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Research: Suppressor mutations in Mecp2-null mice implicate the DNA damage response in Rett syndrome pathology
- Adebola Enikanolaiye,
- Julie Ruston,
- Rong Zeng,
- Christine Taylor,
- Marijke Schrock,
- Christie M. Buchovecky,
- Jay Shendure,
- Elif Acar,
- and Monica J. Justice
Genome Res. April 2020 30: 540-552; Published in Advance April 21, 2020, doi:10.1101/gr.258400.119
...in mice may allow for the discovery of pathways that inform therapeutic strategies in humans. In a preliminary dominant suppressor mutagenesis screen using the supermutagen N-ethyl-N-nitrosourea (ENU), we isolated five modifier loci, named suppressor of methyl CpG binding protein (Sum) 1–5, which suppress...
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Research: Gene regulation and speciation in house mice
- Katya L. Mack,
- Polly Campbell,
- and Michael W. Nachman
Genome Res. April 2016 26: 451-461; Published in Advance February 1, 2016, doi:10.1101/gr.195743.115
...Chromosome in hybrid male sterility in house mice. Quantitative trait locus mapping of sterility phenotypes (White et al. 2011; Bhattacharyya et al. 2014), phenotyping of introgression lines (Oka et al. 2004, 2014; Good et al. 2008b; Campbell et al. 2013), and studies of introgression across the hybrid zone...
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Method: Dissection of complex adult traits in a mouse synthetic population
- David T. Burke,
- Kenneth M. Kozloff,
- Shu Chen,
- Joshua L. West,
- Jodi M. Wilkowski,
- Steven A. Goldstein,
- Richard A. Miller,
- and Andrzej T. Galecki
Genome Res. August 2012 22: 1549-1557; Published in Advance May 15, 2012, doi:10.1101/gr.135582.111
...–2008). Am J Epidemiol 172: 540–548. Feldkamp LA, Goldstein SA, Parfitt AM, Jesion G, Kleerekoper M. 1989. The direct examination of three-dimensional bone architecture in vitro by computed tomography. J Bone Miner 4: 3–11. Flint J, Mackay TFC. 2009. Genetic architecture of quantitative traits in mice, flies...
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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...′ UTR of the CD47 gene, significantly impacts gene splicing and is strongly associated with reproductive phenotypes. Additionally, we observe that neuronal cells generally possess longer 3′ UTRs—a pattern conserved across humans, mice, fruit flies, and pigs. Together, these findings enrich the single...
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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M. Riley,
- Randa Elsayed,
- Mark D. Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C. Nelson
Genome Res. April 2026 36: 695-712; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...including the brain, ear, and craniofacial structures (Fig. 4H; Supplemental Figs. S15, S17, S18). Similarly, putative targets of PFG H3K27ac peaks and sox17E DARs are associated with pancreas development and pancreatic abnormalities in knockout mice, as well as cardiac defects in humans (Fig. 4H...
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Research: Variation in the fitness impact of translationally optimal codons among animals
- Florian Bénitière,
- Tristan Lefébure,
- and Laurent Duret
Genome Res. March 2025 35: 446-458; Published in Advance February 10, 2025, doi:10.1101/gr.279837.124
...), and in practice, codon optimization is essential for the design of heterologous gene expression systems, notably for human mRNA vaccines (Leppek et al. 2022). So, if SCU affects gene expression in humans, why is this trait not under selective pressure? To address this point, and more generally to understand...
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Research: Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype
- Arne Sahm,
- Konstantin Riege,
- Marco Groth,
- Martin Bens,
- Johann Kraus,
- Martin Fischer,
- Hans Kestler,
- Christoph Englert,
- Ralf Schaible,
- Matthias Platzer,
- and Steve Hoffmann
Genome Res. December 2024 34: 2217-2228; Published in Advance December 4, 2024, doi:10.1101/gr.279025.124
...of freshwater polyps with remarkable regeneration abilities and a potentially unlimited life span under laboratory conditions. By sequencing of single cells and whole animals, we found that the mutation rates in Hydra’s stem cells are even slightly higher than in humans or mice. A potential explanation...
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Resource: The Drosophila brain on cocaine at single-cell resolution
- Brandon M. Baker,
- Sneha S. Mokashi,
- Vijay Shankar,
- Jeffrey S. Hatfield,
- Rachel C. Hannah,
- Trudy F.C. Mackay,
- and Robert R.H. Anholt
Genome Res. October 2021 31: 1927-1937; Published in Advance May 25, 2021, doi:10.1101/gr.268037.120
...in humans but can be approached using the Drosophila melanogaster model, where gene expression in the entire brain can be surveyed at once. Flies exposed to cocaine show impaired locomotor activity, including climbing behavior and startle response (a measure of sensorimotor integration), and increased...
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Research: Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans
- Yiguan Wang,
- Paul McNeil,
- Rashidatu Abdulazeez,
- Marta Pascual,
- Susan E. Johnston,
- Peter D. Keightley,
- and Darren J. Obbard
Genome Res. April 2023 33: 587-598; Published in Advance April 10, 2023, doi:10.1101/gr.277383.122
...of this variation is fundamental for parameterizing models of evolution. Here, we provide direct estimates of mutation, recombination, and transposition rates and their variation in a West African and a European population of D. melanogaster and a European population of D. simulans. Across 89 flies, we observe 58...
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Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
- Xuejing Wang and
- Gerald Heckel
Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
...their contributions to the island syndrome in a rodent with an unusually clear history of isolation. Common voles (Microtus arvalis) were introduced by humans on the Orkney archipelago north of Scotland >5000 years ago and rapidly evolved to exceptionally large size. Our analyses show that the s of Orkney voles were...

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