Yeast genome analysis identifies chromosomal translocation, gene conversion events and several sites of Ty element insertion

Saccharomyces cerevisiae Ty elements are transposons closely related to retroviruses. The DNA sequence of a functional Ty element (TyH3) is presented. The long terminal repeat sequences are different, suggesting that TyH3 is a recombinant Ty element. A chromosomal Ty element near the LYS2 gene, Ty173, was found to be nonfunctional, even though it has no detectable insertions or deletions. The defect in Ty173 transposition is caused by a missense mutation giving rise to a Leu-to-Ile substitution in the TYB (pol) open reading frame. Several chromosomal Ty elements carry this lesion in their DNA, indicating that nonfunctional Ty elements are common in the yeast genome.

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Meiotic recombination between repeated transposable elements in Saccharomyces cerevisiae

Molecular and Cellular Biology ◽

10.1128/mcb.8.7.2942-2954.1988 ◽

1988 ◽

Vol 8 (7) ◽

pp. 2942-2954

Author(s):

M Kupiec ◽

T D Petes

Keyword(s):

Saccharomyces Cerevisiae ◽

Transposable Elements ◽

Gene Conversion ◽

Meiotic Recombination ◽

Small Region ◽

Ty Elements ◽

Ty Element ◽

Reciprocal Exchange ◽

Gene Conversions ◽

Conversion Tract

We have measured the frequency of meiotic recombination between marked Ty elements in the Saccharomyces cerevisiae genome. These recombination events were usually nonreciprocal (gene conversions) and sometimes involved nonhomologous chromosomes. The frequency of ectopic gene conversion among Ty elements appeared lower than expected on the basis of previous studies of recombination between artificially constructed repeats. The conversion events involved either a subset of the total Ty elements in the genome or the conversion tract was restricted to a small region of the Ty element. In addition, the observed conversion events were very infrequently associated with reciprocal exchange.

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The Saccharomyces cerevisiae genome contains functional and nonfunctional copies of transposon Ty1.

Molecular and Cellular Biology ◽

10.1128/mcb.8.4.1432 ◽

1988 ◽

Vol 8 (4) ◽

pp. 1432-1442 ◽

Cited By ~ 70

Author(s):

J D Boeke ◽

D Eichinger ◽

D Castrillon ◽

G R Fink

Keyword(s):

Saccharomyces Cerevisiae ◽

Long Terminal Repeat ◽

Missense Mutation ◽

Dna Sequence ◽

Open Reading Frame ◽

Yeast Genome ◽

Reading Frame ◽

Ty Elements ◽

Ty Element ◽

Repeat Sequences

Saccharomyces cerevisiae Ty elements are transposons closely related to retroviruses. The DNA sequence of a functional Ty element (TyH3) is presented. The long terminal repeat sequences are different, suggesting that TyH3 is a recombinant Ty element. A chromosomal Ty element near the LYS2 gene, Ty173, was found to be nonfunctional, even though it has no detectable insertions or deletions. The defect in Ty173 transposition is caused by a missense mutation giving rise to a Leu-to-Ile substitution in the TYB (pol) open reading frame. Several chromosomal Ty elements carry this lesion in their DNA, indicating that nonfunctional Ty elements are common in the yeast genome.

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P-Element-Induced Male Recombination and Gene Conversion in Drosophila

Genetics ◽

10.1093/genetics/144.4.1611 ◽

1996 ◽

Vol 144 (4) ◽

pp. 1611-1622 ◽

Cited By ~ 4

Author(s):

Christine R Preston ◽

William R Engels

Keyword(s):

Gene Conversion ◽

Fragment Length Polymorphism ◽

Great Majority ◽

P Element ◽

Second Step ◽

Male Recombination ◽

Element Insertion ◽

Chromosome Arm ◽

White Locus ◽

Conversion Tract

A P-element insertion flanked by 13 restriction fragment length polymorphism (RFLP) marker sites was used to examine male recombination and gene conversion at an autosomal site. The great majority of crossovers on chromosome arm 2R occurred within the 4-kb region containing the P element and RFLP sites. Of the 128 recombinants analyzed, approximately two-thirds carried duplications or deletions flanking the P element. These rearrangements are described in more detail in the accompanying report. In a parallel experiment, we examined 91 gene conversion tracts resulting from excision of the same autosomal P element. We found the average tract length was 1463 bp, which is essentially the same as found previously at the white locus. The distribution of conversion tract endpoints was indistinguishable from the distribution of crossover points among the nonrearranged male recombinants. Most recombination events can be explained by the “hybrid element insertion” model, but, for those lacking a duplication or deletion, a second step involving double-strand gap repair must be postulated to explain the distribution of crossover points.

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FREQUENCY AND DIRECTIONALITY OF GENE CONVERSION EVENTS INVOLVING THE CYC7-H3 MUTATION IN SACCHAROMYCES CEREVISIAE

Genetics ◽

10.1093/genetics/114.2.347 ◽

1986 ◽

Vol 114 (2) ◽

pp. 347-361

Author(s):

Patricia J Pukkila ◽

Michael D Stephens ◽

David M Binninger ◽

Beverly Errede

Keyword(s):

Saccharomyces Cerevisiae ◽

Gene Conversion ◽

High Frequency ◽

Yeast Genome ◽

Junction Region ◽

Sequence Comparisons ◽

Site Specific ◽

Site Specific Recombination ◽

Conversion Frequency ◽

Aberrant Segregation

ABSTRACT The CYC7-H3 mutation is a 5-kb deletion that causes overproduction of iso-2 cytochrome c. Unlike most mutations in yeast, the CYC7-H3 mutation is preferentially lost when it is involved in a gene conversion event. We have shown that cloned copies of CYC7-H3 DNA that are inserted into the yeast genome are associated with a high frequency of recombination and aberrant segregation events. Since parity in conversion frequency was observed when the extensive insertion/deletion heterozygosity at this locus was eliminated, we conclude that the CYC7-H3 sequences are inherently capable of acting as donors or recipients in gene conversion events, although they are unlikely to act as donors when they are located opposite a large heterology. DNA sequence comparisons revealed similarities between the CYC7-H3 junction region and the 2-µm circle DNA region that is involved in site-specific recombination.

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Rearrangements occurring adjacent to a single Ty1 yeast retrotransposon in the presence and absence of full-length Ty1 transcription.

Genetics ◽

10.1093/genetics/131.4.833 ◽

1992 ◽

Vol 131 (4) ◽

pp. 833-850

Author(s):

P R Sutton ◽

S W Liebman

Keyword(s):

Saccharomyces Cerevisiae ◽

Homologous Recombination ◽

Transposable Element ◽

Gene Conversion ◽

Genetic Background ◽

Repetitive Sequences ◽

Full Length ◽

Yeast Genome ◽

Yeast Saccharomyces Cerevisiae ◽

Ty1 Retrotransposon

Abstract The structures of two unusual deletions from the yeast Saccharomyces cerevisiae are described. These deletions extend from a single Ty1 retrotransposon to an endpoint near a repetitive tRNA(Gly) gene. The deletions suggest that unique sequences flanked by two nonidentical repetitive sequences, or bordered on only one side by a transposable element, have the potential to be mobilized in the yeast genome. Models for the formation of these two unusual deletions were tested by isolating and analyzing 32 additional unusual deletions of the CYC1 region that extend from a single Ty1 retrotransposon. Unlike the most common class of deletions recovered in this region, these deletions are not attributable solely to homologous recombination among repetitive Ty1 or delta elements. They arose by two distinct mechanisms. In an SPT8 genetic background, most unusual deletions arose by transposition of a Ty1 element to a position adjacent to a tRNA(Gly) gene followed by Ty1-Ty1 recombination. In an spt8 strain, where full-length Ty1 transcription and, therefore, transposition are reduced, most deletions were due to gene conversion of a 7-kb chromosomal interval flanked by a Ty1 element and a tRNA(Gly) gene.

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Involvement of cDNA in homologous recombination between Ty elements in Saccharomyces cerevisiae

Molecular and Cellular Biology ◽

10.1128/mcb.12.4.1613-1620.1992 ◽

1992 ◽

Vol 12 (4) ◽

pp. 1613-1620

Author(s):

C Melamed ◽

Y Nevo ◽

M Kupiec

Keyword(s):

Saccharomyces Cerevisiae ◽

Homologous Recombination ◽

Reverse Transcriptase ◽

Gene Conversion ◽

Reverse Transcription ◽

Repeated Sequences ◽

Homologous Gene ◽

Ty Elements ◽

Low Level ◽

Ty Element

Strains carrying a marked Ty element (TyUra) in the LYS2 locus were transformed with plasmids bearing a differently marked Ty1 element (Ty1Neo) under the control of the GAL promoter. When these strains were grown in glucose, a low level of gene conversion events involving TyUra was detected. Upon growth on galactose an increase in the rate of gene conversion was seen. This homologous recombination is not the consequence of increased levels of transposition. When an intron-containing fragment was inserted into Ty1Neo, some of the convertants had the intron removed, implying an RNA intermediate. Mutations that affect reverse transcriptase or reverse transcription of Ty1Neo greatly reduce the induction of recombination in galactose. Thus, Ty cDNA is involved in homologous gene conversion with chromosomal copies of Ty elements. Our results have implications about the way families of repeated sequences retain homogeneity throughout evolution.

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Substrate length requirements for efficient mitotic recombination in Saccharomyces cerevisiae

Molecular and Cellular Biology ◽

10.1128/mcb.13.7.3937-3950.1993 ◽

1993 ◽

Vol 13 (7) ◽

pp. 3937-3950

Author(s):

S Jinks-Robertson ◽

M Michelitch ◽

S Ramcharan

Keyword(s):

Saccharomyces Cerevisiae ◽

Gene Conversion ◽

Mitotic Recombination ◽

Yeast Genome ◽

Inverted Repeats ◽

Ectopic Recombination ◽

Linear Relationships ◽

Recombination System ◽

Efficient Processing ◽

Substrate Size

An ectopic recombination system using ura3 heteroalleles varying in size from 80 to 960 bp has been used to examine the effect of substrate length on spontaneous mitotic recombination. The ura3 heteroalleles were positioned either on nonhomologous chromosomes (heterochromosomal repeats) or as direct or inverted repeats on the same chromosome (intrachromosomal repeats). While the intrachromosomal events occur at rates at least 2 orders of magnitude greater than the corresponding heterochromosomal events, the recombination rate for each type of repeat considered separately exhibits a linear dependence on substrate length. The linear relationships allow estimation of the corresponding minimal efficient processing segments, which are approximately 250 bp regardless of the relative positions of the repeats in the yeast genome. An examination of the distribution of recombination events into simple gene conversion versus crossover events indicates that reciprocal exchange is more sensitive to substrate size than is gene conversion.

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Whole-Genome Analysis of Gene Conversion Events

Comparative Genomics - Lecture Notes in Computer Science ◽

10.1007/978-3-642-04744-2_15 ◽

2009 ◽

pp. 181-192 ◽

Cited By ~ 2

Author(s):

Chih-Hao Hsu ◽

Yu Zhang ◽

Ross Hardison ◽

Webb Miller

Keyword(s):

Gene Conversion ◽

Genome Analysis ◽

Whole Genome ◽

Whole Genome Analysis

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Resection and repair of a Cas9 double-strand break at CTG trinucleotide repeats induces local and extensive chromosomal rearrangements

10.1101/782268 ◽

2019 ◽

Author(s):

Valentine Mosbach ◽

David Viterbo ◽

Stéphane Descorps-Declère ◽

Lucie Poggi ◽

Wilhelm Vaysse-Zinkhöfer ◽

...

Keyword(s):

Gene Conversion ◽

Developmental Disorders ◽

Tandem Repeats ◽

Trinucleotide Repeat ◽

Chromosomal Rearrangements ◽

Strand Break ◽

Double Strand Break ◽

Trinucleotide Repeats ◽

Yeast Genome ◽

Repeat Tract

SummaryMicrosatellites are short tandem repeats, ubiquitous in all eukaryotes and represent ∼2% of the human genome. Among them, trinucleotide repeats are responsible for more than two dozen neurological and developmental disorders. Targeting microsatellites with dedicated DNA endonucleases could become a viable option for patients affected with dramatic neurodegenerative disorders. Here, we used the Streptococcus pyogenes Cas9 to induce a double-strand break within the expanded CTG repeat involved in myotonic dystrophy type 1, integrated in a yeast chromosome. Repair of this double-strand break generated unexpected large chromosomal rearrangements around the repeat tract. These rearrangements depended on RAD52, DNL4 and SAE2, and both non-homologous end-joining and single-strand annealing pathways were involved. Resection and repair of the double-strand break (DSB) were totally abolished in a rad50Δ strain, whereas they were impaired in a sae2Δ mutant, only on the DSB end containing most of the repeat tract. This proved that Sae2 plays significant different roles in resecting a DSB end containing a repeated and structured sequence as compared to a non-repeated DSB end.In addition, we also discovered that gene conversion was less efficient when the DSB could be repaired using a homologous template, suggesting that the trinucleotide repeat may interfer with gene conversion too. Altogether, these data show that SpCas9 is probably not a good choice when inducing a double-strand break at or near a microsatellite, especially in mammalian genomes that contain many more dispersed repeated elements than the yeast genome.

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