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Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
...features of fungal SET domain proteins and uncover a synergistic interplay between H3K36me3 and H3K27me3 in regulating fungal secondary metabolism and virulence. This study advances our understanding of epigenetic regulation in fungi and provides potential targets for controlling fungal pathogens...
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Research: ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters
- Nina L. Haring,
- Elisabeth J. van Bree,
- Whitney S. Jordaan,
- Judith R.E. Roels,
- Gonzalo Congrains Sotomayor,
- Tiziana M. Hey,
- Fred T.G. White,
- Marc D. Galland,
- Marten P. Smidt,
- and Frank M.J. Jacobs
Genome Res. April 2021 31: 551-563; Published in Advance March 15, 2021, doi:10.1101/gr.265348.120
...modifications. Genes close to activated SVAs showed a mild up-regulation, indicating SVAs adopt properties of cis-regulatory elements in the absence of repression. Notably, -wide derepression of SVAs elicited the communal up-regulation of KZNFs that reside in KZNF clusters. This phenomenon may provide new...
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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
...yeast species can be partly owing to the degenerate nature of the regulatory motifs but also indicated that their poly(A) regions are under positive selection.DiscussionThe yeast species have been valuable model systems to dissect basic molecular mechanisms mediating steps of gene expression. Although...
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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
...deamination in yeast cells. Our data indicate that CPD deamination is elevated at minor-in rotational positions where the DNA minor groove faces the histone octamer, likely owing to increased solvent accessibility of the C4 position of the cytosine base. Moreover, we also observe strand-specific enrichment...
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Research: Genome-wide transcript and protein analysis highlights the role of protein homeostasis in the aging mouse heart
- Isabela Gerdes Gyuricza,
- Joel M. Chick,
- Gregory R. Keele,
- Andrew G. Deighan,
- Steven C. Munger,
- Ron Korstanje,
- Steven P. Gygi,
- and Gary A. Churchill
Genome Res. May 2022 32: 838-852; Published in Advance March 11, 2022, doi:10.1101/gr.275672.121
...in protein homeostasis, suggesting that genetic variation can alter the molecular aging process.Cardiovascular (CV) diseases are the leading cause of death in elderly people. Improved understanding of mechanisms that underlie the changes that occur in the aging heart could open new opportunities...
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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
...genes could have large effects on yeast traits. For instance, some strains have extra nonreference genes that allow them to metabolize xylose or melibiose (Naumov et al. 1990; Wenger et al. 2010). Highly diverged alleles of reference genes, as seen for the GAL genes, or copy number variation, as seen...
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Method: Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe
- Arnaud Belcour,
- Jeanne Got,
- Méziane Aite,
- Ludovic Delage,
- Jonas Collén,
- Clémence Frioux,
- Catherine Leblanc,
- Simon M. Dittami,
- Samuel Blanquart,
- Gabriel V. Markov,
- and Anne Siegel
Genome Res. June 2023 33: 972-987; Published in Advance July 19, 2023, doi:10.1101/gr.277056.122
...find module, and ModelSEED on five fungal s. Results on the eukaryotic s showed that AuCoMe predicts the most EC numbers, reactions, and pathways in species distant from the model ones (Supplemental Table S5; Supplemental Fig. S7). A comparison with metabolic pathways contained in YeastCyc for the of S...
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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
...1985; Hey 1988; Lozovskaya et al. 1990; Vela et al. 2014). Hybridization between Arabidopsis thaliana and A. arenosa induces up-regulation of ATHILA retrotransposon expression and reduces hybrid viability (Josefsson et al. 2006). However, such an effect is not observed in crosses between A. thaliana...
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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
...production following heat shock (Supplemental Fig. S1A; Warner 1999; Gasch et al. 2000; Causton et al. 2001; Pincus et al. 2018). K-means clustering revealed two groups of genes strongly up-regulated by heat shock; these groups were both enriched for association with Hsf1 and Msn2 and Msn4 (Supplemental Fig...
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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
...not express Upf proteins, which are the proteins that mediate NMD (Kervestin and Jacobson 2012), do not show IR up-regulation (Gonzalez-Hilarion et al. 2016). By using ribosome profiling data, we obtained evidence that some IR isoforms are likely to translate alternative proteins. Thus, in some cases...

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