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Analysing the impact of extrachromosomal rDNA circles (ERCs) on the ageing yeast transcriptome [genome]

ABSTRACT: Here we analysed the widespread disruption of gene expression that accompanies yeast ageing, and surprisingly observed that this is completely independent of ERCs. Furthermore, we could not find subsets of genes that are differentially regulated in the presence of ERCs. High throughput imaging showed that the accumulation of Tom70-GFP which accompanies the onset of cell division defects at the Senescence Entry Point (SEP) also correlated poorly to ERC abundance, but allowed determination of a gene expression signature for the SEP. This signature included overexpression of mRNA from the chromosome XII region between the rDNA and the telomere (ChrXIIr), which has been previously noted to amplify during ageing.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE207428 | GEO | 2022/07/14

REPOSITORIES: GEO

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Analysing the impact of extrachromosomal rDNA circles (ERCs) on the ageing yeast transcriptome [RNA]

Project description:Here we analysed the widespread disruption of gene expression that accompanies yeast ageing, and surprisingly observed that this is completely independent of ERCs. Furthermore, we could not find subsets of genes that are differentially regulated in the presence of ERCs. High throughput imaging showed that the accumulation of Tom70-GFP which accompanies the onset of cell division defects at the Senescence Entry Point (SEP) also correlated poorly to ERC abundance, but allowed determination of a gene expression signature for the SEP. This signature included overexpression of mRNA from the chromosome XII region between the rDNA and the telomere (ChrXIIr), which has been previously noted to amplify during ageing.

2022-07-14 | GSE207427 | GEO

Analyzing the impact of extrachromosomal rDNA circles (ERCs) on the ageing yeast transcriptome

Project description:Here we analyzed the widespread disruption of gene expression that accompanies yeast ageing, and surprisingly observed that this is completely independent of ERCs. Furthermore, we could not find subsets of genes that are differentially regulated in the presence of ERCs. High throughput imaging showed that the accumulation of Tom70-GFP which accompanies the onset of cell division defects at the Senescence Entry Point (SEP) also correlated poorly to ERC abundance, but allowed determination of a gene expression signature for the SEP. This signature included overexpression of mRNA from the chromosome XII region between the rDNA and the telomere (ChrXIIr), which has been previously noted to amplify during ageing.

2023-06-20 | GSE234869 | GEO

Analysing the impact of extrachromosomal rDNA circles (ERCs) on the ageing yeast transcriptome

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-07-14 | GSE207429 | GEO

Analysing the impact of extrachromosomal rDNA circles (ERCs) on the ageing yeast transcriptome

Project description:Analysing the impact of extrachromosomal rDNA circles (ERCs) on the ageing yeast transcriptome

| PRJNA855459 | ENA

Analysing the impact of extrachromosomal rDNA circles (ERCs) on the ageing yeast transcriptome [genome]

Project description:Analysing the impact of extrachromosomal rDNA circles (ERCs) on the ageing yeast transcriptome [genome]

| PRJNA855462 | ENA

Analysing the impact of extrachromosomal rDNA circles (ERCs) on the ageing yeast transcriptome [RNA]

Project description:Analysing the impact of extrachromosomal rDNA circles (ERCs) on the ageing yeast transcriptome [RNA]

| PRJNA855463 | ENA

Analyzing the impact of extrachromosomal rDNA circles (ERCs) on the ageing yeast transcriptome

Project description:Analyzing the impact of extrachromosomal rDNA circles (ERCs) on the ageing yeast transcriptome

| PRJNA983387 | ENA

Extrachromosomal circles of satellite repeats and 5S ribosomal DNA in human cells.

Project description:BackgroundExtrachomosomal circular DNA (eccDNA) is ubiquitous in eukaryotic organisms and was detected in every organism tested, including in humans. A two-dimensional gel electrophoresis facilitates the detection of eccDNA in preparations of genomic DNA. Using this technique we have previously demonstrated that most of eccDNA consists of exact multiples of chromosomal tandemly repeated DNA, including both coding genes and satellite DNA.ResultsHere we report the occurrence of eccDNA in every tested human cell line. It has heterogeneous mass ranging from less than 2 kb to over 20 kb. We describe eccDNA homologous to human alpha satellite and the SstI mega satellite. Moreover, we show, for the first time, circular multimers of the human 5S ribosomal DNA (rDNA), similar to previous findings in Drosophila and plants. We further demonstrate structures that correspond to intermediates of rolling circle replication, which emerge from the circular multimers of 5S rDNA and SstI satellite.ConclusionsThese findings, and previous reports, support the general notion that every chromosomal tandem repeat is prone to generate eccDNA in eukryoric organisms including humans. They suggest the possible involvement of eccDNA in the length variability observed in arrays of tandem repeats. The implications of eccDNA on genome biology may include mechanisms of centromere evolution, concerted evolution and homogenization of tandem repeats and genomic plasticity.

| S-EPMC3225859 | biostudies-literature

WRN controls formation of extrachromosomal telomeric circles and is required for TRF2DeltaB-mediated telomere shortening.

Project description:Telomere dysfunction has been proposed to contribute to the pathogenesis of Werner syndrome (WS), a premature-aging disorder. The WS protein WRN binds TRF2, a telomere-specific factor that protects chromosome ends. TRF2 possesses an amino-terminal domain that plays an essential role in preventing telomere shortening, as expression of TRF2(DeltaB), which lacks this domain, leads to the formation of telomeric circles, telomere shortening, and cell senescence. Our data show that the TRF2(DeltaB)-induced telomeric-loop homologous-recombination pathway requires WRN helicase. In addition, we show that WRN represses the formation of spontaneous telomeric circles, as demonstrated by the increased levels of telomeric circles observed in telomerase-positive WS fibroblasts. The mechanism of circle formation in WS cells does not involve XRCC3 function. Circle formation in WS cells is reduced by reconstitution with wild-type WRN but not mutant forms lacking either exonuclease or helicase activity, demonstrating that both enzymatic activities of WRN are required to suppress telomeric-circle formation in normal cells expressing telomerase reverse transcriptase. Thus, WRN has a key protective function at telomeres which influences telomere topology and inhibits accelerated attrition of telomeres.

| S-EPMC2268394 | biostudies-literature

Breast tumors

Project description:Additional experiments used for intrinsic gene selection. Sorlie et al. Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10869-74. This Series accompanies Series GSE4335. Experiments that were used to make the "intrinsic" gene list from. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Using regression correlation

2006-03-06 | E-GEOD-4336 | biostudies-arrayexpress

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