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

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

PROVIDER: PRJNA855462 | ENA |

REPOSITORIES: ENA

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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

| PRJNA855459 | 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

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

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

2022-07-14 | GSE207428 | 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

Transcription-induced formation of extrachromosomal DNA during yeast ageing

Project description:Transcription-induced formation of extrachromosomal DNA during yeast ageing

| PRJNA559191 | ENA

The Rio1 kinase downregulates RNA polymerase I to promote rDNA stability and segregation

Project description:To sustain growth, budding yeast actively transcribes its ribosomal gene array (rDNA) in the nucoleolus to produce ribosomes and proteins. However, intense transcription during rDNA replication may provoke collisions between RNA polymerase I (Pol I) and the replisome, may cause replication fork instability, double-strand breaks, local recombinations and rDNA instability. The latter is manifested by rDNA array expansion or reduction and the formation of extrachromosomal rDNA circles, anomalies that accelerate aging in yeast. Transcription also interferes with the resolution, condensation and segregation of the sister chromatid rDNA arrays. As a consequence, rDNA segregation lags behind the rest of the yeast genome and occurs in late anaphase when rDNA transcription is temporarily shut off. How yeast promotes the stability and transmission of its rDNA array while satisfying a constant need for ribosomes remains unclear. Here we show that the downregulation of Pol I by the conserved cell cycle kinase Rio1 spatiotemporally coordinates rDNA transcription, replication and segregation. More specifically, Rio1 activity promotes copy-number stability of the replicating rDNA array by curtailing Pol I activity and by localising the histone deacetylase Sir2, which establishes a heterochromatic state that silences rDNA transcription. At anaphase entry, Rio1 and the Cdc14 phosphatase target Pol I subunit Rpa43 to dissociate Pol I from the 35S rDNA promoter. The rDNA locus then condensates and segregates, thereby concluding the genome transmission process. Rio1 is involved in ribosome maturation in the cytoplasm of budding yeast and human cells. Additional engagements in the cytoplasm or roles in the nucleus are unknown. Our study describes its first nuclear engagement as a Pol I silencing kinase. This activity may prove highly relevant as dysregulated RNA polymerase I activity has been associated with cancer initiation and proliferation.

2017-02-10 | GSE54930 | GEO

Fairy Circles

Project description:Desert Fairy Circles

| PRJEB23251 | 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 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

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