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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
...-Loeffler-Institut, 17493 Greifswald, Germany; 3School of Health Sciences-Biomedical Sciences Program, Missouri State University, Springfield, Missouri 65897, USA A tightly regulated DNA damage response is critical to the overall integrity of the . Here, we combine transcriptomics and proteomics to study DNA damage...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...TE annotation from Lien et al. (2016). The total TE annotation covered 51.92% of the . Consistent with previous findings (Goodier and Davidson 1994; Lien et al. 2016), the dominating TE group was DNA transposons from the Tc1-Mariner superfamily with more than 655,000 copies, covering 327 million base...
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Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
- David C.H. Metzger,
- Imogen Porter,
- Brendan Mobley,
- Benjamin A. Sandkam,
- Lydia J.M. Fong,
- Andrew P. Anderson,
- and Judith E. Mank
Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
..., which typically replicate via a “copy-and-paste” mechanism and require reverse transcription and an intermediate RNA phase, and class II TEs or DNA transposons, which typically replicate via a “cut-and-paste” mechanism facilitated by their encoded protein transposase. Given the distinct differences...
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Method: Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates
- Christopher Faulk
Genome Res. June 2023 33: 948-956; Published in Advance July 13, 2023, doi:10.1101/gr.277743.123
...is unbiased by nature; however, some regions of DNA are enriched compared with single-copy genes; for example, repetitive elements and transposons are present in multiple copies in the nuclear and therefore are more likely to be sequenced by skims than single-copy regions. Importantly, DNA methylation plays...
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Research: Transposon accumulation at xenobiotic gene family loci in aphids
- Tobias Baril,
- Adam Pym,
- Chris Bass,
- and Alex Hayward
Genome Res. October 2023 33: 1718-1733; Published in Advance October 18, 2023, doi:10.1101/gr.277820.123
...gossypiella (Fabrick et al. 2011; Wang et al. 2019); and for Hemiptera, Myzus persicae (Singh et al. 2020; Panini et al. 2021). TEs are DNA sequences capable of moving from one genomic location to another within the . TEs occur in nearly all eukaryotic s, and are implicated in the evolution of host genomic...
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Method: Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie
- Krzysztof H. Banecki,
- Haoxi Chai,
- Yijun Ruan,
- and Dariusz Plewczynski
Genome Res. April 8, 2026 ; Published in Advance April 8, 2026, doi:10.1101/gr.280985.125
...approaches have been far more widely adopted. Especially 3D-FISH and DNA tracing algorithms were proven to be useful in mapping specific 3D chromatin structure folding (Lacen and Lee 2024; Yang and Wang 2024). Several DNA tracing or oligopaint experiments (see Bintu et al. 2018; Su et al. 2020) were used...
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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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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
..., which uncovers a previously underappreciated epigenetic layer modulating 348 IPA. We demonstrate that introns containing IPA sites exhibit elevated DNA methylation 349 compared to non-IPA introns, a pattern that holds true across multiple cell-types. This observation 350 is in line with recent findings...
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Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
- Kehan Lang,
- Chenyang Jia,
- Siyu Li,
- Yi Guo,
- Dingjun Hu,
- and Shengquan Chen
Genome Res. April 2026 36: 769-784; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
...of one modality from another. However, existing methods for cross-modality translation between single-cell RNA sequencing (scRNA-seq) and single-cell DNA methylation (scDNAm) data face limitations, including unidirectionality, inadequate modeling of context-specific DNA methylation...
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Method: Homozygous editing of multiple genes for accelerated generation of xenotransplantation pigs
- Xiaoyue Duan,
- Chaolei Chen,
- Chang Du,
- Liang Guo,
- Jun Liu,
- Naipeng Hou,
- Pan Li,
- Xiaolan Qi,
- Fei Gao,
- Xuguang Du,
- Jiangping Song,
- and Sen Wu
Genome Res. May 2025 35: 1167-1178; Published in Advance March 5, 2025, doi:10.1101/gr.279709.124
...and colleagues that kills cells with unrepaired DNA damage while leaving the cells with precision mutations (Riesenberg et al. 2023). Furthermore, this might facilitate the selection of long-range sequence knock-in as well as multiple genes knockout. We expect that the coselection strategy will be valuable...
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