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Chapter 47 : Mobile Elements in Animal and Plant Genomes

Authors: Prescott L. Deininger1, Astrid M. Roy-Engel1
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Affiliations: 1: Tulane Cancer Center and Department of Environmental Health Sciences, Tulane University Medical Center, 1430 Tulane Ave., New Orleans, LA 70112
Content Type: Monograph
Publication Year: 2002

Category: Microbial Genetics and Molecular Biology

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Abstract:

This chapter discusses the different classes of mobile elements seen in some of the best-characterized animal genome and plant genome. It talks about the some of the general concepts behind the colonization of genomes by mobile elements. There are basically three classes of autonomous mobile elements, all three of which can be found to various extents in different genomes of all animals and plants. These are the DNA transposons, the long terminal repeat (LTR) retrotransposons, and the non-LTR retrotransposons. DNA transposons are very common in the genome, as well as several relatively high-copy-number families of their nonautonomous relatives, miniature inverted-repeat transposable elements (MITEs). Other site-specific mobile elements are the HetA and TART elements that make up the telomeres in . Only sporadic data are available on mobile elements in reptiles, amphibians, and fish. Almost all the classes of mobile elements are present to some degree in almost all animal and plant genomes. The density of mobile elements has also been shown to extend into the centromeric region in . Not only is the impact of mobile elements on their genome a direct result of insertional mutagenesis, but there are also a series of secondary impacts on the genome including recombination and many more subtle changes that may alter the stability or evolution of an organism’s genome. Retrotransposition has also given rise to gene duplications or other useful gene modifications that allowed evolution to new function.

Citation: Deininger P, Roy-Engel A. 2002. Mobile Elements in Animal and Plant Genomes, p 1074-1092. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch47
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Mobile Elements in Animal and Plant Genomes
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Citation: Deininger P, Roy-Engel A. 2002. Mobile Elements in Animal and Plant Genomes, p 1074-1092. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch47
/content/10.1128/9781555817954.chap47.fig47-1
Figure 1.

Major classes of autonomous mobile elements in animals and plants. Schematic diagrams for the three major classes of mobile elements are shown. The DNA transposons have two or three open reading frames coding for enzymes involved in the transposition process. They are also flanked by inverted repeats (arrowheads) at the ends that act as -acting elements in the integration process. The transposition process involves direct integration through DNA intermediates. Both the LTRretrotransposons and the non-LTRretrotransposons use anRNA intermediate in the amplification process. They generally encode two open reading frames coding for RNA-binding proteins and enzymes involved in reverse transcription and endonuclease cleavage at the site of integration. The LTRretrotransposons have LTRs that contain signals for transcription of the elements and are involved in the integration process. The non-LTRretrotransposons use a promoter region found in the 5′ noncoding region of the RNA and terminate in a poly(A) tract like a typical mRNA.

10.1128/9781555817954/fig47-1_thmb.gif
10.1128/9781555817954/fig47-1.gif
Image of Figure 1.
Figure 1.

Major classes of autonomous mobile elements in animals and plants. Schematic diagrams for the three major classes of mobile elements are shown. The DNA transposons have two or three open reading frames coding for enzymes involved in the transposition process. They are also flanked by inverted repeats (arrowheads) at the ends that act as -acting elements in the integration process. The transposition process involves direct integration through DNA intermediates. Both the LTRretrotransposons and the non-LTRretrotransposons use anRNA intermediate in the amplification process. They generally encode two open reading frames coding for RNA-binding proteins and enzymes involved in reverse transcription and endonuclease cleavage at the site of integration. The LTRretrotransposons have LTRs that contain signals for transcription of the elements and are involved in the integration process. The non-LTRretrotransposons use a promoter region found in the 5′ noncoding region of the RNA and terminate in a poly(A) tract like a typical mRNA.

Citation: Deininger P, Roy-Engel A. 2002. Mobile Elements in Animal and Plant Genomes, p 1074-1092. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch47
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Figure 2.

Genomic patterns for mobile elements. The patterns show schematically some of the basic density patterns found for mobile elements in animal and plant genomes. These include elements that are distributed fairly randomly, some showing either a combined centromeric/telomeric preference, and many with a preference for the juxtacentromeric region. In more complex genomes, it is typical to see a complex series of clusters spread throughout the genome. There are also classes of mobile elements with a very high degree of specificity for very specific gene or chromosomal regions.

10.1128/9781555817954/fig47-2_thmb.gif
10.1128/9781555817954/fig47-2.gif
Image of Figure 2.
Figure 2.

Genomic patterns for mobile elements. The patterns show schematically some of the basic density patterns found for mobile elements in animal and plant genomes. These include elements that are distributed fairly randomly, some showing either a combined centromeric/telomeric preference, and many with a preference for the juxtacentromeric region. In more complex genomes, it is typical to see a complex series of clusters spread throughout the genome. There are also classes of mobile elements with a very high degree of specificity for very specific gene or chromosomal regions.

Citation: Deininger P, Roy-Engel A. 2002. Mobile Elements in Animal and Plant Genomes, p 1074-1092. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch47
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/content/10.1128/9781555817954.chap47.fig47-3
Figure 3.

Schematic of evolutionary peaks of mobile element amplification. Each of the different line types represents a theoretical amplification rate versus evolutionary time for a different mobile element. These simply show the concept that when a mobile element enters or is activated in a naïve genome, they often amplify efficiently and reach a peak amplification rate. Processes such as mobile elements regulating their own amplification, development of genomic suppression mechanisms, or simply negative selection due to the damage caused by the elements, eventually lead most elements to greatly decrease or lose all amplification capability. Because very few elements are actively removed from the genome, the modern genome will be littered with pseudogene copies of the older elements, as well as members of any active families of elements. Also, some of the highest-copy-number elements are nonautonomous and therefore only amplify in conjunction with an active, autonomous family of elements. The modern genome is littered with both the elements that amplified earlier in evolution and families of currently active elements.

10.1128/9781555817954/fig47-3_thmb.gif
10.1128/9781555817954/fig47-3.gif
Image of Figure 3.
Figure 3.

Schematic of evolutionary peaks of mobile element amplification. Each of the different line types represents a theoretical amplification rate versus evolutionary time for a different mobile element. These simply show the concept that when a mobile element enters or is activated in a naïve genome, they often amplify efficiently and reach a peak amplification rate. Processes such as mobile elements regulating their own amplification, development of genomic suppression mechanisms, or simply negative selection due to the damage caused by the elements, eventually lead most elements to greatly decrease or lose all amplification capability. Because very few elements are actively removed from the genome, the modern genome will be littered with pseudogene copies of the older elements, as well as members of any active families of elements. Also, some of the highest-copy-number elements are nonautonomous and therefore only amplify in conjunction with an active, autonomous family of elements. The modern genome is littered with both the elements that amplified earlier in evolution and families of currently active elements.

Citation: Deininger P, Roy-Engel A. 2002. Mobile Elements in Animal and Plant Genomes, p 1074-1092. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch47
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Tables

Mobile Elements in Animal and Plant Genomes
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Citation: Deininger P, Roy-Engel A. 2002. Mobile Elements in Animal and Plant Genomes, p 1074-1092. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch47
/content/10.1128/9781555817954.chap47.tab47-1
Table 1

Abundance of human mobile elements on chromosomes 21, 22, and X

10.1128/9781555817954/tab47-1_thmb.gif
10.1128/9781555817954/tab47-1.gif
Generic image for table
Table 1

Abundance of human mobile elements on chromosomes 21, 22, and X

Citation: Deininger P, Roy-Engel A. 2002. Mobile Elements in Animal and Plant Genomes, p 1074-1092. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch47
/content/10.1128/9781555817954.chap47.tab47-2
Table 2

Species and population variation in mobile elements

10.1128/9781555817954/tab47-2_thmb.gif
10.1128/9781555817954/tab47-2.gif
Generic image for table
Table 2

Species and population variation in mobile elements

Citation: Deininger P, Roy-Engel A. 2002. Mobile Elements in Animal and Plant Genomes, p 1074-1092. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch47

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