Ontology highlight
ABSTRACT:
PROVIDER: PRJNA746007 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Ribosome is the most abundant RNA-protein complex in a cell and many copies of the ribosomal RNA gene (rDNA) have to be maintained. However, arrays of tandemly repeated rDNA genes can lose the copies by intra-repeat recombination. Loss of the rDNA copies of Saccharomyces cerevisiae is counteracted by gene amplification whereby the number of rDNA repeats stabilizes around 150 copies, suggesting the presence of a monitoring mechanism that counts and adjusts the number. Here, we report that in response to rDNA copy loss, the upstream activating factor (UAF) for RNA polymerase I which transcribes the rDNA is released and directly bind to a RNA polymerase II transcribed gene, SIR2 to repress, whose gene products silence rDNA recombination. We show that the amount of UAF determines rDNA copies number that is stably maintained. UAF ensures rDNA production not only by rDNA transcription activation but also by its copy number maintenance.
2019-01-03 | GSE116661 | GEO
Project description:Ribosomal DNA (rDNA) is organized as large arrays of tandem repeats that vary in copy number from a few dozen to hundreds. In the budding yeast Saccharomyces cerevisiae, each rDNA repeat includes a potential origin of replication. Previous work has led to the model that the rDNA replication origins compete for limiting replication initiation factors with origins in the rest of the genome, suggesting that reduction in rDNA copy number would reduce competition for these limiting factors and therefore promote origin usage in the rest of the genome. To test this hypothesis, we compared genome-wide replication in strains with either wild type rDNA copy number of ~180 (“180 rDNA”) or just ~35 copies (“35 rDNA”) by performing dense-to-light isotope transfer experiments to physically separate replicated, hybrid-density (HL or heavy-light) DNA from unreplicated, HH (heavy-heavy) DNA in cell samples collected at different times in S phase. Contrary to our expectations, we find that although there are no apparent differences in non-rDNA origin activity between the two strains, the 35 rDNA strain shows a genome-wide delay in progression through S phase compared to the 180 rDNA strain.
2023-02-17 | GSE205068 | GEO
Project description:In this study we perform ATAC-seq of budding yeast strains with variable copy number of the rRNA genes (rDNA CN). We aim to better understand the relationship between DNA accessibility and replicative lifespan in strains with variable rDNA CN.
2022-04-05 | GSE193598 | GEO
Project description:Copy number variant (CNV) and Single nucleotide polymorphism (SNP) of UCLA hESC lines
| PRJNA356825 | ENA
Project description:In this study we perform RNA-seq of budding yeast strains with variable copy number of the rRNA genes (rDNA CN) to assess the relationship between rDNA CN and gene expression. RNA-seq was performed on samples both with and without polyA selection (for all transcripts and for rRNA transcripts, respectively).
2022-04-05 | GSE193599 | GEO
Project description:Please see publication. These experiments were performed to ascertain the contribution of Y-linked rDNA copy number variation in the modulation of gene expression. Males (XY) and female (XXY) genotypes were probed.
2011-08-01 | GSE27695 | GEO
Project description:The diet consumed by fathers prior to procreation impacts metabolic phenotypes in their offspring, but the mechanisms underlying such intergenerational information transfer remain obscure. Here, we carried out extensive analysis of cytosine methylation patterns in murine sperm, generating whole genome methylation maps for 4 pools of sperm samples and for 12 individual sperm samples, as well as 61 genome-scale reduced-representation bisulfite sequencing (RRBS) methylation maps, using samples obtained from male mice consuming various diets. We found that epivariation, either stochastic or due to unknown demographic or environmental factors, was a far stronger contributor to the sperm methylome than was the diet consumed. Variation in cytosine methylation was particularly dramatic over tandem repeat families, including ribosomal DNA (rDNA) repeats, and rDNA methylation levels were heritable from one generation to the next. However, rDNA methylation was strongly correlated with genetic variation in rDNA copy number, and analysis of hundreds of sperm samples revealed no consistent effect of diet on rDNA copy number or methylation level in sperm, indicating that paternal diet exerts an rDNA methylation-independent effect on offspring gene expression. These results reveal loci of genetic and epigenetic lability in the mammalian genome, but strongly argue against a direct mechanistic role for sperm cytosine methylation in dietary reprogramming of offspring metabolism.
2015-12-17 | GSE75323 | GEO
Project description:Nasopharyngeal carcinoma cell lines (copy number analysis)
| PRJNA123147 | ENA