A distant 10-bp sequence specifies the boundaries of a programmed DNA deletion in Tetrahymena.

Godiska, Ronald; James, C. David; Yao, Meng-Chao

doi:10.1101/gad.7.12a.2357

Cited by 80 publications

(74 citation statements)

References 24 publications

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“…cis-acting signals have been identified for only one of the five developmentally regulated rearrangements studied to date in T. thermophila. Ten-base-pair A5G5 polypurine tracts near the junctions of the M rearrangement have been shown to be both necessary and sufficient cis-acting sequences (5,23,24). Since the other four rearrangements in T. thennophila analyzed to date all lack A5G5 sequences, the polypurine tracts cannot be the universal signal for DNA rearrangement in T. thermophila.…”

Section: Discussionmentioning

confidence: 96%

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A small family of elements with long inverted repeats is located near sites of developmentally regulated DNA rearrangement in Tetrahymena thermophila.

Wells¹,

Ellingson²,

Catt³

et al. 1994

Mol. Cell. Biol.

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Extensive DNA rearrangement occurs during the development of the somatic macronucleus from the germ line micronucleus in ciliated protozoans. The micronuclear junctions and the macronuclear product of a developmentally regulated DNA rearrangement in Tetrahymena thermophila, Tlrl, have been cloned. The intrachromosomal rearrangement joins sequences that are separated by more than 13 kb in the micronucleus with the elimination of moderately repeated micronucleus-specific DNA sequences. There is a long, 825-bp, inverted repeat near the micronuclear junctions. The inverted repeat contains two diferent 19-bp tandem repeats. The 19-bp repeats are associated with each other and with DNA rearrangements at seven locations in the micronuclear genome. Southern blot analysis is consistent with the occurrence of the 19-bp repeats within pairs of larger repeated sequences. Another family member was isolated. The 19-mers in that clone are also in close proximity to a rearrangement junction. We propose that the 19-mers define a small family of developmentally regulated DNA rearrangements having elements with long inverted repeats near the junction sites. We discuss the possibility that transposable elements evolve by capture of molecular machinery required for essential cellular functions.Ciliated protozoa have two different kinds of nuclei: diploid, germ line micronuclei and transcriptionally active macronuclei. During sexual reproduction (conjugation), the old macronucleus is degraded and a new macronucleus develops from a mitotic product of the zygotic micronucleus.The developing macronucleus undergoes radical changes in genome organization. In the holotrichous ciliate Tetrahymena thermophila, there is a period of DNA replication which brings the DNA content of the macronucleus to 45 times the haploid DNA content of the micronucleus. When the developing nucleus is between 4C and 8C, about 15% of the germ line DNA sequences are eliminated from the somatic macronucleus (11,36,58). Since DNA sequence elimination is site specific, highly regular, and developmentally controlled, it is expected that DNA rearrangement involves the interaction of specific cis-acting sequences with the rearrangement machinery.Developmentally regulated DNA rearrangements in T. thermophila fall into two classes with respect to the fate of the macronucleus-destined sequences which flank the eliminated DNA (reviewed in reference 56

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Section: Discussionmentioning

confidence: 96%

“…The polypurine tracts are outside the deleted DNA and direct DNA rearrangement at a distance of 41 to 54 bp. Short direct repeats at the in vivo junctions of M are not required for rearrangement but may play a role in fine tuning the choice of junction site (24). The R rearrangement, the deletion near the calmodulin gene, and mse2.9 all lack polypurine tracts.…”

mentioning

confidence: 99%

A small family of elements with long inverted repeats is located near sites of developmentally regulated DNA rearrangement in Tetrahymena thermophila.

Wells¹,

Ellingson²,

Catt³

et al. 1994

Mol. Cell. Biol.

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“…Similar methods were previously developed for T. thermophila (29), and studies of eliminated sequences in this organism have shown that flanking DNA plays an important role in these events (3,8,14,20). In the case of the Tetrahymena M element, it is clear that a 10-bp sequence (A 5 G 5 ) located 50 bp outside the deleted region is sufficient to specify one end of the DNA splice junction (9). Interestingly, our results demonstrate the importance of flanking sequences in elimination of the Paramecium 28-bp internal IES.…”

Section: Discussionmentioning

confidence: 91%

“…Analysis of the M element revealed a requirement for a 10-bp DNA sequence (A 5 G 5 ) located about 45 bp outside the left boundary that has a corresponding partner found in inverted orientation about 45 bp outside the right boundary (8). Inserting different lengths of DNA between the 10-bp sequence and the normal splice boundary does not prevent excision but alters the boundary in a corresponding manner so that a distance of about 45 bp is maintained (9). Therefore, the sequence element not only is required but also specifies the deletion boundary.…”

mentioning

confidence: 99%

Developmentally Regulated Excision of a 28-Base-Pair Sequence from the Paramecium Genome Requires Flanking DNA

Mayer²,

Forney

2000

Molecular and Cellular Biology

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The micronuclear DNA of Paramecium tetraurelia is estimated to contain over 50,000 short DNA elements that are precisely removed during the formation of the transcriptionally active macronucleus. Ciliated protozoa provide a unique biological system for the study of DNA rearrangements. During sexual reproduction, a transcriptionally active macronucleus is formed from the germ line DNA in the micronucleus. The precise details of the process vary among different ciliates, but common features include fragmentation of germ line chromosomes, elimination of specific DNA elements, and amplification of the macronucleusdestined linear fragments (reviewed in references 2, 13, and 21). Elimination of relatively small regions of the genome (14 bp to several kilobases) followed by rejoining of the adjacent sequences has been observed in a wide variety of ciliate species. These excised DNA elements are commonly referred to as internal eliminated sequences (IESs) to distinguish them from elimination that results from fragmentation events.In Paramecium tetraurelia, the micronuclear genome contains relatively short IESs (26 bp to about 1 kb) that always begin and end with a 5Ј-TA-3Ј dinucleotide. Excision results in precise removal of the element, leaving a single TA within the macronuclear DNA (4,5,15,23,26,27). No significant open reading frames are encoded by these elements, and comparison of evolutionarily related IESs within the variable surface antigen genes of P. tetraurelia revealed substantial variation in the size and sequence of an IES relative to the adjacent macronuclear DNA (23). The ends of the element generally include a perfect inverted repeat that includes the TA and extends either into the IES or out toward the macronucleusdestined DNA (26). Statistical analysis of 20 IESs from P. tetraurelia identified an 8-bp consensus inverted terminal repeat that includes the invariant TA dinucleotide (12). This consensus repeat is inside the IES and therefore does not necessarily include the perfect inverted repeats. The functional significance of the consensus repeat is supported by the analysis of Paramecium mutant cell lines defective in IES excision.Isolated cell lines that are unable to excise a specific IES contain single nucleotide mutations in the consensus region (16,17).The structure of a Paramecium IES can be complex. There are at least two examples in which one IES is located inside a larger IES (6,16,17). In this report (which focuses on one of the complex IESs), we will refer to the smaller IES located inside another as an internal IES. The enzymatic machinery responsible for IES excision has not been identified, but analysis of a pleiotropic mutant line has shown that excision of one IES (or a small subclass) is inhibited by a mutation in an unlinked locus (19).Paramecium is not the only ciliate that contains TA IESs (IESs bounded by TA repeats). Euplotes crassus contains IESs bounded by 5Ј-TA-3Ј direct repeats, and they have similar consensus terminal inverted repeats (reviewed in reference 11). Interesting...

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“…In fact, mechanistic studies in Tetrahymena revealed that the sequences at the boundaries of IESs were not essential. Instead, sequences located a short distance (45-50 bp) outside the excision boundaries, which are in the DNA that remains in the somatic genome, were shown to determine the boundaries of excision (Godiska et al 1993;Chalker et al 1999;Patil and Karrer 2000;Fillingham et al 2001). These regulatory sequences that specify the excision boundaries share little, if any, similarity with one another, a fact that has always been hard to reconcile with a transposon origin.…”

Section: Piggymac: the Domestication Of A Transposasementioning

confidence: 99%

Subtraction by addition: domesticated transposases in programmed DNA elimination: Figure 1.

Motl¹,

Chalker²

2009

Genes Dev.

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The ciliate Paramecium tetraurelia must eliminate ∼60,000 short sequences from its genome to generate uninterrupted coding sequences in its somatic macronucleus. In this issue of Genes & Development, Baudry and colleagues (pp. 2478–2483) identify the protein that excises these noncoding sequences: a domesticated piggyBac transposase that has been adapted to remove what are likely the remnants of transposon insertions. This new study reveals how addition of a transposase to small RNA-directed silencing machinery can guide major genome reorganization.

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A distant 10-bp sequence specifies the boundaries of a programmed DNA deletion in Tetrahymena.

Cited by 80 publications

References 24 publications

A small family of elements with long inverted repeats is located near sites of developmentally regulated DNA rearrangement in Tetrahymena thermophila.

A small family of elements with long inverted repeats is located near sites of developmentally regulated DNA rearrangement in Tetrahymena thermophila.

Developmentally Regulated Excision of a 28-Base-Pair Sequence from the Paramecium Genome Requires Flanking DNA

Subtraction by addition: domesticated transposases in programmed DNA elimination: Figure 1.

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