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Transcription-induced formation of extrachromosomal DNA during yeast ageing

ABSTRACT: Transcription-induced formation of extrachromosomal DNA during yeast ageing

PROVIDER: PRJNA559191 | ENA |

REPOSITORIES: ENA

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Transcription-induced formation of extrachromosomal DNA during yeast ageing

Project description:Extrachromosomal circular DNA (eccDNA) facilitates adaptive evolution by allowing rapid and extensive gene copy number variation, and is implicated in the pathology of cancer and ageing. Here, we demonstrate that yeast aged under environmental copper accumulate high levels of eccDNA containing the copper resistance gene CUP1. Transcription of CUP1 causes CUP1 eccDNA accumulation, which occurs in the absence of phenotypic selection. We have developed a sensitive and quantitative eccDNA sequencing pipeline that reveals CUP1 eccDNA accumulation on copper exposure to be exquisitely site specific, with no other detectable changes across the eccDNA complement. eccDNA forms de novo from the CUP1 locus through processing of DNA double-strand breaks (DSBs) by Sae2 / Mre11 and Mus81, and genome-wide analyses show that other protein coding eccDNA species in aged yeast share a similar biogenesis pathway. Although abundant we find that CUP1 eccDNA does not replicate efficiently, and high copy numbers in aged cells arise through frequent formation events combined with asymmetric DNA segregation. The transcriptional stimulation of CUP1 eccDNA formation shows that age-linked genetic change varies with transcription pattern, resulting in gene copy number profiles tailored by environment.

2019-10-18 | GSE135542 | GEO

Transcription-induced formation of extrachromosomal DNA during yeast ageing.

Project description: Not available

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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

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

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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]

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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 [genome]

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 | GSE207428 | GEO

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Yeast transcriptome profiling in replicative ageing

Project description:Yeast transcriptome profiling in replicative ageing

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Genome-scale purification of extrachromosomal circular DNA in yeast.

Project description:Extrachromosomal circular DNA is common in yeast.

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