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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
..., Källberg M, Cox AJ, Kruglyak S, Saunders CT. 2016. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics 32: 1220–1222. doi:10.1093/bioinformatics/btv710 ↵Chen C, Qi H, Shen Y, Pickrell J, Przeworski M. 2017. Contrasting determinants...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...hypersensitivity), high nucleosomal turnover (e.g., high levels of rapid-turnover histones H2A.Z and H3.3), specific epigenetic markers (e.g., high ratio of H3K4me1 and H3K4me2 to H3K4me3, high ratio of 5hmC to 5mC, enrichment of H3K27ac), chromatin loops in direct contact with the core promoter (enrichment...
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Research: Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary
- Satyam P. Srivastav,
- Cédric Feschotte,
- and Andrew G. Clark
Genome Res. May 2024 34: 711-724; Published in Advance May 15, 2024, doi:10.1101/gr.278062.123
...with high-quality long-read assemblies. We perform annotations of ovary piCs and -wide TE content in each strain. Our analysis uncovers extensive variation in piC activity across strains and signatures of rapid birth and death of piCs. Most TEs inferred to be recently active show an enrichment of insertions...
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Research: Extensive variation in germline de novo mutations in Poecilia reticulata
- Yuying Lin,
- Iulia Darolti,
- Wouter van der Bijl,
- Jake Morris,
- and Judith E. Mank
Genome Res. August 2023 33: 1317-1324; Published in Advance July 13, 2023, doi:10.1101/gr.277936.123
...the short guppy generation time. Overall, our study shows remarkable variation in germline mutation rate and provides insights into rapid evolution of guppies.Mutations underlie much of the diversity of life on earth. Moreover, the timing, rate, and spectra of germline mutations are fundamental aspects...
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Resource: Large-scale discovery of mouse transgenic integration sites reveals frequent structural variation and insertional mutagenesis
- Leslie O. Goodwin,
- Erik Splinter,
- Tiffany L. Davis,
- Rachel Urban,
- Hao He,
- Robert E. Braun,
- Elissa J. Chesler,
- Vivek Kumar,
- Max van Min,
- Juliet Ndukum,
- Vivek M. Philip,
- Laura G. Reinholdt,
- Karen Svenson,
- Jacqueline K. White,
- Michael Sasner,
- Cathleen Lutz,
- and Stephen A. Murray
Genome Res. March 2019 29: 494-505; Published in Advance January 18, 2019, doi:10.1101/gr.233866.117
...transgene insertions in these lines is largely unknown. Here, expanding on prior work, we show that TLA represents a rapid and efficient means to precisely identify the site of insertion, and critically, the corresponding molecular consequences. These events are associated with structural variations...
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Research: Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species-dependent essential genes
- Monica R. Sanchez,
- Celia Payen,
- Frances Cheong,
- Blake T. Hovde,
- Sarah Bissonnette,
- Adam P. Arkin,
- Jeffrey M. Skerker,
- Rachel B. Brem,
- Amy A. Caudy,
- and Maitreya J. Dunham
Genome Res. March 2019 29: 396-406; Published in Advance January 11, 2019, doi:10.1101/gr.232330.117
...species.ResultsGenerating Tn7 insertional libraries in S. uvarum to predict essential and nonessential genesOne of the most straightforward mutant phenotypes to characterize is cell viability, which reveals if a given gene is involved in an essential cellular process. Therefore, we first sought...
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Research: Gene regulation underlies environmental adaptation in house mice
- Katya L. Mack,
- Mallory A. Ballinger,
- Megan Phifer-Rixey,
- and Michael W. Nachman
Genome Res. November 2018 28: 1636-1645; Published in Advance September 7, 2018, doi:10.1101/gr.238998.118
..., Maretzky T, Issuree PD, Niu XD, Reiss K, Saftig P, Khokha R, Lundell D, Blobel CP. 2010. ADAM17 is regulated by a rapid and reversible mechanism that controls access to its catalytic site. J Cell Sci 123: 3913–3922. ↵Lee DC, Sunnarborg SW, Hinkle CL, Myers TJ, Stevenson M, Russell W, Castner BJ, Gerhart MJ...
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Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
- Mikhail O. Maksimov,
- Cynthia Wu,
- David G. Ashbrook,
- Flavia Villani,
- Vincenza Colonna,
- Nima Mousavi,
- Nichole Ma,
- Lu Lu,
- Jonathan K. Pritchard,
- Alon Goren,
- Robert W. Williams,
- Abraham A. Palmer,
- and Melissa Gymrek
Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
...that are only identified upon molecular interrogation (Sasani et al. 2022). Identifying genetic factors controlling this variation can provide insight into mutation processes and DNA repair mechanisms.Short tandem repeats (STRs), typically consisting of repeated sequence motifs of 1–6 bp, show rapid mutation...
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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...content in affected regions (Duret and Galtier 2009a). To date, gBGC has been found to be widespread in mammals and birds and contributes to GC content variation, rapid evolution of sequences, and even fixation of deleterious mutations (Galtier et al. 2009; Glémin 2010; Pessia et al. 2012; Capra et al...
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Method: A HIT-trapping strategy for rapid generation of reversible and conditional alleles using a universal donor
- Hengxing Lu,
- Jun Liu,
- Tao Feng,
- Zihang Guo,
- Yunjun Yin,
- Fei Gao,
- Gengsheng Cao,
- Xuguang Du,
- and Sen Wu
Genome Res. May 2021 31: 900-909; Published in Advance April 1, 2021, doi:10.1101/gr.271312.120
...for gene functional annotation and biomedical research. Despite technological advances in gene editing by the CRISPR-Cas9 systems, rapid and efficient introduction of site-directed mutations remains a challenge in large animal models. Here, we developed a robust and flexible insertional mutagenesis...

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