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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
..., an insignificant difference (ART cohort as baseline, IRR = 1.14, 95% CI: 0.41–3.19, P = 0.796) (Supplemental Table S5). Approximately half of these SV calls localize to a cluster of C2H2 KRAB zinc finger proteins on distal Chromosome 4 (145.3 Mb), a locus recently shown to be highly copy number variable in house...
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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 testes. Using editing, we generated knock-in fly lines with gfp-tagged endogenous mcm2, orc1, and caf1-105, genes considered differentially enriched in GSC-like cells (Fig. 2G; Table 1; Supplemental Fig. S3D). We then performed immunostaining on nontumor testes to examine the expression patterns...
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Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
- Wenyu Zhang,
- Anja Guenther,
- Yuanxiao Gao,
- Kristian Ullrich,
- Bruno Huettel,
- Aftab Ahmad,
- Lei Duan,
- Kaizong Wei,
- and Diethard Tautz
Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
...and closely related outgroup species. Using an optimized protocol to capture predominantly full-length capped transcripts, we identify widespread brain isoform diversity. We assess whether the individual isoform landscape can be used to trace the differentiation history of house mouse natural populations. We...
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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
...of Chromosome 8 and restore euploidy in cells derived from an individual with a complex rearrangement of Chromosome 8p. Transcriptomic analysis revealed 361 differentially expressed genes between the proband and the euploid revertant, highlighting genes both within and outside the 8p region that may contribute...
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Research: Inference of selective forces on house mouse genomes during secondary contact in East Asia
- Kazumichi Fujiwara,
- Shunpei Kubo,
- Toshinori Endo,
- Toyoyuki Takada,
- Toshihiko Shiroishi,
- Hitoshi Suzuki,
- and Naoki Osada
Genome Res. March 2024 34: 366-375; Published in Advance March 20, 2024, doi:10.1101/gr.278828.123
..., studies into the demographic history of M. musculus in East Asia using a -wide data set have not been performed.Although the genetic diversity of maternally inherited mitochondrial haplotypes in wild house mice has been well studied, natural variation in the paternally inherited Y Chromosome has remained...
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Research: Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes
- Diana Lobo,
- Hernán E. Morales,
- Cock Van Oosterhout,
- José Vicente López-Bao,
- Pedro Silva,
- Luis Llaneza,
- Carolina Pacheco,
- Diana Castro,
- Germán Hernández-Alonso,
- George Pacheco,
- John Archer,
- M. Thomas P. Gilbert,
- Nuno Ferrand,
- and Raquel Godinho
Genome Res. March 2025 35: 432-445; Published in Advance February 14, 2025, doi:10.1101/gr.279093.124
...levels between these groups along Chromosome 2 in nonoverlapping windows of 500 kb using VCFtools. Levels of differentiation between the Δblock and the genomic background (defined as the entire Chromosome 2 excluding the introgressed block) were compared using a Welch two-sample t-test in R. To identify...
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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...decayed during early primate evolution (>50 million years ago [MYA]) before stabilizing since the separation of Old World monkeys (<50 MYA). Taken together, our results suggest ancient and lineage-specific transposon subfamilies contributed to mammalian NF-kB regulatory networks.Transposable elements (TEs...
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Research: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
- Koichi Kitao,
- Kenji Ichiyanagi,
- and So Nakagawa
Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
..., and Diptera, and the 800 Mb grasshopper X Chromosome is homologous to the fly ancestral X Chromosome despite 400 million years of divergence, suggesting either repeated origin of sex chromosomes with highly similar gene content, or long-term conservation of the X Chromosome. We use this broad conservation...
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Method: A minimally destructive protocol for DNA extraction from ancient teeth
- Éadaoin Harney,
- Olivia Cheronet,
- Daniel M. Fernandes,
- Kendra Sirak,
- Matthew Mah,
- Rebecca Bernardos,
- Nicole Adamski,
- Nasreen Broomandkhoshbacht,
- Kimberly Callan,
- Ann Marie Lawson,
- Jonas Oppenheimer,
- Kristin Stewardson,
- Fatma Zalzala,
- Alexandra Anders,
- Francesca Candilio,
- Mihai Constantinescu,
- Alfredo Coppa,
- Ion Ciobanu,
- János Dani,
- Zsolt Gallina,
- Francesco Genchi,
- Emese Gyöngyvér Nagy,
- Tamás Hajdu,
- Magdolna Hellebrandt,
- Antónia Horváth,
- Ágnes Király,
- Krisztián Kiss,
- Barbara Kolozsi,
- Péter Kovács,
- Kitti Köhler,
- Michaela Lucci,
- Ildikó Pap,
- Sergiu Popovici,
- Pál Raczky,
- Angela Simalcsik,
- Tamás Szeniczey,
- Sergey Vasilyev,
- Cristian Virag,
- Nadin Rohland,
- David Reich,
- and Ron Pinhasi
Genome Res. March 2021 31: 472-483; Published in Advance February 12, 2021, doi:10.1101/gr.267534.120
...a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other...

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