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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...and Lyson 2022; Brownstein et al. 2023), Atractosteus spatula and Lepisosteus osseus exhibit an extraordinary degree of genomic similarity. The three gar s exhibit high synteny (Fig. 1A) with bowfins as well (e.g., Amia calva), the living sister lineage of gars. Gar s maintain higher synteny with tetrapod s...
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Research: Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence
- Manuela Baquero Pérez,
- Gertjan Laenen,
- Isabelle Loïodice,
- Mickaël Garnier,
- Ugo Szachnowski,
- Antonin Morillon,
- Myriam Ruault,
- and Angela Taddei
Genome Res. October 2025 35: 2226-2239; Published in Advance August 12, 2025, doi:10.1101/gr.279874.124
...relocate from the nuclear periphery to the center of the nucleus into a hypercluster; chromatin is found in a compacted, hypoacetylated state; and transcription is globally shutdown. Yet, Q cells can restart transcription within minutes of refeeding. Here, we follow the global decrease of transcription...
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Method: Examining the dynamics of three-dimensional genome organization with multitask matrix factorization
- Da-Inn Lee and
- Sushmita Roy
Genome Res. May 2025 35: 1179-1193; Published in Advance March 20, 2025, doi:10.1101/gr.279930.124
...a tree structure. Finally, TGIF is motivated by a dimensionality reduction (matrix factorization) framework to reduce the noisy, high-dimensional count profile of each genomic locus into a low-dimensional space of different ranks. This enables TGIF to be a general framework that identifies TADs...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...(Fig. 1E; Supplemental Figs. S21–S23) display expected genomic features in which more gene-poor chromosomes are located more frequently toward the nuclear periphery (Supplemental Figs. S24–S26). Our 3D modeling of all three cell types reveals major differences between 10A cells versus T1 and C1 cells...
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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
...and accessibility of assemblies for global cattle breeds and other bovine species. Genome Biol 24: 139. doi:10.1186/s13059-023-02975-0 ↵Tavakoli N, Gibney D, Aluru S. 2022. Haplotype-aware variant selection for graphs. In Proceedings of the 13th ACM International Conference on Bioinformatics, Computational Biology...
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Research: H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity
- Kei Fukuda,
- Chikako Shimura,
- and Yoichi Shinkai
Genome Res. October 2025 35: 2199-2210; Published in Advance August 5, 2025, doi:10.1101/gr.280732.125
...maintaining proper 3D organization. At least five H3K9 methyltransferases exist in mammals (Setdb1, Suv39h1, Suv39h2, Ehmt1, Ehmt2) (Allshire and Madhani 2018), and they regulate H3K9 methylation redundantly or independently, depending on genomic regions (Fukuda et al. 2021). For example, H3K9me2...
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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
....gossmann@tu-dortmund.deAbstractSporadically, genetic material that originates from an organelle integrates into the nuclear . However, it is unclear what processes maintain such integrations over evolutionary time. Recently, it was shown that nuclear DNA of mitochondrial origin (NUMT) may harbor genes with intact mitochondrial reading frames despite...
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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
...approximately once in every 4000 births (Wei et al. 2022), with a higher rate in cancer cells (Ju et al. 2015; Wei et al. 2022), leading to high NUMT diversity across the human population. The insertion of mtDNA into the nuclear can cause genomic instability via mutations or disruption of normal gene function...
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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
...). This is necessary to escape the plant immune system and to confer the ability to infect new host varieties.Recent progress in heterokaryotic fungi genomics, such as in arbuscular mycorrhizal fungi, has revealed extensive nuclear variations in structural and gene content (Li et al. 2019; Sperschneider et al. 2023b...
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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
...-type strains, it will be important to use CGC1 to develop a pan of N2 sequences in the future. Global traits of C. elegans chromosomes such as meiotic recombination rates and the densities of various genomic elements should be more correctly ascertained (Carlton et al. 2022). The full sequencing of 45S r...
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