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Nucleolar morphology is a well-established indicator of ribosome biogenesis activity that has served as the foundation of many screens investigating ribosome production. Missing from this field of study is a broad-scale investigation of the regulation of ribosomal DNA morphology, despite the essential role of rRNA gene transcription in modulating ribosome output. We hypothesized that the morphology of rDNA arrays reflects ribosome biogenesis activity. We established GapR-GFP, a prokaryotic DNA-binding protein that recognizes transcriptionally-induced overtwisted DNA, as a live visual fluorescent marker for quantitative analysis of rDNA organization in Schizosaccharomyces pombe. We found that the morphology—which we refer to as spatial organization—of the rDNA arrays is dynamic throughout the cell cycle, under glucose starvation, RNA pol I inhibition, and TOR activation. Screening the haploid S. pombe Bioneer deletion collection for spatial organization phenotypes revealed large ribosomal protein (RPL) gene deletions that alter rDNA organization. Further work revealed RPL gene deletion mutants with altered rDNA organization also demonstrate resistance to the TOR inhibitor Torin1. A genetic analysis of signaling pathways essential for this resistance phenotype implicated many factors including a conserved MAPK, Pmk1, previously linked to extracellular stress responses. We propose RPL gene deletion triggers altered rDNA morphology due to compensatory changes in ribosome biogenesis via multiple signaling pathways, and we further suggest compensatory responses may contribute to human diseases such as ribosomopathies. Altogether, GapR-GFP is a powerful tool for live visual reporting on rDNA morphology under myriad conditions. Author summary: Cells devote significant energy and resources to produce ribosomes, large protein complexes that carry out protein synthesis. To ensure that ribosome production matches cellular needs, activation of ribosome assembly is regulated by many inputs. One key regulatory target is transcription of the tandemly repeated rRNA genes in the ribosomal DNA arrays. A broad understanding of how cells regulate the organization of the rDNA under different cellular conditions and transcriptional states has been difficult to assess with current tools and model systems. We present a new imaging reporter, a fluorescently tagged DNA-binding protein called GapR, that highlights rDNA spatial organization in fission yeast, a model system that shares similar regulatory networks with mammals. Using GapR, we found that the 3D organization of the rDNA arrays changes with the cell cycle, glucose starvation, RNA pol I inhibition, and TOR signaling. We surveyed hundreds of yeast mutants to identify factors that regulate rDNA spatial organization, discovering that the deletion of ribosome protein genes causes rDNA array expansion. Further experiments indicated that ribosome protein insufficiency activates conserved regulatory signaling pathways as part of a compensatory response. Our work presents the first broad investigation for regulators of rDNA spatial organization in any organism. Importantly, we identify a compensatory response to compromised ribosome biogenesis that could be conserved in mammals. [ABSTRACT FROM AUTHOR]

A century of genetic analysis has revealed that multiple mechanisms control the distribution of meiotic crossover events. In Drosophila melanogaster, two significant positional controls are interference and the strongly polar centromere effect. Here, we assess the factors controlling the distribution of crossovers (COs) and noncrossover gene conversions (NCOs) along all five major chromosome arms in 196 single meiotic divisions to generate a more detailed understanding of these controls on a genome-wide scale. Analyzing the outcomes of single meiotic events allows us to distinguish among different classes of meiotic recombination. In so doing, we identified 291 NCOs spread uniformly among the five major chromosome arms and 541 COs (including 52 double crossovers and one triple crossover). We find that unlike COs, NCOs are insensitive to the centromere effect and do not demonstrate interference. Although the positions of COs appear to be determined predominately by the long-range influences of interference and the centromere effect, each chromosome may display a different pattern of sensitivity to interference, suggesting that interference may not be a uniform global property. In addition, unbiased sequencing of a large number of individuals allows us to describe the formation of de novo copy number variants, the majority of which appear to be mediated by unequal crossing over between transposable elements. This work has multiple implications for our understanding of how meiotic recombination is regulated to ensure proper chromosome segregation and maintain genome stability. [ABSTRACT FROM AUTHOR]