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Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
...< 0.0001) (Supplemental Table S30). Similarly, wild yeast strains that are aneuploidy tolerant show down-regulation of mitochondrial ribosomal proteins and genes involved in respiration, and up-regulation of oxidoreductases (Hose et al. 2015). The clusters and enrichment patterns remain even when...
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Research: Extensive protein dosage compensation in aneuploid human cancers
- Klaske M. Schukken and
- Jason M. Sheltzer
Genome Res. July 2022 32: 1254-1270; Published in Advance June 14, 2022, doi:10.1101/gr.276378.121
...on aneuploid chromosomes in human cancers and in budding yeast (corr = 0.214, P < 5 × 10−9) (Supplemental Fig. S6C; Supplemental Table S3). For instance, the ribosomal subunit gene RPL38, the splicing factor gene SF3A1, and the ER membrane complex gene EMC3 showed consistent dosage compensation at the protein...
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Research: Mediator dynamics during heat shock in budding yeast
- Debasish Sarkar,
- Z. Iris Zhu,
- Elizabeth R. Knoll,
- Emily Paul,
- David Landsman,
- and Randall H. Morse
Genome Res. January 2022 32: 111-123; Published in Advance November 16, 2021, doi:10.1101/gr.275750.121
...depletion (Petrenko et al. 2016); however, no -wide analysis has been reported examining whether promoter occupancy by Mediator is stabilized by Kin28 depletion at strongly induced genes or depends on PIC components as it does in yeast grown in rich medium (YPD). In this work, we examine -wide Mediator...
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Research: Intragenic repeat expansion in the cell wall protein gene HPF1 controls yeast chronological aging
- Benjamin P. Barré,
- Johan Hallin,
- Jia-Xing Yue,
- Karl Persson,
- Ekaterina Mikhalev,
- Agurtzane Irizar,
- Sylvester Holt,
- Dawn Thompson,
- Mikael Molin,
- Jonas Warringer,
- and Gianni Liti
Genome Res. May 2020 30: 697-710; Published in Advance April 10, 2020, doi:10.1101/gr.253351.119
...that buoyancy-induced methionine oxidation in natural yeast strains impinges on a metabolic trait regulating aging in organisms from yeasts to mice.HPF1 and FLO11, like the vast majority of genes encoding cell wall proteins, contain intragenic tandem repeats (Verstrepen et al. 2005). Intragenic tandem repeats...
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Research: Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters
- Danny Zeevi,
- Shai Lubliner,
- Maya Lotan-Pompan,
- Eran Hodis,
- Rita Vesterman,
- Adina Weinberger,
- and Eran Segal
Genome Res. December 2014 24: 1991-1999; Published in Advance October 7, 2014, doi:10.1101/gr.179259.114
...by expressing in S. cerevisiae 668 ribosomal protein (RP) gene promoters taken from nine yeast species and by further examining several pairs of orthologous promoters through a library of 91 chimeric promoters. Our results shed new light on how yeast promoters can evolve in sequencewhile preserving...
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Resource: Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach
- Pablo Meyer,
- Geoffrey Siwo,
- Danny Zeevi,
- Eilon Sharon,
- Raquel Norel,
- DREAM6 Promoter Prediction Consortium,
- Eran Segal,
- and Gustavo Stolovitzky
Genome Res. November 2013 23: 1928-1937; Published in Advance August 15, 2013, doi:10.1101/gr.157420.113
...protein genes. Nature 432: 1054–1058. Zeevi D, Sharon E, Lotan-Pompan M, Lubling Y, Shipony Z, Raveh-Sadka T, Keren L, Levo M, Weinberger A, Segal E. 2011. Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters. Genome Res 21: 2114–2128. Zhu C...
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Research: Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates
- Étienne Fafard-Couture,
- Pierre-Étienne Jacques,
- and Michelle S. Scott
Genome Res. April 2023 33: 525-540; Published in Advance April 18, 2023, doi:10.1101/gr.277483.122
...RNAs) are structured noncoding RNAs present in multiple copies within eukaryotic s. snoRNAs guide chemical modifications on their target RNA and regulate processes like ribosome assembly and splicing. Most human snoRNAs are embedded within host gene introns, the remainder being independently expressed from intergenic...
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Research: Improved redox homeostasis owing to the up-regulation of one-carbon metabolism and related pathways is crucial for yeast heterosis at high temperature
- Liang Song,
- Jun-Yan Shi,
- Shou-Fu Duan,
- Da-Yong Han,
- Kuan Li,
- Ri-Peng Zhang,
- Peng-Yu He,
- Pei-Jie Han,
- Qi-Ming Wang,
- and Feng-Yan Bai
Genome Res. April 2021 31: 622-634; Published in Advance March 15, 2021, doi:10.1101/gr.262055.120
...) and Sinha et al. (2006) showed that both dominance and epistasis at three quantitative trait genes—MKT1, END3, and RHO2—contributed to growth heterosis at high temperatures in some yeast hybrids but were not conserved in others. Plech et al. (2014) reported that heterosis was prevalent among domesticated...
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Research: Natural genetic variation in yeast longevity
- Stefan W. Stumpferl,
- Sue E. Brand,
- James C. Jiang,
- Boguslawa Korona,
- Anurag Tiwari,
- Jianliang Dai,
- Jae-Gu Seo,
- and S. Michal Jazwinski
Genome Res. October 2012 22: 1963-1973; Published in Advance September 5, 2012, doi:10.1101/gr.136549.111
...,000–387,742). It contains 12 genes within a region of 18 kbp; one of them is SIR2. (B) QTL 5 is located on chromosome XII (bp 446,389–487,500). It contains 23 protein-coding genes, one tRNA gene, some ARS consensus sequences, and the rDNA cluster (RDN1). Two copies of the rDNA are shown here, but the rDNA cluster contains...
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Research: Preservation of genetic and regulatory robustness in ancient gene duplicates of Saccharomyces cerevisiae
- Orla M. Keane,
- Christina Toft,
- Lorenzo Carretero-Paulet,
- Gary W. Jones,
- and Mario A. Fares
Genome Res. November 2014 24: 1830-1841; Published in Advance August 22, 2014, doi:10.1101/gr.176792.114
...associated with the deletion of singletons compared to duplicates in yeast (Gu et al. 2003), functional compensation of deleted gene copies (VanderSluis et al. 2010), higher robustness of duplicates to transient gene knockdowns in Caenorhabditis elegans (Conant andWagner 2004), and the contribution of gene...

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