The Origins of Gene Instability in Yeast

Roeder, G. Shirleen; Farabaugh, Philip J.; Chaleff, D.; Fink, Gereon R.

doi:10.1126/science.6251544

Cited by 193 publications

(109 citation statements)

References 24 publications

Supporting

Mentioning

105

Contrasting

Order By: Relevance

“…This class includes Tyl-H3 and Tyl-Hl, both of which were found to activate the promoterless his3A4 gene by insertion (2). We have also studied Ty2-917, which inserted into the HIS4 locus to create the his4-917 mutation (33).…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Transpositional competence and transcription of endogenous Ty elements in Saccharomyces cerevisiae: implications for regulation of transposition.

Curcio¹,

Sanders²,

Garfinkel³

1988

Mol. Cell. Biol.

View full text Add to dashboard Cite

Transposition of Ty elements in the yeast Saccharomyces cerevisiae occurs through an RNA intermediate. Although Ty RNA accounts for 5 to 10% of the total polyadenylated RNA in a haploid cell, the transposition frequency is only i0' to 10-8 per gene. To determine whether Ty elements native to the yeast genome are transpositionally competent, two elements were fused to the GALI promoter and tested for their ability to transpose. These native elements, Tyl-588 and Ty2-117, transposed at high levels when the GAL) promoter was induced. Three Ty's identified as spontaneous transpositions in specific target genes were also tested. Of these three, Ty2-917 and the previously characterized element Tyl-H3 were shown to be transpositionafly competent. The third element, Tyl-Hi, was transposition defective. In addition, we marked the chromosomal copy of Tyl-588 with the NEO gene and demonstrated that Tyl-588NEO was actively transcribed in yeast cells. Tyl-588NEO transcription was regulated by the SPT3 and MAT loci in the same manner as that observed for Ty's collectively. These results indicate that the yeast genome contains functional Ty elements. The presence of a transpositionally competent, actively transcribed element suggests that regulation of Ty transposition occurs at a posttranscriptional level.

show abstract

Section: Resultsmentioning

confidence: 99%

“…The transcriptional orientation of Ty2-917 is opposite to that of the HIS4 gene (15,33). The insert of pGTy2-917NEO extends from the XhoI site in the 5' 8 to the BgIII site in the HIS4 promoter region (Fig.…”

mentioning

confidence: 99%

Transpositional competence and transcription of endogenous Ty elements in Saccharomyces cerevisiae: implications for regulation of transposition.

Curcio¹,

Sanders²,

Garfinkel³

1988

Mol. Cell. Biol.

View full text Add to dashboard Cite

show abstract

“…This process is reflected by the presence of solo LTRs and partially deleted LTR-RTs in all plant genomes investigated to date . Based on studies in yeast (Roeder et al 1980), solo LTRs are thought to be formed by unequal intraelement homologous recombination (UR) between two highly identical LTRs. In contrast, partially deleted or truncated elements are thought to be the outcome of illegitimate (nonhomologous) recombination (IR) (Devos et al 2002;Wicker et al 2003;).…”

mentioning

confidence: 99%

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

Tian

Rizzon²,

Du³

et al. 2009

Genome Res.

146

176

View full text Add to dashboard Cite

In flowering plants, the accumulation of small deletions through unequal homologous recombination (UR) and illegitimate recombination (IR) is proposed to be the major process counteracting genome expansion, which is caused primarily by the periodic amplification of long terminal repeat retrotransposons (LTR-RTs). However, the full suite of evolutionary forces that govern the gain or loss of transposable elements (TEs) and their distribution within a genome remains unclear. Here, we investigated the distribution and structural variation of LTR-RTs in relation to the rates of local genetic recombination (GR) and gene densities in the rice (Oryza sativa) genome. Our data revealed a positive correlation between GR rates and gene densities and negative correlations between LTR-RT densities and both GR and gene densities. The data also indicate a tendency for LTR-RT elements and fragments to be shorter in regions with higher GR rates; the size reduction of LTR-RTs appears to be achieved primarily through solo LTR formation by UR. Comparison of indica and japonica rice revealed patterns and frequencies of LTR-RT gain and loss within different evolutionary timeframes. Different LTR-RT families exhibited variable distribution patterns and structural changes, but overall LTR-RT compositions and genes were organized according to the GR gradients of the genome. Further investigation of non-LTR-RTs and DNA transposons revealed a negative correlation between gene densities and the abundance of DNA transposons and a weak correlation between GR rates and the abundance of long interspersed nuclear elements (LINEs)/short interspersed nuclear elements (SINEs). Together, these observations suggest that GR and gene density play important roles in shaping the dynamic structure of the rice genome.

show abstract

“…If, on the contrary, the 1. found to move over short time scales in yeast (3,4) and occupy different chromosomal locations in closely related strains of Drosophila (6,27). In the absence of genetic markers, it is difficult to provide direct evidence oftransposition in other DNAs, but the identification of precisely duplicated discrete-length sequences suggests that a similar mechanism may be responsible for the multiplication of many moderately repeated sequences in eukaryotic genomes.…”

Section: Discussionmentioning

confidence: 99%

“…Detailed information has become available on the organization, distribution, and evolution of many satellite and repeated structural gene DNAs, but few details are known about the arrangement of the bulk of the moderately repeated, interspersed DNA sequences present in most eukaryotes. Recent work that links genetic and structural studies on.repeated sequences in yeast (3,4) and Drosophila (5-7) indicates that some eukaryotic repeated sequences are transposable elements analogous to those found in prokaryotes. These eukaryotic transposable elements are >5000 nucleotides (Nt) long, much longer than the short repeated sequences found throughout the metazoa (1).…”

mentioning

confidence: 99%

Discrete-length repeated sequences in eukaryotic genomes.

Pearson¹,

Morrow²

1981

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Two of the four repeated DNA sequences near the 5' end of the silk fibroin gene hybridize with discrete-length families of repeated DNA. These two families comprise 0.5% of the animal's genome. A repeated sequence with a conserved length has also been-found in the short class of moderately repeated sequences in the sea urchin. The discrete length, interspersion, and sequence fidelity ofthese moderately repeated sequences suggests that each has been multiplied as a discrete unit. Thus, transposition mechanisms may be responsible for the multiplication and dispersion of a large class of repeated sequences in phylogenetically diverse eukaryotic genomes. The repeat we have studied in most detail differs from previously described eukaryotic transposable elements: it is much shorter (1300 base pairs) and does not have terminal repetitions detectable by DNA hybridization. A simple technique for identifying such discrete-length repeated sequences is described, Repeated DNA sequences comprise 20-50% of most animal genomes (1) and >50% of many plant genomes (2). Detailed information has become available on the organization, distribution, and evolution of many satellite and repeated structural gene DNAs, but few details are known about the arrangement of the bulk of the moderately repeated, interspersed DNA sequences present in most eukaryotes. Recent work that links genetic and structural studies on.repeated sequences in yeast (3,4) and Drosophila (5-7) indicates that some eukaryotic repeated sequences are transposable elements analogous to those found in prokaryotes. These eukaryotic transposable elements are >5000 nucleotides (Nt) long, much longer than the short repeated sequences found throughout the metazoa (1).In most eukaryotes, and in silk moths and sea urchins in particular, repeated sequences that average -400 Nt are interspersed with single-copy DNA averaging 1000-3000 Nt. In contrast, some animals, including Drosophila, seem to have few short repeated sequences interspersed with nonrepeated DNA (8-10). Our studies have been concerned with repeated sequence organization in genomes that have a repeat interspersion typical of most animals (1, 11-13).The length ofa repeated sequencerefers to the duplex region formed when a repeated sequence renatures. The unreacted single-strand tails mark the ends. These single-strand tails have been visualized with the electron microscope (14) or degraded with nuclease S1 and the remaining duplexes were fractionated on the basis of length (13). We have used Southern transfer hybridization of populations of nuclease Sl-trimmed repeated sequences to examine the distribution of lengths of individual members of various repeated-sequence families. We find that some repeated-sequence families consist of members that have the same length, while other families have members that differ in length (15). Three discrete-length repeated sequences are described, two in the DNA of the silk moth Bombyx moti near the 5' end of the silk fibroin gene (15)

show abstract

The Origins of Gene Instability in Yeast

Cited by 193 publications

References 24 publications

Transpositional competence and transcription of endogenous Ty elements in Saccharomyces cerevisiae: implications for regulation of transposition.

Transpositional competence and transcription of endogenous Ty elements in Saccharomyces cerevisiae: implications for regulation of transposition.

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

Discrete-length repeated sequences in eukaryotic genomes.

Contact Info

Product

Resources

About