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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...and human melanomas are elevated at fast-deaminating TCG sequences, occurring about three- to fivefold more frequently than expected from the levels of damage formation (Fig. 3H).CPD deamination is suppressed near the transcription start and end sites of yeast genesTo determine how CPD deamination...
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Research: Genomic environments scale the activities of diverse core promoters
- Clarice K.Y. Hong and
- Barak A. Cohen
Genome Res. January 2022 32: 85-96; Published in Advance December 27, 2021, doi:10.1101/gr.276025.121
.... Determining whether the specificity of gene expression is governed by enhancers and chromatin features or by enhancer-promoter compatibility is crucial to understanding a variety of biological processes including cell type–specific regulatory programs and models of gene evolution.The core promoter is the ∼100...
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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
...relevant genetic differences is linkage mapping on a biparental cross (Ehrenreich et al. 2009). Two haploid yeast strains are mated to produce a diploid strain, which undergoes meiosis to produce haploid progeny strains known as segregants. Researchers determine genotypes and phenotypes for hundreds...
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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
...to transcription by RNA polymerase II (Pol II) in eukaryotes. In budding yeast (Saccharomyces cerevisiae), Mediator is recruited by activators and associates with core promoter regions, where it facilitates preinitiation complex (PIC) assembly, only transiently before Pol II escape. Interruption...
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Research: Reactivation of transposable elements following hybridization in fission yeast
- Sergio Tusso,
- Fang Suo,
- Yue Liang,
- Li-Lin Du,
- and Jochen B.W. Wolf
Genome Res. February 2022 32: 324-336; Published in Advance December 14, 2021, doi:10.1101/gr.276056.121
...evidence for this “genomic shock hypothesis” in the fission yeast Schizosaccharomyces pombe. In this species, two divergent lineages (Sp and Sk) have experienced recent, likely human-induced, hybridization. We used long-read sequencing data to assemble s of 37 samples derived from 31 S. pombe strains...
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Research: Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation
- Răzvan V. Chereji,
- Peter R. Eriksson,
- Josefina Ocampo,
- Hemant K. Prajapati,
- and David J. Clark
Genome Res. December 2019 29: 1985-1995; Published in Advance September 11, 2019, doi:10.1101/gr.249326.119
...in chromatinOur data indicate that access to most of the is blocked by nucleosomes in yeast (∼78%) and in mouse hepatocytes (∼68%), consistent with average nucleosome spacings of ∼165 bp and ∼195 bp, respectively, and a protected inner core of ∼133 bp. Thus, nucleosome spacing is the major determinant...
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Resource: Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms
- José Carlos Montañés,
- Marta Huertas,
- Simone G. Moro,
- William R. Blevins,
- Mercè Carmona,
- José Ayté,
- Elena Hidalgo,
- and M. Mar Albà
Genome Res. June 2022 32: 1215-1227; Published in Advance May 26, 2022, doi:10.1101/gr.276516.121
...), 08003 Barcelona, Spain; 2Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; 3Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain Corresponding author: malba@imim.esAbstractThe unicellular yeast Schizosaccharomyces pombe...
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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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Research: The organization of genome duplication is a critical determinant of the landscape of genome maintenance
- Blanca Gómez-Escoda and
- Pei-Yun Jenny Wu
Genome Res. August 2018 28: 1179-1192; Published in Advance June 22, 2018, doi:10.1101/gr.224527.117
...in the fission yeast does not alter sensitivity to replication stress (Hayano et al. 2012). First, we evaluated the effect of rif1Δ in our experimental setup and determined origin usage in cdc25-22 rif1Δ cells synchronized in G2 and released in 6 mM HU (Supplemental Fig. S5A). Consistent with previous reports...
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Research: Polymorphic centromere locations in the pathogenic yeast Candida parapsilosis
- Mihaela Ola,
- Caoimhe E. O'Brien,
- Aisling Y. Coughlan,
- Qinxi Ma,
- Paul D. Donovan,
- Kenneth H. Wolfe,
- and Geraldine Butler
Genome Res. May 2020 30: 684-696; Published in Advance May 18, 2020, doi:10.1101/gr.257816.119
...- or trimethylation at lysine 9 of histone H3 (H3K9me2/3). The position of the centromere in most species is determined by the presence of a variant of histone H3, called CENPA in mammals or Cse4 in yeast.Centromere repositioning occurs on an evolutionary timescale, leading to the formation of evolutionarily new...
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