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Research: Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes
- Yu-Chi Chen,
- David L.J. Vendrami,
- Maximilian L. Huber,
- Luisa E.Y. Handel,
- Christopher R. Cooney,
- Joseph I. Hoffman,
- and Toni I. Gossmann
Genome Res. June 2025 35: 1313-1324; Published in Advance March 31, 2025, doi:10.1101/gr.279428.124
...integrated into the nuclear accumulate missense mutations that ultimately lead to a broken reading frame. However, if the integration is very recent, if the local mutation rate is very low, or if selection actively maintains the coding properties of the integration, the former mitochondrial coding genes may...
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Research: Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in Oryza
- Chenbo Gong,
- Yicheng Huang,
- Mengmeng Liu,
- Yong Zhou,
- Yinwei Xu,
- Nahed Mohammed,
- Xintong Qiao,
- Andrea Zuccolo,
- Weibo Xie,
- Rod A. Wing,
- Jianwei Zhang,
- Fei Zhou,
- and Yongjun Lin
Genome Res. June 2025 35: 1349-1363; Published in Advance April 25, 2025, doi:10.1101/gr.279609.124
...-strand break repair pathways and replication-based mechanisms play important roles in integrating organelle DNA into the nuclear . Further investigation indicates that complex NORGs are formed through single mutational events before or during the insertion process via ligation of multiple plastid and...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...explore the impact of dikaryotism on the biology of a long-term asexual clone of the wheat pathogenic fungus Puccinia striiformis f. sp. tritici. We use Oxford Nanopore Technologies (ONT) duplex sequencing combined with Hi-C to generate a T2T nuclear-phased assembly with >99.999% consensus accuracy. We...
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Research: Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth
- Hadar Medini and
- Dan Mishmar
Genome Res. March 2025 35: 459-474; Published in Advance March 4, 2025, doi:10.1101/gr.279700.124
..., it is plausible that its involvement in regulation of mitonuclear gene expression occurs via regulating the regulators of both mitochondrial and nuclear OXPHOS genes. This thought is partially supported by our observed elevated expression of the mitochondrial RNA polymerase, POLRMT, in certain tissues and species...
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Research: Prepatterning of differentiation-driven nuclear lamin A/C-associated chromatin domains by GlcNAcylated histone H2B
- Torunn Rønningen,
- Akshay Shah,
- Anja R. Oldenburg,
- Kristin Vekterud,
- Erwan Delbarre,
- Jan Øivind Moskaug,
- and Philippe Collas
Genome Res. December 2015 25: 1825-1835; Published in Advance September 10, 2015, doi:10.1101/gr.193748.115
...causing partial lipodystrophies (Guenantin et al. 2014), coupling A-type lamins to cellular metabolic state. Specific lipodystrophic LMNA mutation hot spots disrupt lamin A/C interaction with DNA in vitro (Stierlé et al. 2003) and could affect LADs. The common metabolic disorders caused by deregulation...
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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
...Jena, Germany Corresponding author: arne.sahm@rub.deAbstractGrowing evidence suggests that somatic mutations may be a major cause of the aging process. However, it remains to be tested whether the predictions of the theory also apply to species with longer life spans than humans. Hydra is a genus...
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Research: Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction
- Kimberly N. Griffin,
- Benjamin William Walters,
- Haixin Li,
- Huafeng Wang,
- Giulia Biancon,
- Toma Tebaldi,
- Carolyn B. Kaya,
- Jean Kanyo,
- TuKiet T. Lam,
- Andy L. Cox,
- Stephanie Halene,
- Jean-Ju Chung,
- and Bluma J. Lesch
Genome Res. September 2022 32: 1655-1668; Published in Advance September 15, 2022, doi:10.1101/gr.276578.122
...) is a ubiquitously expressed protein critical for regulation of mRNA translation and vital to animal development. AGO2 protein is found in both cytoplasmic and nuclear compartments, and although its cytoplasmic role is well studied, the biological relevance of nuclear AGO2 is unclear. Here, we address this problem...
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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
....5%–56%) increase in the dnSNV rate with ART compared with naturally conceived mice (P = 0.017). Analysis of the dnSNV mutation spectrum identifies signatures attributable to germline DNA repair activity but reveals no differentially enriched signatures between cohorts. We observe no enrichment of dn...
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Method: Surveying mutation density patterns around specific genomic features
- Hui Yu,
- Scott Ness,
- Chung-I Li,
- Yongsheng Bai,
- Peng Mao,
- and Yan Guo
Genome Res. October 2022 32: 1930-1940; Published in Advance September 13, 2022, doi:10.1101/gr.276770.122
...positions help to sharpen the potential mutation density pattern.Comparison to similar toolsCurrently, there is no dedicated application to explore mutation density spatial trends with complete flexibility on genomic features. Three other tools have partially similar features (Table 1). Asymmetron...
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Research: Widespread specific intron retention events in nuclear RNA complexes identified by sedimentation analysis of pluripotent cellular extracts
- Isabela T. Pereira,
- Izabela Mamede,
- Paulo P. Amaral,
- Gloria R. Franco,
- and John L. Rinn
Genome Res. October 2025 35: 2189-2198; Published in Advance August 26, 2025, doi:10.1101/gr.280431.125
...predominantly nuclear, metabolically stable, and they were not the major splice isoforms, but instead they were mostly retained-intron isoforms, each containing a specific retained intron, and this intron retention phenomenon is conserved in humans and mice. Collectively, our study reveals a widespread...

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