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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
...to UV mutagenesis. However, the impact of genomic context and chromatin architecture on CPD deamination rates in cells remains poorly understood. Here, we develop a method known as dCPD-seq to map deaminated CPDs (dCPDs) across the of repair-deficient yeast cells at single-nucleotide resolution. Our d...
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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
...-frozen tissues), and their current elevated costs make these technologies applicable to few tissue sections, thus avoiding generating multiomic integrative views of their molecular complexity.Previously, we have presented a double-barcoded DNA array strategy for SrT, allowing us to interrogate large numbers...
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Method: OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
- Siavash Raeisi Dehkordi,
- Zhaoyang Jia,
- Joey Estabrook,
- Jen Hauenstein,
- Neil Miller,
- Naz Güleray-Lafci,
- Jürgen Neesen,
- Alex Hastie,
- Alka Chaubey,
- Andy Wing Chun Pang,
- Paul Dremsek,
- and Vineet Bafna
Genome Res. December 2025 35: 2671-2681; Published in Advance November 14, 2025, doi:10.1101/gr.280536.125
...OMKar automates karyotyping using optical maps to identify constitutional abnormalities Siavash Raeisi Dehkordi1,2,5, Zhaoyang Jia1,5, Joey Estabrook2, Jen Hauenstein2, Neil Miller2, Naz Güleray-Lafci3, Jürgen Neesen3, Alex Hastie2, Alka Chaubey2, Andy Wing Chun Pang2, Paul Dremsek3 and Vineet...
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Research: Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer
- Yueqiang Song,
- Fuyuan Li,
- Shangzi Wang,
- Yuntong Wang,
- Cong Lai,
- Lian Chen,
- Ning Jiang,
- Jin Li,
- Xingdong Chen,
- Swneke D. Bailey,
- and Xiaoyang Zhang
Genome Res. October 2024 34: 1514-1527; Published in Advance October 18, 2024, doi:10.1101/gr.278418.123
...-specific. We develop a HiChIP-based methodology that navigates enhancer–promoter contact maps to prioritize the target genes for the duplication hotspots harboring enhancer elements. The methodology identifies many novel enhancer duplication events activating oncogenes such as ESR1, FOXA1, GATA3, GATA6, TP63...
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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
...of near-cognate poly(A) signals.Recent advances in mapping 3′-ends of RNA isoforms in S. cerevisiae using deep sequencing showed that the cleavage heterogeneity is quite extensive for some mRNAs (Moqtaderi et al. 2013). A cleavage zone can span dozens of nucleotides in a yeast mRNA, which rarely happens...
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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: The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores
- Yulong Liu,
- Gang Zhai,
- Jingzhi Su,
- Yulong Gong,
- Bingyuan Yang,
- Qisheng Lu,
- Longwei Xi,
- Yutong Zheng,
- Jingyue Cao,
- Haokun Liu,
- Junyan Jin,
- Zhimin Zhang,
- Yunxia Yang,
- Xiaoming Zhu,
- Zhongwei Wang,
- Gaorui Gong,
- Jie Mei,
- Zhan Yin,
- Rodolphe E. Gozlan,
- Shouqi Xie,
- and Dong Han
Genome Res. July 2024 34: 981-996; Published in Advance August 9, 2024, doi:10.1101/gr.278476.123
...Figure 4. miR-216b is responsible for regulating the expression of tas1r3. (A) Volcano map of intestine miRNAs expression levels in grass carp before or after the FHT from carnivore to herbivore. (B) The miRNAs putative binding to tas1r3 3′ UTR. Gray means no significantly difference; red means...
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Research: Ultraviolet damage and repair maps in Drosophila reveal the impact of domain-specific changes in nucleosome repeat length on repair efficiency
- Benjamin Morledge-Hampton,
- Kathiresan Selvam,
- Manish Chauhan,
- Alan G. Goodman,
- and John J. Wyrick
Genome Res. February 2025 35: 257-267; Published in Advance January 6, 2025, doi:10.1101/gr.279605.124
...in humans and yeast (Mao et al. 2016, 2017; Brown et al. 2018; Gonzalez-Perez et al. 2019). To study the influence of nucleosomes on UV damage formation in Drosophila, we used CPD-seq (Mao et al. 2016; Mao and Wyrick 2020) to map CPDs at single-nucleotide resolution in S2 cells immediately after UV...
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Method: A new compression strategy to reduce the size of nanopore sequencing data
- Kavindu Jayasooriya,
- Sasha P. Jenner,
- Pasindu Marasinghe,
- Udith Senanayake,
- Hassaan Saadat,
- David Taubman,
- Roshan Ragel,
- Hasindu Gamaarachchi,
- and Ira W. Deveson
Genome Res. July 2025 35: 1574-1582; Published in Advance May 15, 2025, doi:10.1101/gr.280090.124
...data compression strategy that helps address the large size of raw signal data generated during nanopore experiments. Ex-zd encompasses both a lossless compression method, which modestly outperforms all current methods for nanopore signal data compression, and a ‘lossy’ method, which can be used...
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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
...of the silencing factor Sir3 on the regulation of the yeast 3D folding. We show that Sir3 is both necessary and limiting for telomere clustering.Sir3 mediates interactions between telomeresHi-C contact maps clearly show that interactions between subtelomeric regions decrease in the absence of Sir3 and increase...

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