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Chapter 10 : Transposable Elements and Repeat-Induced Point Mutation

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Abstract:

This chapter concentrates on the impact of repeat-induced point mutation (RIP) on transposable elements (TEs). It is clear that RIP does not follow an identical pattern in all fungi: whereas RIP in is intense enough to reduce the C+G content of the most affected elements to below 30% and widespread enough for unmutated TEs to be absent from the sequenced genome, in and RIP is described as "light" or "mild", and init was observed only in late-maturing ascospores. The genomes of and other filamentous fungi show a large variety of sequences homologous to TEs found in other organisms. The distribution of TEs in fungal genomes suggests that there are a limited number of innocuous genomic locations. A striking feature of some of the TE sequences is illustrated. Like other genomic components, TEs provide a record of the evolutionary processes to which they were subjected, but unlike most genomic components, their turnover is rapid and the record they leave is largely one of decay, including defeat by the defense mechanisms of the host. RIP is the most potent genome defense system known in eukaryotes. It is perhaps surprising that RIP is apparently unique to filamentous ascomycetes, but genome defense mechanisms appear to be unusually labile in evolution perhaps because they have to be retailored to meet each new emergency encountered by the host.

Citation: Clutterbuck A, Selker E. 2010. Transposable Elements and Repeat-Induced Point Mutation, p 124-131. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch10
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Image of FIGURE 1
FIGURE 1

Diagram of RIP in . Two haploid strains of opposite mating type are illustrated, one containing an unlinked duplication (open boxes). For clarity, only two chromosomes are shown. The lightning bolt indicates the time that RIP occurs, and the filled boxes indicate new alleles created by RIP. The four possible combinations of chromosomes in the meiotic progeny are represented below. In cases in which an essential gene was duplicated, only the left-hand two products would be expected to be viable. Unlinked gene-sized duplications pass through a cross without being discovered and mutated by RIP at an appreciable frequency (~50%), but direct duplications of the same sequences rarely survive untouched. Most products of RIP are left methylated at remaining cytosines.

Citation: Clutterbuck A, Selker E. 2010. Transposable Elements and Repeat-Induced Point Mutation, p 124-131. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch10
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Image of FIGURE 2
FIGURE 2

Graphic list of TEs in . Each vertical line represents one element, elements being ranked by length within families. In each element the black, upper portion of the line represents A+T content while the gray lower part represents C+G; the predominance of A+T in some elements is suggestive of the action of RIP. (A) Long elements and their fragments. (B) Small elements, including solo LTRs and nonautonomous elements.

Citation: Clutterbuck A, Selker E. 2010. Transposable Elements and Repeat-Induced Point Mutation, p 124-131. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch10
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