A natural mutator allele shapes mutation spectrum variation in mice
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Abstract
Although germline mutation rates and spectra can vary within and between species, common genetic modifiers of the mutation rate have not been identified in nature 1. Here we searched for loci that influence germline mutagenesis using a uniquely powerful resource: a panel of recombinant inbred mouse lines known as the BXD, descended from the laboratory strains C57BL/6J (B haplotype) and DBA/2J (D haplotype). Each BXD lineage has been maintained by brother-sister mating in the near absence of natural selection, accumulating de novo mutations for up to 50 years on a known genetic background that is a unique linear mosaic of B and D haplotypes 2. We show that mice inheriting D haplotypes at a quantitative trait locus on chromosome 4 accumulate C>A germline mutations at a 50% higher rate than those inheriting B haplotypes, primarily owing to the activity of a C>A-dominated mutational signature known as SBS18. The B and D quantitative trait locus haplotypes encode different alleles of Mutyh, a DNA repair gene that underlies the heritable cancer predisposition syndrome that causes colorectal tumors with a high SBS18 mutation load 3,4. Both B and D Mutyh alleles are present in wild populations of Mus musculus domesticus, providing evidence that common genetic variation modulates germline mutagenesis in a model mammalian species.
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The contextual fear conditioning protocol used matches that previously used in the AD-BXD F1s.
“The protocol used matches that previously used in the AD-BXD F1s10 83.”
From Magnetic resonance microscopy maps widespread effects of Alzheimer’s disease on brain structures and behavior in mice (2026) · cites this paper as [83]
The Methods section on construction of BXD lines describes breeding, and the Methods section on whole-genome sequencing describes tissue collection and genetic analysis. Neither describes contextual fear conditioning or compares its protocol with one used in AD-BXD F1s (searched: “contextual fear conditioning AD-BXD F1s” and “fear conditioning protocol behavioral testing Alzheimer BXD F1”). (LLM, conf=0.75)
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Self-citationHigh-recombining genomic regions affect demography inference based on ancestral recombination graphs
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Wang, X., Bajpai, A. K., Gu, Q., Ashbrook, D. G., Starlard‐Davenport, A., & Lu, L. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1009462 · Cited by 9 · see citing works
Self-citationmutyper: assigning and summarizing mutation types for analyzing germline mutation spectra
DeWitt, W. S., Zhu, L., Vollger, M. R., Goldberg, M. E., Talenti, A., Beichman, A. C., & Harris, K. (2023) · The Journal of Open Source Software · doi:10.21105/joss.05227 · Cited by 9 · see citing works
Self-citationVariation in the Spectrum of New Mutations among Inbred Strains of Mice
López‐Cortegano, E., Chebib, J., Jonas, A., Vock, A., Künzel, S., Tautz, D., & Keightley, P. D. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae163 · Cited by 8 · see citing works
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A maternal germline mutator phenotype in a family affected by heritable colorectal cancer
Young, C. L., Beichman, A., Ponte, D. M., Hemker, S. L., Zhu, L., Kitzman, J., Shirts, B., & Harris, K. (2024) · Genetics · doi:10.1093/genetics/iyae166 · Cited by 7 · see citing works
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Self-citationHigh-recombining genomic regions affect demography inferencePreprint
Ishigohoka, J., & Liedvogel, M. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.05.579015 · Cited by 6 · see citing works
Unprecedented female mutation bias in the aye-aye, a highly unusual lemur from Madagascar
Wang, R. J., Peña-García, Y., Raveendran, M., Harris, R. A., Nguyen, T. H. D., Gingras, M., Wu, Y., Perez, L. M., Yoder, A. D., Simmons, J. H., et al. (2025) · PLoS Biology · doi:10.1371/journal.pbio.3003015 · Cited by 5 · see citing works
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Ball, R. L., Bogue, M. A., Liang, H., Srivastava, A., Ashbrook, D. G., Lamoureux, A., Gerring, M. W., Hatoum, A. S., Kim, M. J., He, H., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.08.552506 · Cited by 4 · see citing works
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The Smarcal1-Usp37 locus modulates glycogen aggregation in astrocytes of the aged hippocampus
Gómez-Pascual, A., Glikman, D. M., Ng, H. X., Tomkins, J. E., Lu, L., Xu, Y., Ashbrook, D. G., Kaczorowski, C. C., Kempermann, G., KILLMAR, J. T., et al. (2026) · Cell Systems · doi:10.1016/j.cels.2025.101488 · Cited by 2 · see citing works
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Selection shapes the landscape of functional variation in wild house micePreprint
Lawal, R. A., Arora, U. P., & Dumont, B. L. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.12.443838 · Cited by 3 · see citing works
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Self-citationMutation and recombination parameters in zebra finch are similar to those in mammalsPreprint
Prentout, D., Bykova, D., Hoge, C., Hooper, D. M., McDiarmid, C. S., Wu, F., Griffith, S. C., de Manuel, M., & Przeworski, M. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.05.611523 · Cited by 2 · see citing works
The evolution of mutation rates in the light of development and cell-lineage selectionPreprint
Majic, P., Srivastava, M., & Crocker, J. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.16.633395 · Cited by 2 · see citing works
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Enhancing the diversity of self-replicating structures using active self-adapting mechanisms
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Sasani, T. A., Quinlan, A. R., & Harris, K. (2023) · doi:10.7554/elife.89096.1 · Cited by 1 · see citing works
Self-citationJoint dog and wolf genealogies reveal the evolution of the canine genomePreprint
Rees, J., Sherman, M., Teofilov, D., Colomer-Vilaplana, A., Myers, S. R., Bergström, A., & Speidel, L. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.18.729863 · Cited by 1 · see citing works
Determining susceptibility loci in triple negative breast cancer using a novel pre-clinical modelPreprint
Simon, S. E., Simmons, B. W., Kim, M., Joseph, S. C., Korba, E. B., Marathe, S. J., Bohm, M. S., Mahajan, S., Bohl, C. J., Read, R. W., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.08.579359
Self-citationThe Population-Genetic Environment
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Little impact of new mutations on mammalian trait variation
Dumont, B. L. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002825
Unprecedented female mutation bias in aye-ayesPreprint
Wang, R. J., Peña-García, Y., Raveendran, M., Harris, R. A., Nguyen, T. H. D., Gingras, M., Wu, Y., Perez, L. M., Yoder, A. D., Simmons, J. H., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.13.628352
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Self-citationIdentification of susceptibility loci using a novel murine model for triple-negative breast cancer
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Self-citationAdditional file 5 of geneHapR: an R package for gene haplotypic statistics and visualization
Zhang, R., Jia, G., & Diao, X. (2024) · Figshare · doi:10.6084/m9.figshare.26589771
Additional file 6 of geneHapR: an R package for gene haplotypic statistics and visualization
Zhang, R., Jia, G., & Diao, X. (2024) · Figshare · doi:10.6084/m9.figshare.26589774
Additional file 2 of geneHapR: an R package for gene haplotypic statistics and visualization
Zhang, R., Jia, G., & Diao, X. (2024) · Figshare · doi:10.6084/m9.figshare.26589762
Additional file 1 of geneHapR: an R package for gene haplotypic statistics and visualization
Zhang, R., Jia, G., & Diao, X. (2024) · Figshare · doi:10.6084/m9.figshare.26589759
Genetic control of local mutation rates.
Caballero, M., & Koren, A. (2026) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.2625619123
Additional file 3 of geneHapR: an R package for gene haplotypic statistics and visualization
Zhang, R., Jia, G., & Diao, X. (2024) · Figshare · doi:10.6084/m9.figshare.26589765
Additional file 4 of geneHapR: an R package for gene haplotypic statistics and visualization
Zhang, R., Jia, G., & Diao, X. (2024) · Figshare · doi:10.6084/m9.figshare.26589768
A sibling study of variation in parental mutation ratesPreprint
Getseva, V., POYRAZ, P., Stolyarova, A. V., Agarwal, I., & Przeworski, M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.10.724105
The rate and spectrum of germline mutations in chicken from a commercial pedigree line
López‐Cortegano, E., Sosa‐Madrid, B. S., & Kranis, A. (2026) · Genetics Selection Evolution · doi:10.1186/s12711-026-01085-2
- Authors
- Sasani, T. A., Ashbrook, D. G., Beichman, A. C., Lu, L., Palmer, A. A., Williams, R. W., Pritchard, J. K., & Harris, K.
- Affiliations
- University of Washington (US)
- University of Tennessee Health Science Center (US)
- University of California San Diego (US)
- Stanford University (US)
- Corresponding author
- Harris, Kelley
- ORCID
- Venue
- Nature
- Published
- 2022-05-11
- Volume
- 605
- Issue
- 7910
- Pages
- 497-502
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC9272728
- OpenAlex
- W4280525469
- Cited by
- 64
- References
- 54
- Citations by year
- 2026: 7 · 2025: 11 · 2024: 11 · 2023: 24 · 2022: 6 · 2021: 5
- FWCI
- 4.74
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Nature (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- Wellcome Trust
- National Institutes of Health (NIH T32, NIH-R01, DA044223)
- National Institute on Aging (T32AG066574)
- National Institute on Drug Abuse (P30DA044223, DA044223, P50DA037844, U01DA051234)
- National Human Genome Research Institute (R01HG008140, T32HG000035)
- National Institute of General Medical Sciences (R01GM123489, R35GM133428)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Health Sciences › Medicine › Pathology and Forensic Medicine › Genetic factors in colorectal cancer
- Keywords
- germline mutagenesis, mutation rate, mutation spectrum, MUTYH, haplotypes, quantitative trait loci, DNA repair, natural genetic variation, Mus musculus domesticus, colorectal cancer predisposition
- MeSH terms
- Alleles, Animals, Haplotypes, Male, Mammals, Mice, Inbred C57BL, Mice, Inbred DBA, Mutation, Genetic Variation, Germ-Line Mutation, Quantitative Trait Loci, Mice
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