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Research: Characterization of the role of spatial proximity of DNA double-strand breaks in the formation of CRISPR-Cas9-induced large structural variations
- Mikkel Dahl-Jessen,
- Thorkild Terkelsen,
- Rasmus O. Bak,
- and Uffe Birk Jensen
Genome Res. February 2025 35: 231-241; Published in Advance January 13, 2025, doi:10.1101/gr.278575.123
...diversity, evolution, and carcinogenesis and are, as such, important for human health. However, it remains unclear how spatial proximity of double-strand breaks (DSBs) affects the formation of SVs. To investigate if spatial proximity between two DSBs affects DNA repair, we used data from 3C experiments (Hi...
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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: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...factors bind directly to the DNA to activate or repress transcription (Marr et al. 2021; Minnoye et al. 2021). Recent advances in sequencing technology have enabled the characterization of chromatin remodelers, nucleosome positioning, and chromatin accessibility using high-throughput assays like Ch...
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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
...in double-stranded DNA and ∼200 years in single-stranded DNA (Frederico et al. 1990). In contrast, the rate of deamination is vastly accelerated for cytosine bases in CPDs, with a half-life of tens to hundreds of hours (Taylor 2022). Because even error-free replicative bypass of a deaminated CPD (d...
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Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
- Jingwei Zhou,
- Yuhong Huang,
- Huan Ma,
- Yiqian Chen,
- Chuanye Chen,
- Fangpu Han,
- and Handong Su
Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
...chromosomes exhibited reduced signal intensities (Fig. 1A,B; Supplemental Fig. S1), consistent with previous reports of centromeric DNA loss during misdivision (Koo et al. 2015; Guo et al. 2016). Residual centromeric signals were predominantly localized at the breakpoints of long-arm telosomes (1AL, 1BL, 6AL...
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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
...governing PARP expression, 582 localization, and activity in cells. Crit Rev Biochem Mol Biol 55: 541–554. 583 Sandoval PY, Lee P-H, Meng X, Kapler GM. 2015. Checkpoint activation of an 584 unconventional DNA replication program in tetrahymena. PLoS Genet 11: 1005405. 585 Schärer OD. 2013. Nucleotide...
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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
...state, and local gene activity in addition to the DNA sequence (Szerlong and Hansen 2011; Jiang and Zhang 2021; Singh and Mueller-Planitz 2021). However, to what extent variations in NRL impact cellular processes such as DNA repair is unclear.Drosophila melanogaster (hereafter referred to as Drosophila...
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Research: Transcriptome analyses of rhesus monkey preimplantation embryos reveal a reduced capacity for DNA double-strand break repair in primate oocytes and early embryos
- Xinyi Wang,
- Denghui Liu,
- Dajian He,
- Shengbao Suo,
- Xian Xia,
- Xiechao He,
- Jing-Dong J. Han,
- and Ping Zheng
Genome Res. April 2017 27: 567-579; Published in Advance February 21, 2017, doi:10.1101/gr.198044.115
..., Petroff M, et al. 2012. Altered subcellular localization of Reduced DNA DSB repair in monkey early embryos Genome Research 577 www..org transcription factor TEAD4 regulates first mammalian cell lineage commitment. Proc Natl Acad Sci 109: 7362–7367. Huang Y, Yu X, Sun N, Qiao N, Cao Y, Boyd-Kirkup JD, Shen...
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Research: Rtt109 promotes nucleosome replacement ahead of the replication fork
- Felix Jonas,
- Gilad Yaakov,
- and Naama Barkai
Genome Res. June 2022 32: 1089-1098; Published in Advance May 24, 2022, doi:10.1101/gr.276674.122
...is composed of replication-dependent and -independent components. The former localizes to regions surrounding the fork, whereas the latter also occurs in regions not actively replicating (associated, e.g., with transcription). To distinguish these contributions, we defined the temporal progression of DNA...
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Research: Sister chromatid telomere fusions, but not NHEJ-mediated inter-chromosomal telomere fusions, occur independently of DNA ligases 3 and 4
- Kate Liddiard,
- Brian Ruis,
- Taylor Takasugi,
- Adam Harvey,
- Kevin E. Ashelford,
- Eric A. Hendrickson,
- and Duncan M. Baird
Genome Res. May 2016 26: 588-600; Published in Advance March 3, 2016, doi:10.1101/gr.200840.115
...evolution. [Supplemental material is available for this article.] Short telomeres inadequately protected by the shelterin complex (de Lange 2005) are recognized as double-stranded DNA breaks (DSBs), activating nonhomologous end-joining (NHEJ) DNA repair that can result in chromosomal fusions (Cowell...
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