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Research: Sir3 mediates long-range chromosome interactions in budding yeast
- Myriam Ruault,
- Vittore F. Scolari,
- Luciana Lazar-Stefanita,
- Antoine Hocher,
- Isabelle Loïodice,
- Romain Koszul,
- and Angela Taddei
Genome Res. March 2021 31: 411-425; Published in Advance February 12, 2021, doi:10.1101/gr.267872.120
..., the molecular mechanisms responsible for settling and maintaining such interactions remain poorly understood. Here, we investigate the well-conserved interactions between heterochromatin loci. In budding yeast, the 32 telomeres cluster in 3–5 foci in exponentially growing cells. This clustering is functionally...
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Method: Delineating yeast cleavage and polyadenylation signals using deep learning
- Emily Kunce Stroup and
- Zhe Ji
Genome Res. July 2024 34: 1066-1080; Published in Advance June 24, 2024, doi:10.1101/gr.278606.123
...address this issue by developing deep learning models to deconvolute degenerate cis-regulatory elements and quantify their positional importance in mediating yeast poly(A) site formation, cleavage heterogeneity, and strength. In S. cerevisiae, cleavage heterogeneity is promoted by the depletion of U...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...to high homogenization within a single cluster (Ganley and Kobayashi 2011; Hori et al. 2021; Garcia et al. 2024). The complex IGS region, similarly to what is observed in humans and budding yeast (Ganley and Kobayashi 2011; Hori et al. 2021), is composed of tandemly arranged repeats and can undergo...
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Research: Highly complete long-read genomes reveal pangenomic variation underlying yeast phenotypic diversity
- Cory A. Weller,
- Ilya Andreev,
- Michael J. Chambers,
- Morgan Park,
- NISC Comparative Sequencing Program,
- Joshua S. Bloom,
- and Meru J. Sadhu
Genome Res. May 2023 33: 729-740; Published in Advance May 1, 2023, doi:10.1101/gr.277515.122
.... A popular method for studying the genetic basis of trait variation is linkage mapping, which identifies quantitative trait loci (QTLs), regions of the that harbor causative genetic variants. Large-scale linkage mapping in the budding yeast Saccharomyces cerevisiae has found thousands of QTLs affecting...
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Research: Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast
- Vahid Aslanzadeh,
- Yuanhua Huang,
- Guido Sanguinetti,
- and Jean D. Beggs
Genome Res. February 2018 28: 203-213; Published in Advance December 18, 2017, doi:10.1101/gr.225615.117
...efficiency and that faster elongation reduces cotranscriptional splicing and splicing efficiency in budding yeast, suggesting that splicing is more efficient when cotranscriptional. Moreover, we demonstrate that altering the RNA polymerase II elongation rate in either direction compromises splicing fidelity...
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Research: Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast
- Gregory T. Booth,
- Isabel X. Wang,
- Vivian G. Cheung,
- and John T. Lis
Genome Res. June 2016 26: 799-811; Published in Advance May 12, 2016, doi:10.1101/gr.204578.116
...@cornell.edu AbstractComplex regulation of gene expression in mammals has evolved from simpler eukaryotic systems, yet the mechanistic features of this evolution remain elusive. Here, we compared the transcriptional landscapes of the distantly related budding and fission yeast. We adapted the Precision Run...
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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
...effects in humans restrict its usage (Kaeberlein 2014).The budding yeast Saccharomyces cerevisiae has been pivotal in elucidating mechanisms regulating aging. Yeast aging can be studied through two approaches: replicative life span (RLS) and chronological life span (CLS). Replicative lifespan...
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Research: Independent evolution of transcript abundance and gene regulatory dynamics
- Gat Krieger,
- Offir Lupo,
- Avraham A. Levy,
- and Naama Barkai
Genome Res. July 2020 30: 1000-1011; Published in Advance July 22, 2020, doi:10.1101/gr.261537.120
..., but providing limited information about variation across different conditions. To close this gap, we profiled mRNA levels of two related yeast species in hundreds of conditions and used coexpression analysis to distinguish variation in the dynamic pattern of gene expression from variation in expression levels...
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Research: Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
- Clotilde Garrido,
- Cintia Gómez-Muñoz,
- Etienne Kornobis,
- Nicolas Agier,
- Oana Ilioaia,
- Gilles Fischer,
- and Zhou Xu
Genome Res. March 2026 36: 522-533; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125
...response and inappropriate repair. In the budding yeast Saccharomyces cerevisiae, these include Rap1 and its cofactors Rif1/Rif2, which are bound to double-stranded DNA (dsDNA) in numbers roughly proportional to TL (Marcand et al. 1997; Levy and Blackburn 2004). In addition, owing to the incomplete...
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Research: Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast
- Wu Wei,
- Bianca P. Hennig,
- Jingwen Wang,
- Yujie Zhang,
- Ilaria Piazza,
- Yerma Pareja Sanchez,
- Christophe D. Chabbert,
- Sophie H. Adjalley,
- Lars M. Steinmetz,
- and Vicent Pelechano
Genome Res. December 2019 29: 1974-1984; Published in Advance November 18, 2019, doi:10.1101/gr.243378.118
...the existence of all predicted truncated proteins by direct methods such as MS and characterize their functional relevance in the particular cell systems studied.N-terminal proteomics approaches showed that downstream in-frame methionines often define alternative N termini in the budding yeast proteome...

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