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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J Smith,
- and Falk Butter
Genome Res. January 28, 2026 gr.281000.125; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...–58. 489 Fayyad N, Kobaisi F, Beal D, Mahfouf W, Ged C, Morice-Picard F, Fayyad-Kazan M, 490 Fayyad-Kazan H, Badran B, Rezvani HR, et al. 2020. Xeroderma Pigmentosum C 491 (XPC) Mutations in Primary Fibroblasts Impair Base Excision Repair Pathway and 492 Increase Oxidative DNA Damage. Front Genet 11...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
....5%–56%) increase in the dnSNV rate with ART compared with naturally conceived mice (P = 0.017). Analysis of the dnSNV mutation spectrum identifies signatures attributable to germline DNA repair activity but reveals no differentially enriched signatures between cohorts. We observe no enrichment of dn...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells Jennifer A. Urban1, Daniel Ringwalt1, John M. Urban2,3, Wingel Xue1,5, Ryan Gleason1, Keji Zhao4 and Xin Chen1,2 1Department of Biology, The Johns Hopkins University...
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Research: Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype
- Arne Sahm,
- Konstantin Riege,
- Marco Groth,
- Martin Bens,
- Johann Kraus,
- Martin Fischer,
- Hans Kestler,
- Christoph Englert,
- Ralf Schaible,
- Matthias Platzer,
- and Steve Hoffmann
Genome Res. December 2024 34: 2217-2228; Published in Advance December 4, 2024, doi:10.1101/gr.279025.124
...GenomiPhi Kit was used for cell lysis and multiple displacement amplification. Sequencing was performed using Illumina sequencing methodology (Bentley et al. 2008). In detail, 2 µg of amplified DNA was introduced into Illumina's TruSeq DNA PCR-free library preparation. Paired-end sequencing was conducted...
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Research: Tyrosine 1–phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage
- Kamal Ajit,
- Adele Alagia,
- Kaspar Burger,
- and Monika Gullerova
Genome Res. February 2024 34: 201-216; Published in Advance March 11, 2024, doi:10.1101/gr.278644.123
...Tyrosine 1–phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage Kamal Ajit1, Adele Alagia1, Kaspar Burger2,3 and Monika Gullerova1 1Sir William Dunn School of Pathology, Oxford, OX1 3RE...
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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
...cancers because it induces mutagenic damage to DNA (Pfeifer et al. 2005; Brash 2015). The primary class of UV damage is the cyclobutane pyrimidine dimer (CPD), which forms between adjacent pyrimidine bases (i.e., TT, TC, CT, and CC) (Friedberg et al. 2006). Although CPDs form most frequently at TT...
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Research: Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types
- Arnoud Boot,
- Alvin W.T. Ng,
- Fui Teen Chong,
- Szu-Chi Ho,
- Willie Yu,
- Daniel S.W. Tan,
- N. Gopalakrishna Iyer,
- and Steven G. Rozen
Genome Res. June 2020 30: 803-813; Published in Advance July 6, 2020, doi:10.1101/gr.255620.119
...H, Battistini F, Bouwman BAM, Iftekhar A, Katainen R, Cajuso T, Crosetto N, Orozco M, Aaltonen LA, et al. 2020. Colibactin DNA-damage signature indicates mutational impact in colorectal cancer. Nat Med doi:10.1038/s41591-020-0908-2 ↵Ellrott K, Bailey MH, Saksena G, Covington KR, Kandoth C, Stewart C...
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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
..., the wrapping of DNA around the histone octamer in individual nucleosomes significantly modulates UV damage formation and repair, generating nucleosome-associated patterns that correlate with somatic mutation rates in skin cancers (Brown et al. 2018; Pich et al. 2019). For example, the formation of UV...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...author: ryan.lister@uwa.edu.auAbstractIn plants, cytosine DNA methylation (mC) is largely associated with transcriptional repression of transposable elements, but it can also be found in the body of expressed genes, referred to as gene body methylation (gbM). gbM is correlated with ubiquitously expressed...
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Research: Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in Oryza
- Chenbo Gong,
- Yicheng Huang,
- Mengmeng Liu,
- Yong Zhou,
- Yinwei Xu,
- Nahed Mohammed,
- Xintong Qiao,
- Andrea Zuccolo,
- Weibo Xie,
- Rod A. Wing,
- Jianwei Zhang,
- Fei Zhou,
- and Yongjun Lin
Genome Res. June 2025 35: 1349-1363; Published in Advance April 25, 2025, doi:10.1101/gr.279609.124
...-strand break repair pathways and replication-based mechanisms play important roles in integrating organelle DNA into the nuclear . Further investigation indicates that complex NORGs are formed through single mutational events before or during the insertion process via ligation of multiple plastid and...

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