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Project description:Aneuploidy is a hallmark of tumor cells and yet the precise relationship between aneuploidy and a cell’s proliferative ability, or cellular fitness, has remained elusive. In this study we have combined a detailed analysis of aneuploid clones isolated from laboratory-evolved populations of Saccharomyces cerevisiae with a systematic, genome-wide screen for the fitness effects of telomeric amplifications to address the relationship between aneuploidy and cellular fitness. We found that aneuploid clones rise to high population frequencies in nutrient-limited evolution experiments and show increased fitness relative to wild-type. Direct competition experiments confirmed that three out of four aneuploid events isolated from evolved populations were themselves sufficient to improve fitness. To expand the scope beyond this small number of exemplars, we created a genome-wide collection of >1,800 diploid yeast strains each containing a different telomeric amplicon (Tamp) ranging in size from 0.4 to 1,000kb. Using pooled competition experiments in nutrient-limited chemostats followed by high-throughput sequencing of strain-identifying barcodes, we determined the fitness effects of these >1,800 Tamps under three different conditions. Our data revealed that the fitness landscape explored by telomeric amplifications is much broader than that explored by single-gene amplifications. As also observed in the evolved clones, we found the fitness effects of most Tamps to be condition specific with a minority showing common effects in all three conditions. By integrating our data with previous work that examined the fitness effects of single-gene amplifications genome wide, we found that a small number of genes within each Tamp are centrally responsible for each Tamp’s fitness effects. Our genome-wide Tamp screen confirmed that telomeric amplifications identified in laboratory-evolved populations generally increased fitness. Our results show that Tamps are mutations that produce large, typically condition-dependent changes in fitness that are important drivers of increased fitness in asexually evolving populations. Each of these arrays is a Comparative Genomic Hybridization experiment to detect copy number differences between a reference strain and a strain of interest.
2015-04-12 | E-GEOD-67769 | biostudies-arrayexpress
Project description:Loc1 RIP-chip Experimental procedure: C-terminally TAP-tagged Loc1p from yeast S. cerevisiae was purified from 1 L of cells grown in YPD medium as previously described (Gerber et al. 2004, PLoS Biol. 2, E79). Untagged control cells (BY4741) cells served as a negative control. cDNA was synthesized from 3 μg of total RNA derived from the extract and 500 ng of affinity-isolated RNA and labeled with Cy3 and Cy5 fluorescent dyes, respectively. Samples were mixed and hybridized to cDNA microarrays. Publication: Niedner-Boblenz A. et al. 2024, Nucleic Acids Res, in press. Title: Intrinsically disordered RNA-binding motifs cooperate to catalyze RNA folding and drive phase separation Abstract: RNA-binding proteins are essential for gene regulation and the spatial organization of cells. Here, we report that the yeast ribosome biogenesis factor Loc1p is an intrinsically disordered RNA-binding protein with eight repeating positively charged, unstructured nucleic acid binding (PUN) motifs. While a single of these previously undefined motifs stabilizes folded RNAs, multiple copies strongly cooperate to catalyze RNA folding. In the presence of RNA, these multivalent PUN motifs drive phase separation. Proteome-wide searches in pro- and eukaryotes for proteins with similar arrays of PUN motifs reveal a strong enrichment in RNA-mediated processes and DNA remodeling. Thus, PUN motifs are potentially involved in a large variety of RNA- and DNA-related processes by concentrating them in membrane-less organelles. The general function and wide distribution of PUN motifs across species suggests that in an ancient “RNA world” PUN-like motifs may have supported the correct folding of early ribozymes.
2024-10-23 | GSE273374 | GEO
Project description:Array-based comparative genome hybridization. The aneuploid progeny could return to euploid state.
2015-01-07 | GSE42359 | GEO
Project description:Reproduced from P. T. Spellman, G. Sherlock, M. Q. Zhang, V. R. Iyer, K. Anders, M. B. Eisen, P. O. Brown, D. Botstein and B. Futcher, "Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization," Molecular Biology of the Cell 9 (12), pp. 3273--3297 (December 1998).
2005-10-05 | E-SMDB-1887 | biostudies-arrayexpress
Project description:Reproduced from P. T. Spellman, G. Sherlock, M. Q. Zhang, V. R. Iyer, K. Anders, M. B. Eisen, P. O. Brown, D. Botstein and B. Futcher, "Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization," Molecular Biology of the Cell 9 (12), pp. 3273--3297 (December 1998).
2005-10-05 | E-SMDB-1886 | biostudies-arrayexpress
Project description:Living yeast-based biostimulants: different genes for the same results?
| PRJEB57693 | ENA