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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
...mutagens can alter the spectrum of mutations that accumulate in somatic tissues (Pleasance et al. 2010; Alexandrov et al. 2020), prompting us to ask whether the altered hormonal milieu and in vitro environment encountered during the generation of ART-born mice modify the prevalence of specific types...
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Research: Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage
- Emily Lowry,
- Yiqing Wang,
- Tal Dagan,
- and Amir Mitchell
Genome Res. August 2024 34: 1154-1164; Published in Advance August 16, 2024, doi:10.1101/gr.279517.124
....mitchell@umassmed.eduAbstractColibactin produced primarily by Escherichia coli strains of the B2 phylogroup cross-links DNA and can promote colon cancer in human hosts. Here, we investigate the toxin's impact on colibactin producers and on bacteria cocultured with producing cells. Using -wide genetic screens and mutation accumulation experiments...
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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
..., France; 5Clareo Biosciences, Louisville, Kentucky 40222, USA ↵6 These authors contributed equally to this work. Corresponding authors: andreas.lossius@medisin.uio.no, corey.watson@louisville.eduAbstractGenetic diversity within the human immunoglobulin heavy-chain (IGH) locus influences the expressed...
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Research: Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells
- Nick Riddiford,
- Katarzyna Siudeja,
- Marius van den Beek,
- Benjamin Boumard,
- and Allison J. Bardin
Genome Res. August 2021 31: 1419-1432; Published in Advance June 24, 2021, doi:10.1101/gr.268441.120
...understood. To explore mutational processes in the early stages of cancer evolution, we exploited neoplasia arising spontaneously in the Drosophila intestine. Analysing whole- sequencing data with a dedicated bioinformatic pipeline, we found neoplasia formation to be driven largely through the inactivation...
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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
...” variations are strictly biallelic and are present in all cells of the genet—unless a locus is affected by a second mutation and the resulting allele is transmitted to a subset of cells.In Hydra oligactis, lowering the water temperature can induce aging. Gene expression comparisons between aging and nonaging...
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Method: BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries
- Yangyang Liu,
- Bingqiang Liu,
- and Juntao Liu
Genome Res. May 2025 35: 1194-1208; Published in Advance March 17, 2025, doi:10.1101/gr.279647.124
.... In comparison with other leading TAD callers, BINDER shows significant improvement in identifying hierarchical TADs and exhibits the strongest robustness with ultrasparse data, which supports the importance of boundary identification in calling hierarchical TADs. Applying BINDER to experimental data and mouse...
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Research: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly
- Kang Du,
- Oliver Deusch,
- Ilja Bezrukov,
- Christa Lanz,
- Yann Guiguen,
- Margarete Hoffmann,
- Anette Habring,
- Detlef Weigel,
- Manfred Schartl,
- and Christine Dreyer
Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
...Poecilia wingei and Poecilia obscura (Nanda et al. 2014). This analysis revealed polymorphisms in heterochromatin content of the Y as well as differences in distance of the genetic marker M_229 to the physical chromosome end between populations. The sex determination locus (SDL) was mapped to the most...
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Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
- John Beaulaurier,
- Lynn Ly,
- J. Andrew Duty,
- Carly Tyer,
- Christian Stevens,
- Chuan-Tien Hung,
- Akash Sookdeo,
- Alex W. Drong,
- Shreyas Kowdle,
- Axel Guzman-Solis,
- Domenico Tortorella,
- Daniel J. Turner,
- Sissel Juul,
- Scott Hickey,
- and Benhur Lee
Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
...repertoire, we combined sequencing of the germline IG loci with single-cell transcriptome sequencing of B cells from the same donor. Sequencing and assembly of the germline IG loci captured the IGH locus in a single fully phased contig where the maternal and paternal contributions to the germline V, D, and J...
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ARTICLE: The modifier of Min 2 (Mom2) locus: Embryonic lethality of a mutation in the Atp5a1 gene suggests a novel mechanism of polyp suppression
- Amy A. Baran,
- Karen A. Silverman,
- Joseph Zeskand,
- Revati Koratkar,
- Ashley Palmer,
- Kristen McCullen,
- Walter J. Curran, Jr,
- Tina Bocker Edmonston,
- Linda D. Siracusa,
- and Arthur M. Buchberg
Genome Res. May 2007 17: 566-576; Published in Advance March 26, 2007, doi:10.1101/gr.6089707
...that inherit mutations in the Apc gene. We identified a new modifier locus of Apc Min -induced intestinal tumorigenesis called M odifier o f M in 2 ( Mom2 ). The polyp-resistant Mom2 R phenotype resulted from a spontaneous mutation and linkage analysis localized Mom2 to distal chromosome 18. To obtain...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...genomics and phylogeny analyses identified regions of organismal s that show patterns of accelerated evolution (Ferris et al. 2018; Foley et al. 2023). The usage of mutation rate patterns, species sequence alignments, and the identification of highly conserved regions can provide insights into phenotypic...
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