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Research: Natural variation in C. elegans short tandem repeats
- Gaotian Zhang,
- Ye Wang,
- and Erik C. Andersen
Genome Res. October 2022 32: 1852-1861; Published in Advance October 4, 2022, doi:10.1101/gr.277067.122
..., Andersen EC. 2018. Extreme allelic heterogeneity at a Caenorhabditis elegans beta-tubulin locus explains natural resistance to benzimidazoles. PLoS Pathog 14: e1007226. doi:10.1371/journal.ppat.1007226 ↵Hannan AJ. 2018. Tandem repeats mediating genetic plasticity in health and disease. Nat Rev Genet 19...
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Method: Multisample motif discovery and visualization for tandem repeats
- Yaran Zhang,
- Marc Hulsman,
- Alex Salazar,
- Niccolò Tesi,
- Lydian Knoop,
- Sven van der Lee,
- Sanduni Wijesekera,
- Jana Krizova,
- Erik-Jan Kamsteeg,
- and Henne Holstege
Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
...) population structure due to their high mutability (Rosenberg et al. 2002; Ellegren 2004; Course et al. 2021; Lu et al. 2023). Course et al. demonstrated significant differences in repeat length among VNTRs in genes, including ADP-ribosyltransferase 1 (ART1), PROP paired-like homeobox 1 (PROP1), and dynein 2...
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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...in the human may help to address the “missing heritability” problem, explaining a portion of complex trait heritability not yet identified (Hannan 2018).However, STRs are difficult to characterize with short-read sequencing (SRS) technologies owing to often long repeat tracts and lack of flanking sequence...
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Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
...structural mutations (SMs; 2%). We found that the degree of DNA repetitiveness is positively correlated with SNM and indel rates and that a substantial fraction of SMs can be explained by homology-dependent mechanisms associated with repeat sequences. Most (90%) indels can be attributed to microsatellite...
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Research: Oxidative stress accelerates intestinal tumorigenesis by enhancing 8-oxoguanine-mediated mutagenesis in MUTYH-deficient mice
- Mizuki Ohno,
- Noriko Takano,
- Kyoko Hidaka,
- Fumiko Sasaki,
- Kazumi Yamauchi,
- Yasunobu Aoki,
- Takehiko Nohmi,
- Yusaku Nakabeppu,
- Yoshimichi Nakatsu,
- and Teruhisa Tsuzuki
Genome Res. January 2024 34: 47-56; Published in Advance January 30, 2024, doi:10.1101/gr.278326.123
...triggering tumorigenesis is not well understood. Here, we aimed to explore the causal relationship between oxidative stress, somatic mutations in pre-tumor-initiated normal tissues, and tumor incidence in the small intestines of MUTYH-proficient and MUTYH-deficient mice. MUTYH is a base excision repair...
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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
..., USA ↵3 These authors contributed equally to this work. Corresponding author: mxs2589@psu.eduAbstractA tandem repeat is a sequence of nucleotides that appear as multiple contiguous, near-identical copies arranged consecutively. Tandem repeats are widespread across natural s, play critical roles...
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Research: Autism spectrum disorder risk genes have convergent effects on transcription and neuronal firing patterns in primary neurons
- Alekh Paranjapye,
- Rili Ahmad,
- Steven Su,
- Abraham J. Waldman,
- Jennifer E. Phillips-Cremins,
- Shuo Zhang,
- and Erica Korb
Genome Res. November 2025 35: 2433-2444; Published in Advance October 20, 2025, doi:10.1101/gr.280698.125
...-associated factor CHD8 during cortical development. Mol Autism 12: 16. doi:10.1186/s13229-020-00409-3 ↵Iossifov I, O'Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, Stessman HA, Witherspoon KT, Vives L, Patterson KE, et al. 2014. The contribution of de novo coding mutations to autism spectrum disorder. Nature 515...
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Research: Chromatin structure influences rate and spectrum of spontaneous mutations in Neurospora crassa
- Mariana Villalba de la Peña,
- Pauliina A.M. Summanen,
- Martta Liukkonen,
- and Ilkka Kronholm
Genome Res. April 2023 33: 599-611; Published in Advance March 15, 2023, doi:10.1101/gr.276992.122
...an effect for H3K9me3 like we observed, which may indicate that there are species specific differences in heterochromatin.Differential exposure of heterochromatin to natural mutagens, such as oxidative damage, does not seem to explain our results. As mutations typically associated with oxidative damage...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...complete and gap-free (Hillier et al. 2005). It was thus surprising when, 14 years later, our attempt to reproduce a perfect isogenic copy of the reference C. elegans instead showed that it was neither complete nor gap-free (Yoshimura et al. 2019), as discrepancies observed by others were by then also...
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Research: Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
- Clotilde Garrido,
- Cintia Gómez-Muñoz,
- Etienne Kornobis,
- Nicolas Agier,
- Oana Ilioaia,
- Gilles Fischer,
- and Zhou Xu
Genome Res. March 2026 36: 522-533; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125
.... This study reveals the diversity of TL in S. cerevisiae and highlights key factors shaping TL distributions both -wide and at individual chromosome extremities.Telomeres are repeated sequences found at chromosome extremities, which are essential for integrity and control of cell proliferation (Jain...

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