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Method: Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase
- Maria Grazia Mendoza-Ferri,
- Gwendoline Lozachmeur,
- Maximilien Duvina,
- Laetitia Perret,
- Didier Merciris,
- Anne Gigout,
- and Marco Antonio Mendoza-Parra
Genome Res. July 2025 35: 1633-1645; Published in Advance May 13, 2025, doi:10.1101/gr.280305.124
...) a modified version of double-barcoded DNA arrays for capturing cleaved chromatin with the CUT&Tag chemistry (Kaya-Okur et al. 2019); (2) a modified bioinformatics pipeline allowing us to demultiplex spatial read-counts retrieved around gene promoter regions and their visualization within our tool MULTILAYER...
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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: 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
...deaminated samples, because complete deamination results in similar levels of dCPDs (i.e., enrichment value of about 1.0).One possible explanation of this finding is that protein–DNA interactions associated with the TSS and TES of yeast genes may suppress CPD deamination in cells, as suggested by previous...
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Research: Ultra-long-range interactions between active regulatory elements
- Elias T. Friman,
- Ilya M. Flyamer,
- Davide Marenduzzo,
- Shelagh Boyle,
- and Wendy A. Bickmore
Genome Res. August 2023 33: 1269-1283; Published in Advance July 14, 2023, doi:10.1101/gr.277567.122
.... Investigating factors that contribute to such chromatin interactions is therefore important for understanding gene regulation. Here, we have determined contact frequencies between millions of pairs of cis-regulatory elements from chromosome conformation capture data sets and analyzed a collection of hundreds...
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Method: ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies
- Jordan H. Little,
- Guillermo Hoffmann Meyer,
- Aakash Grover,
- Alex Michael Francette,
- Raghavendran Partha,
- Karen M. Arndt,
- Martin Smith,
- Nathan Clark,
- and Maria Chikina
Genome Res. September 2025 35: 2041-2051; Published in Advance August 7, 2025, doi:10.1101/gr.280586.125
...; AUC = 0.581). The true-positive set are interactions from STRING with combined scores that are more than 700. ERC scores were calculated on a phylogeny of 18 yeast species.Better: ERC2.0 outperforms previous ERC methodology and improves with larger data setsThe faster methodology can calculate ERC...
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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
....ji@northwestern.eduAbstract3′-end cleavage and polyadenylation is an essential process for eukaryotic mRNA maturation. In yeast species, the polyadenylation signals that recruit the processing machinery are degenerate and remain poorly characterized compared with the well-defined regulatory elements in mammals. Here we...
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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
...) Three copies of an HA tag were introduced into both alleles of the endogenous CSE4 gene in C. parapsilosis CLIB214 and 90-137 using CRISPR-Cas9 editing. The gene was cut between glycine 69 and glycine 70, and a repair template containing the HA tags was inserted by homologous recombination...
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Method: Harnessing agent-based frameworks in CellAgentChat to unravel cell–cell interactions from single-cell and spatial transcriptomics
- Vishvak Raghavan,
- Yumin Zheng,
- Yue Li,
- and Jun Ding
Genome Res. July 2025 35: 1646-1663; Published in Advance May 2, 2025, doi:10.1101/gr.279771.124
...Harnessing agent-based frameworks in CellAgentChat to unravel cell–cell interactions from single-cell and spatial transcriptomics Vishvak Raghavan1,2,3, Yumin Zheng2, Yue Li1,3 and Jun Ding1,2,3 1School of Computer Science, McGill University, Montreal, Quebec H3A 2A7, Canada; 2Meakins...
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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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Method: The oligogenic inheritance test GCOD detects risk genes and their interactions in congenital heart defects
- Maureen Pittman,
- Kihyun Lee,
- Franco Felix,
- Yu Huang,
- Adrienne Lam,
- Mauro W. Costa,
- Deepak Srivastava,
- and Katherine S. Pollard
Genome Res. February 2026 36: 330-347; Published in Advance December 12, 2025, doi:10.1101/gr.281141.125
...genetic interactions. As sequencing is applied to more families and other disorders, GCOD will enable detection of increasingly large, novel gene combinations, shedding light on combinatorial causes of genetic diseases.Many diseases are genetically heterogeneous such that damaging variants at different...
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