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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: Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication
- Vinay Tripuraneni,
- Gonen Memisoglu,
- Heather K. MacAlpine,
- Trung Q. Tran,
- Wei Zhu,
- Alexander J. Hartemink,
- James E. Haber,
- and David M. MacAlpine
Genome Res. May 2021 31: 775-788; Published in Advance April 2, 2021, doi:10.1101/gr.271155.120
...the context of chromatin (Hauer and Gasser 2017). The canonical access-repair-restore model (Soria et al. 2012; Polo and Almouzni 2015) for DNA repair in eukaryotic s recognizes that chromatin presents a significant obstacle for DNA double-strand break recognition and repair processes. Chromatin must thus...
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Method: Highly efficient and scarless genome editing via essential gene-coupled homology-directed repair
- Joo Hye Yeo,
- Hyongbum Henry Kim,
- Sang Ho Oh,
- and Jinu Lee
Genome Res. April 15, 2026 gr.281194.125; Published in Advance April 15, 2026, doi:10.1101/gr.281194.125
...-proficient cells. By 35 leveraging essential-gene co-editing, ESS-HDR enables precise and scarless 36 modification with enhanced efficiency. CRISPR–Cas9 induces double-strand breaks at 37 both the target locus and an essential gene, accompanied by two donor templates: one 38 introducing the desired edit...
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Method: Nanopore sequencing of complex genomic rearrangements in yeast reveals mechanisms of repeat-mediated double-strand break repair
- Ryan J. McGinty,
- Rachel G. Rubinstein,
- Alexander J. Neil,
- Margaret Dominska,
- Denis Kiktev,
- Thomas D. Petes,
- and Sergei M. Mirkin
Genome Res. December 2017 27: 2072-2082; Published in Advance November 7, 2017, doi:10.1101/gr.228148.117
..., Durham, North Carolina 27710, USA Corresponding author: sergei.mirkin@tufts.eduAbstractImproper DNA double-strand break (DSB) repair results in complex genomic rearrangements (CGRs) in many cancers and various congenital disorders in humans. Trinucleotide repeat sequences, such as (GAA)n repeats...
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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
...damage signaling and homology-directed DNA double-strand break repair. This study highlights the utility of monkey models to better understand the molecular basis for reprogramming, ZGA, and genomic stability surveillance in human early embryogenesis and may provide insights for improved homologous...
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Method: Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases
- Ming Yan,
- Thea O. Andersen,
- Phillip B. Pope,
- and Zhongtang Yu
Genome Res. February 2025 35: 368-378; Published in Advance December 27, 2024, doi:10.1101/gr.279825.124
...and protozoa from those of prokaryotes. Overall, the newly developed package GutEuk and its associated databases create new opportunities for the in-depth study of GI tract eukaryotes.The complex and multikingdom microbial ecosystem unique to the rumen supplies ruminants with up to 70% of their energy...
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Method: MCHelper automatically curates transposable element libraries across eukaryotic species
- Simon Orozco-Arias,
- Pío Sierra,
- Richard Durbin,
- and Josefa González
Genome Res. December 2024 34: 2256-2268; Published in Advance December 9, 2024, doi:10.1101/gr.278821.123
.... Genome-wide TE annotations are also improved, including larger unfragmented insertions. Moreover, MCHelper is an easy-to-install and easy-to-use tool.After two decades of sequencing projects, reference s for thousands of eukaryotic species are already available and many more are currently being sequenced...
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Method: GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes
- Tomáš Brůna,
- Alexandre Lomsadze,
- and Mark Borodovsky
Genome Res. May 2024 34: 757-768; Published in Advance June 12, 2024, doi:10.1101/gr.278373.123
...Mark-ETP delivers state-of-the-art gene-prediction accuracy, with the margin of outperforming existing approaches increasing in its application to larger and more complex eukaryotic s.Massive sequencing of eukaryotic s, for example, the Earth BioGenome Project (Lewin et al. 2022), should be complemented with fast...
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Corrigendum: Corrigendum: 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. September 2017 27: 1621.2; doi:10.1101/gr.226613.117
...double-strand break repair in primate oocytes and early embryos 650223 CAS Center for Excellence in Molecular Cell Science Key Laboratory of Computational Biology Kunming College of Life Science 100049 Primate Research Center Kunming Institute of Zoology China; Chinese Academy of Sciences–Max Planck...
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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
....DiscussionNucleosomes are ubiquitous throughout the s of higher eukaryotes and have indispensable roles in organization (McGinty and Tan 2015). Exploring the influences of nucleosomes on DNA repair systems such as NER is critical to our understanding of maintenance and stability. Here, we produced the first CPD damage map...

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