Sciences 17, 492–497 (1931) (link to article)

Feschotte, C., et al. Plant transposable elements: Where genetics meets genomics. Nature Reviews Genetics 3, 339–341 (2002) doi:10.1038/nrg793 (link to article)

McClintock, M. The Order of the Genes C, Sh and Wx in Zea Mays with Reference to a Cytologically Known Point in the Chromosome. Proceedings of the National Academy of Sciences 17, 485–491 (1931)

McClintock, B. Mutable loci in maize. Carnegie Institution of Washington Yearbook 50, 174–181 (1951) (link to article)

McLean, P. McClintock and the Ac/Ds transposable elements of corn, www.ndsu.nodak.edu/instruct/mcclean/plsc431/transelem/trans1.htm (1997)