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Chapter 5 : Transposable Elements as Sources of Genomic Variation

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Abstract:

This chapter provides a general description of the types of genetic variation caused by transposable elements in animals and plants, and examines this variation within an evolutionary framework. It focuses on the variation induced by transposable elements in their host organisms. The host variation associated with transposable elements can result from several interconnected aspects of transposable element activity. Estimates of the frequencies of new transposable element-induced mutations have been made under laboratory conditions and varied over an enormous range. The partial or complete sterility associated with several systems of hybrid dysgenesis in provides an interesting aspect of variation associated with transposable element activity. Heterochromatin proteins can recognize and silence transposable elements, some of which target heterochromatin for insertion. Thus, the evolution of heterochromatin could have led to a self-perpetuating expansion of domains rich in transposable elements. Two mechanisms are considered most likely to be responsible for transposable element-induced karyotypic changes. The best known mechanism is ectopic recombination, in which homologous recombination occurs between multiple copies of a transposable element present in a genome. A second mechanism for inducing genomic rearrangements is alternative transposition of class II elements in bacteria, plants, and animals. Some features of both transposable elements and hosts suggest coadaptations to mitigate the reduction of fitness expected from unfettered transposition, and to provide a wide range of new variations on which natural selection can act.

Citation: Kidwell M, Lisch D. 2002. Transposable Elements as Sources of Genomic Variation, p 59-90. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch5

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Figures

Image of Figure 1
Figure 1

transposon insertion into an intron causes ectopic expression of the gene in maize. In the presence of the transposase, function of a putative leaf-specific repressor in the intron is blocked. In the absence of transposase, the repressor functions normally and expression in the leaf is blocked. Thus, in this case, the transposase becomes part of a regulatory pathway in plant development. Adapted from ( ) with permission from the publisher.

Citation: Kidwell M, Lisch D. 2002. Transposable Elements as Sources of Genomic Variation, p 59-90. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch5
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Image of Figure 2
Figure 2

Insertions of a element into the first intron of the locus in have opposite effects depending on the orientation of the transposon. In one orientation the result of an insertion is a recessive homeotic conversion of sex organs to sterile perianth organs because of loss of expression in the inner two whorls of the flower. Insertion in the opposite orientation leads to a semidominant conversion of sterile organs into sex organs caused by ectopic expression of plena in the outer two whorls of the flower and vegetative organs for promoting sex organ development within the context of the flower. Adapted from ( ) with permission from the publisher.

Citation: Kidwell M, Lisch D. 2002. Transposable Elements as Sources of Genomic Variation, p 59-90. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch5
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Image of Figure 3
Figure 3

A histogram showing total genome sizes and the percentage of those sizes occupied by transposable elements (TEs) for eight species: barley ( species) ( ), maize () ( ), human () ( ), rice () ( ), fruit fly () ( ), vetch () ( ), worm () ( ), and yeast () ( ). Genome sizes for each of these species except barley and maize are taken from http://www.cbs.dtu.dk/databases/DOGS/.

Citation: Kidwell M, Lisch D. 2002. Transposable Elements as Sources of Genomic Variation, p 59-90. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch5
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Image of Figure 4
Figure 4

Preferential insertion of elements near the 5′ end of transcription units. The insertion sites of 56 different mutagenic elements are shown. Each insertion site is plotted with respect to a simplified standard gene containing one intron before, and one intron after, the AUG initiation site. Reprinted from the ( ) with permission from the publisher.

Citation: Kidwell M, Lisch D. 2002. Transposable Elements as Sources of Genomic Variation, p 59-90. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch5
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Image of Figure 5
Figure 5

A Y chromosome inversion generated by recombination between LINE elements in hominids. At the top is depicted a schematic representation of a prototypical, full-length human LINE element showing the location of two long open reading frames (ORFs) and the polyadenylated tail. Below that is shown a model of an inversion between two LINE elements drawn out of register. Reprinted from ( ) with permission from the publisher.

Citation: Kidwell M, Lisch D. 2002. Transposable Elements as Sources of Genomic Variation, p 59-90. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch5
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Image of Figure 6
Figure 6

Association of a retrovirus-related element with androgen regulation of the sex-limited protein () gene in mouse. Adapted from ( ) with permission from the publisher.

Citation: Kidwell M, Lisch D. 2002. Transposable Elements as Sources of Genomic Variation, p 59-90. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch5
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Image of Figure 7
Figure 7

A gypsy insertion blocks a subset of upstream enhancers of the yellow gene in The gypsy transposon carries a chromatin insulator which binds to the protein product of () (circle). Because this insulator acts in a polar fashion, when the element is inserted between the promoter and the enhancers specific for wing and body expression, the yellow gene only expresses in the mouth, whose enhancer remains unaffected. Adapted from ( ) with permission from the publisher.

Citation: Kidwell M, Lisch D. 2002. Transposable Elements as Sources of Genomic Variation, p 59-90. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch5
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Image of Figure 8
Figure 8

Promoter scrambling in plants. The original insertion of a transposon into the TATA box of the gene caused a tissue-specific change in expression. Subsequent excision and promoter “scrambling” caused additional changes in tissue specificity. Reprinted from the ( ) with permission from the publisher.

Citation: Kidwell M, Lisch D. 2002. Transposable Elements as Sources of Genomic Variation, p 59-90. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch5
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