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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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Method: Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation
- Richa Rashmi,
- Abhinaya Muruganandham,
- Pranita Borkar,
- Sumana Mallick,
- Taylor Hubbs,
- Ari Aviles,
- Daniel Chung,
- and Irtisha Singh
Genome Res. April 13, 2026 gr.281044.125; Published in Advance April 13, 2026, doi:10.1101/gr.281044.125
...1 Dynamics of intronic polyadenylation in the hematopoietic lineage and its 1 regulation by DNA methylation 2 Richa Rashmi1, Abhinaya Muruganandham1,2, Pranita Borkar1, Sumana Mallick1,2, Taylor 3 Hubbs1, Ari Aviles1,3, Daniel Chung1, Irtisha Singh1,2,3* 4 1Department of Cell Biology & Genetics...
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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 A.C. Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J. Smith,
- and Falk Butter
Genome Res. January 28, 2026 ; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...damage response transcripts. NER: nucleotide excision repair, ICL: inter crosslink repair, BER: base excision repair, DSBR: double-strand break repair, MMR:mismatch repair, DDR: DNA damage response, UV: ultraviolet light, CPT: cisplatin, HP: hydrogen peroxide, MMS: methyl methanesulfonate, IR: ionizing...
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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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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. April 2026 36: 802-813; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
..., and three independent biological replicates were processed. (E) DNA yields (total ng) obtained from each sorted population. (F) Integrity analysis and size distribution of purified and fragmented genomic DNA. (G) Electropherogram of purified and fragmented genomic DNA. (H) RNA yields copurified with the DNA...
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