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Chapter 30 : Genome-Wide Rearrangements of DNA in Ciliates

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Abstract:

This chapter provides an update of the molecular analysis in DNA rearrangements. Sufficient progress has been made to provide good insights into their regulatory mechanisms and allow meaningful speculations on their relationships to other DNA rearrangement processes. The chapter focuses on the studies of the two processes (chromosome fragmentation and internal DNA deletion), which also occur, but separately, in nematodes (chromosome fragmentation) and crustaceans (DNA deletion). These processes are described briefly to complete the picture of DNA rearrangements in ciliates. The chapter discusses the unusual epigenetic effects on chromosome breakage and DNA deletion, and is concluded by offering the authors' views on the possible functions of these processes. The degree of fragmentation in the oligohymenophorans such as , , and is nearly two orders of magnitude lower than in the hypotrichous ciliates. The differences in the chromosome fragmentation process are quite extensive among the ciliates studied. Even in and , for which sequences controlling breakage have been identified, there is little evidence that they share a common mechanism of fragmentation. Site-specific deletion of DNA sequences, like chromosome fragmentation, occurs in all ciliates examined, but its extent varies greatly among species. In , the study of internal eliminated sequences (IESs) started much later than in other ciliates, but a few dozen IESs have already been sequenced in this organism.

Citation: Yao M, Duharcourt S, Chalker D. 2002. Genome-Wide Rearrangements of DNA in Ciliates, p 730-758. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch30

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Figure 1

Ciliate species frequently used in the study of DNA rearrangements and their taxonomic grouping.

Citation: Yao M, Duharcourt S, Chalker D. 2002. Genome-Wide Rearrangements of DNA in Ciliates, p 730-758. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch30
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Image of Figure 2
Figure 2

Nuclear dualism of This image of a living cell was taken using Nomarski optics.DNA is stained with DAPI to enhance visualization of the micronucleus (Mi) and the macronucleus (Ma). CV, contractile vacuole. Scale bar = 10 μm.

Citation: Yao M, Duharcourt S, Chalker D. 2002. Genome-Wide Rearrangements of DNA in Ciliates, p 730-758. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch30
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Image of Figure 3
Figure 3

Chromosome fragmentation and internal DNA deletion. This diagram represents sections of ciliate chromosomes undergoing the two major types of DNA rearrangements. Open bars represent chromosome segments retained in the macronucleus, and the solid bar represents the segment eliminated from the macronucleus. Bars with vertical stripes are telomeric DNAs added to the broken ends.

Citation: Yao M, Duharcourt S, Chalker D. 2002. Genome-Wide Rearrangements of DNA in Ciliates, p 730-758. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch30
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Image of Figure 4
Figure 4

Conservation of the Cbs of (A) The 15-bp Cbs is conserved both within and among related species. The sequences of the nine characterized breakage sites of are shown. The Cbs at eight of these are identical; the ninth differs by a single T to A change at position 13 ( ). The Cbs from the breakage sites at the 3′ end of the rDNA from several related species is also shown ( ). The sequence differences from the predominant Cbs are given. Dashes denote the conserved nucleotide positions. (B) Mutational analysis of the Cbs. Single nucleotide substitutions were introduced into a copy of Cbs and tested for activity using an rDNA-based transformation assay ( ). The observed activity of each altered Cbs is given to the right of each sequence:+, full activity; p, partial activity;-, no detectable activity.

Citation: Yao M, Duharcourt S, Chalker D. 2002. Genome-Wide Rearrangements of DNA in Ciliates, p 730-758. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch30
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Image of Figure 5
Figure 5

A model for chromosome breakage in At the top are the micronuclear (mic) and macronuclear (mac) sequences of an actual chromosome breakage site found in clone Tt 701 ( ). The sequences that are retained in the macronucleus are underlined; telomeric repeats are shown. The 15-bp Cbs is denoted by the gray box. In this model, the Cbs is recognized in the developing nucleus by a protein complex consisting of a recognition domain (hatched oval) and two endonuclease subunits (black symbols). These could be encoded in a single or multiple genes. This Cbs recognition complex also recruits the multiprotein telomerase complex (gray ovals). Cleavage occurs on each side of the Cbs, resulting in its removal from the chromosome. Limited exonuclease digestion of the broken ends on each side occurs, probably by telomerase itself, creating a favorable substrate for end healing. Addition of GGGGTT repeats then ensues to produce the mature macronuclear chromosomes.

Citation: Yao M, Duharcourt S, Chalker D. 2002. Genome-Wide Rearrangements of DNA in Ciliates, p 730-758. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch30
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Image of Figure 6
Figure 6

A model for fragmentation/telomere addition in A segment of micronuclear DNA with an E-Cbs core is shown at the top. The E-Cbs directs a double-strand break in the DNA to generate fragmentation intermediates with 6-bp, 3′ overhangs. Telomerase then adds GGGGTTTT telomeric repeats to the 3′ ends, and a DNA polymerase synthesizes the complementary CCCCAAAA strand. In the situation shown, both products of fragmentation become the ends of the macronuclear DNA molecules. In other cases, either the right or left segment would be developmentally eliminated spacer DNA. Reprinted from with permission of the publisher ( ).

Citation: Yao M, Duharcourt S, Chalker D. 2002. Genome-Wide Rearrangements of DNA in Ciliates, p 730-758. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch30
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Image of Figure 7
Figure 7

Organization of some internal eliminated sequences in various ciliates. Brackets define the excision boundaries of the DNA deleted elements that are indicated as rectangles. Thick arrows indicate inverted repeats. (1) IESs, with XY denoting the 1-to 8-bp terminal direct repeats that vary for different IESs. The black boxes indicate the macronuclear flanking sequences that have been shown in some cases to be required for IES excision. (2) and IESs, with XYZ denoting the 2-to 7-bp terminal direct repeats that vary for different IESs. Arrows below the TBE1 transposon-like element denote three conserved open reading frames. (3) and IESs, with TA terminal direct repeats. Arrows below the Tec1 transposon-like element again denote three major open reading frames. Modified from with permission of the publisher ( ).

Citation: Yao M, Duharcourt S, Chalker D. 2002. Genome-Wide Rearrangements of DNA in Ciliates, p 730-758. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch30
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Image of Figure 8
Figure 8

Comparisons of the deduced consensus sequences of ( ) and IESs ( ) with the termini of the Tec1 and Tec2 transposon-like elements ( ) and the terminal consensus sequence for the Tc1-related transposons ( ). The derived consensus sequence of IESs is TAYAGYNRand of TATrGCR. (Subscripts indicate the percentage of IES ends conforming the consensus.) In each case the first two bases (TA) represent the terminal direct repeat. Identical bases are highlighted with a black background, and similar positions are highlighted with a gray background. R = G or A, Y = C or T, K = G or T, S = C or G, N = any base. Reprinted from with permission of the publisher ( ).

Citation: Yao M, Duharcourt S, Chalker D. 2002. Genome-Wide Rearrangements of DNA in Ciliates, p 730-758. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch30
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Image of Figure 9
Figure 9

Model for IES excision in A germ line IES is shown at the top of the figure as a rectangle. An initiating cleavage event occurs at one end of the IES. Cleavage occurs at specific sites (arrows) and generates two DNA ends with 4-bp 5′ overhangs and 3′ A residues. The 3′-hydroxyl group of theA residue on the macronucleus-destined end serves as a nucleophile in a transesterification reaction with a corresponding site on the opposite side of the IES. This creates a macronuclear junction on one strand. Additional processing steps are required to join covalently the opposite strand of the macronuclear DNA. Modified from the with permission of the publisher ( ).

Citation: Yao M, Duharcourt S, Chalker D. 2002. Genome-Wide Rearrangements of DNA in Ciliates, p 730-758. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch30
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Image of Figure 10
Figure 10

. Formation of the palindromic rDNA of the macronucleus. During macronuclear development, the single micronuclear rDNA is transformed into a large palindromic structure. Chromosome breakage occurs at the 3′ Cbs and at one of the three 5′ Cbs. At the 3′ breakage site, telomeric repeats are added to the end. Located at the 5′ end are a pair of 42-bp inverted repeats separated by a 28-bp spacer. Breakage next to these repeats is usually healed by creation of a head-to-head palindromic molecule with the spacer at the center.

Citation: Yao M, Duharcourt S, Chalker D. 2002. Genome-Wide Rearrangements of DNA in Ciliates, p 730-758. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch30
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Image of Figure 11
Figure 11

The scrambled and unscrambled actin I gene of The scrambled micronuclear version of the actin I gene is at the top, and the unscrambled macronuclear version is at the bottom. MDSs are shown as open boxes, and the IESs are shown as solid lines. The size of each MDS is given. The number above each MDS corresponds to the order of segments in the unscrambled gene. Removal of the IESs during macronuclear development reorders the MDS to create the intact coding sequence of the actin gene ( ).

Citation: Yao M, Duharcourt S, Chalker D. 2002. Genome-Wide Rearrangements of DNA in Ciliates, p 730-758. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch30
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Image of Figure 12
Figure 12

Maternal inheritance of an alternative fragmentation site in In the wild-type (wt) strain, macronuclear (mac) telomeres (gray boxes) are added in three locations downstream of the gene (arrows). In strain d48, the micronuclear (mic) genome is wild type, and macronuclear telomeres are added in a single region upstream of the coding sequence. In conjugation between the wild type and d48, this alternative fragmentation site is maternally inherited.

Citation: Yao M, Duharcourt S, Chalker D. 2002. Genome-Wide Rearrangements of DNA in Ciliates, p 730-758. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch30
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Figure 13

Maternal regulation of IES excision. Transformation of the wild-type macronucleus (mac) with a plasmid containing an IES (black rectangle) specifically inhibits the excision of the homologous germ-line IES (black rectangle) in the next sexual generation but does not affect the excision of other germ-line IESs (gray rectangle). Reprinted from with permission of the publisher ( ).

Citation: Yao M, Duharcourt S, Chalker D. 2002. Genome-Wide Rearrangements of DNA in Ciliates, p 730-758. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch30
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