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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE207429 | GEO | 2022/07/14

REPOSITORIES: GEO

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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

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

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: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

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 the tandemly repeated CUP1 gene 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.

| S-EPMC6890164 | biostudies-literature

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

DNA circles promote yeast ageing in part through stimulating the reorganization of nuclear pore complexes.

Project description:The nuclear pore complex (NPC) mediates nearly all exchanges between nucleus and cytoplasm, and in many species, it changes composition as the organism ages. However, how these changes arise and whether they contribute themselves to ageing is poorly understood. We show that SAGA-dependent attachment of DNA circles to NPCs in replicatively ageing yeast cells causes NPCs to lose their nuclear basket and cytoplasmic complexes. These NPCs were not recognized as defective by the NPC quality control machinery (SINC) and not targeted by ESCRTs. They interacted normally or more effectively with protein import and export factors but specifically lost mRNA export factors. Acetylation of Nup60 drove the displacement of basket and cytoplasmic complexes from circle-bound NPCs. Mutations preventing this remodeling extended the replicative lifespan of the cells. Thus, our data suggest that the anchorage of accumulating circles locks NPCs in a specialized state and that this process is intrinsically linked to the mechanisms by which ERCs promote ageing.

| S-EPMC9020822 | biostudies-literature

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