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Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
- Kai Otsuka,
- Akihiko Sakashita,
- So Maezawa,
- Richard M. Schultz,
- and Satoshi H. Namekawa
Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
...spermatogenesis and meiotic sex chromosome inactivation (MSCI), an essential process in the male germline (Turner 2015; Alavattam et al. 2022).ResultsExpression of KZFPs and ERVs changes dynamically during spermatogenesis in miceBecause the KZFP family of proteins evolved rapidly in mammals and contributed...
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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
....5%–56%) increase in the dnSNV rate with ART compared with naturally conceived mice (P = 0.017). Analysis of the dnSNV mutation spectrum identifies signatures attributable to germline DNA repair activity but reveals no differentially enriched signatures between cohorts. We observe no enrichment of dn...
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Method: Characterization of meiotic recombination intermediates through gene knockouts in founder hybrid mice
- Benjamin Davies,
- Gang Zhang,
- Daniela Moralli,
- Samy Alghadban,
- Daniel Biggs,
- Chris Preece,
- Peter Donnelly,
- and Anjali Gupta Hinch
Genome Res. November 2023 33: 2018-2027; Published in Advance November 17, 2023, doi:10.1101/gr.278024.123
...with a benchmark for validating our method. Although Dmc1−/− male mice undergo DSBs and load RAD51 with normal kinetics, the breaks remain unrepaired, and the chromosomes fail to synapse, which leads to meiotic arrest.The aims of this study were, first, to establish and validate an efficient knockout strategy...
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Research: Parental methylome reprogramming in human uniparental blastocysts reveals germline memory transition
- Jiawei Xu,
- Yimin Shu,
- Guidong Yao,
- Yu Zhang,
- Wenbin Niu,
- Yile Zhang,
- Xueshan Ma,
- Haixia Jin,
- Fuli Zhang,
- Senlin Shi,
- Yang Wang,
- Wenyan Song,
- Shanjun Dai,
- Luyao Cheng,
- Xiangyang Zhang,
- Wei Xie,
- Aaron J. Hsueh,
- and Yingpu Sun
Genome Res. September 2021 31: 1519-1530; Published in Advance July 30, 2021, doi:10.1101/gr.273318.120
...are derived from only the mother (parthenogenetic/gynogenetic [GG]) or the father (androgenetic [AG]). Interfering with the meiotic reduction in oocytes leads to the development of a diploid or haploid embryo with maternal chromosomes only, thus producing parthenogenetic embryos. In contrast, reconstructing...
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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
...on Chromosome 13 at which strains inheriting the C57BL/6J (B) haplotype have a higher rate of STR expansions than those inheriting the DBA/2J (D) haplotype. The strongest candidate gene in this locus is Msh3, a known modifier of STR stability in cancer and at pathogenic repeat expansions in mice and humans...
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Method: Early embryonic mutations reveal dynamics of somatic and germ cell lineages in mice
- Arikuni Uchimura,
- Hirotaka Matsumoto,
- Yasunari Satoh,
- Yohei Minakuchi,
- Sayaka Wakayama,
- Teruhiko Wakayama,
- Mayumi Higuchi,
- Masakazu Hashimoto,
- Ryutaro Fukumura,
- Atsushi Toyoda,
- Yoichi Gondo,
- and Takeshi Yagi
Genome Res. May 2022 32: 945-955; Published in Advance May 9, 2022, doi:10.1101/gr.276363.121
.... Mutation rates and characteristics of the postzygotic mutations. (A) Schematic of the number of spontaneous mutations along with the developmental period. (B) The trinucleotide context of postzygotic mutations (validated mosaic mutations detected during deep-coverage WGS on five mice), germline mutations...
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Research: Germline mutation rates and the long-term phenotypic effects of mutation accumulation in wild-type laboratory mice and mutator mice
- Arikuni Uchimura,
- Mayumi Higuchi,
- Yohei Minakuchi,
- Mizuki Ohno,
- Atsushi Toyoda,
- Asao Fujiyama,
- Ikuo Miura,
- Shigeharu Wakana,
- Jo Nishino,
- and Takeshi Yagi
Genome Res. August 2015 25: 1125-1134; Published in Advance June 30, 2015, doi:10.1101/gr.186148.114
...that affects the amount of genetic variation and the rate of evolution. However, neither the rate of germline mutations in laboratory mice nor the biological significance of the mutation rate in mammalian populations is clear. Here we studied -wide mutation rates and the long-term effects of mutation...
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Research: Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability
- Richard J. Wang,
- Gregg W.C. Thomas,
- Muthuswamy Raveendran,
- R. Alan Harris,
- Harshavardhan Doddapaneni,
- Donna M. Muzny,
- John P. Capitanio,
- Predrag Radivojac,
- Jeffrey Rogers,
- and Matthew W. Hahn
Genome Res. June 2020 30: 826-834; Published in Advance May 27, 2020, doi:10.1101/gr.255174.119
.... 2015; Francioli et al. 2015; Jónsson et al. 2017). This male bias in the number of de novo mutations has been attributed to the continuous nature of spermatogenesis, which results in the accumulation of errors in the male germline (Crow 2000). As new mutations are responsible for the incidence...
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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
...-type-specific replication timing differences align with cell-type-specific chromatin features. For the first time, our results enable precise identification of specific chromosomal regions that differ in replication timing and chromatin landscapes between germline and somatic stem-cell populations in the in vivo context...
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Research: Small chromosomal regions position themselves autonomously according to their chromatin class
- Harmen J.G. van de Werken,
- Josien C. Haan,
- Yana Feodorova,
- Dominika Bijos,
- An Weuts,
- Koen Theunis,
- Sjoerd J.B. Holwerda,
- Wouter Meuleman,
- Ludo Pagie,
- Katharina Thanisch,
- Parveen Kumar,
- Heinrich Leonhardt,
- Peter Marynen,
- Bas van Steensel,
- Thierry Voet,
- Wouter de Laat,
- Irina Solovei,
- and Boris Joffe
Genome Res. June 2017 27: 922-933; Published in Advance March 24, 2017, doi:10.1101/gr.213751.116
...chromosomal segments of different chromatin classes are able to correctly segregate in the nucleus and whether they can establish the correct pattern of lamina association. For this purpose, we studied a human chromosome segregating in a xenospecific mouse background. Although cell lines and mice carrying...

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