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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
...Medicine, Oslo University Hospital, 0424 Oslo, Norway Corresponding authors: david.tremethick@anu.edu.au, jonas.paulsen@ibv.uio.noAbstractBreast cancer entails intricate alterations in organization and expression. However, how three-dimensional (3D) chromatin structure changes in the progression from...
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Method: Three-dimensional missense tolerance ratio analysis
- Riley E. Perszyk,
- Anders S. Kristensen,
- Polina Lyuboslavsky,
- and Stephen F. Traynelis
Genome Res. August 2021 31: 1447-1461; Published in Advance July 22, 2021, doi:10.1101/gr.275528.121
...consist of nonadjacent residues, but together function as a unit. We therefore developed an approach to analyze nearest neighbors in three-dimensional space as determined by crystallography rather than on the polypeptide chain. We used members of the GRIN gene family that encode subunits of NMDA...
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Research: The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence
- Xianglin Zhang,
- Xuehui Liu,
- Zhenhai Du,
- Lei Wei,
- Huan Fang,
- Qiongye Dong,
- Jing Niu,
- Yanda Li,
- Juntao Gao,
- Michael Q. Zhang,
- Wei Xie,
- and Xiaowo Wang
Genome Res. July 2021 31: 1121-1135; Published in Advance June 17, 2021, doi:10.1101/gr.275235.121
...The loss of heterochromatin is associated with multiscale three-dimensional reorganization and aberrant transcription during cellular senescence Xianglin Zhang1,2,9, Xuehui Liu1,2,3,9, Zhenhai Du4,5,6,9, Lei Wei1,2, Huan Fang1,2, Qiongye Dong1,2, Jing Niu7, Yanda Li1,2, Juntao Gao1,2, Michael Q...
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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
...documents evolutionary stasis across multiple levels of organization in gars, including structural features, chromosome evolution, TE dynamics, and ancient gene flow. By integrating these findings, we provide a mechanistic explanation for the exceptional genomic stability observed in this lineage over deep...
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Research: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
- Yali Zhang,
- Yayi Zhou,
- Yangyang Chen,
- Xueyu Wang,
- Boyan Hu,
- Shahid Siddique,
- Romnick A. Latina,
- Veronica I. Casey,
- Dexin Bo,
- Yucheng Liao,
- Min Zhang,
- Ming Sun,
- Fengjuan Zhang,
- and Dadong Dai
Genome Res. March 23, 2026 ; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
...resolution.miniMDSwas used to convert the contact frequency matrix into relative positions in a three-dimensional Euclidean coordinate system. The higher the contact frequency, the closer the three-dimensional distance between the fragments. Finally, the inferred 3D coordinate datawere imported into...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...architecture, with stretches of heterochromatic DNA dominated by long retrotransposon insertions interspersed with compact, gene-rich regions. The absence of an enrichment of SSPs within TE-rich regions suggest a partially different genomic organization compared with the frequent TE...
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Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
- Christine R. Keenan,
- Hannah D. Coughlan,
- Nadia Iannarella,
- Andres Tapia del Fierro,
- Andrew Keniry,
- Timothy M. Johanson,
- Wing Fuk Chan,
- Alexandra L. Garnham,
- Lachlan W. Whitehead,
- Marnie E. Blewitt,
- Gordon K. Smyth,
- and Rhys S. Allan
Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
.... Examination of the three-dimensional (3D) nucleome reveals that transcriptomic dysregulation occurs in euchromatic regions close to the nuclear periphery in 3D space. Moreover, this transcriptomic dysregulation is highly correlated with altered 3D organization in Suv39DKO cells. Together, our results suggest...
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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
..., Yamanashi 400-8510, Japan Corresponding authors: yshinkai@riken.jp, k.fukuda@yamanashi.ac.jpAbstractThe three-dimensional (3D) structure is essential for gene regulation and various genomic functions. CTCF plays a key role in organizing topologically associated domains (TADs) and promoter-enhancer loops...
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Method: Defining the separation landscape of topological domains for decoding consensus domain organization of the 3D genome
- Dachang Dang,
- Shao-Wu Zhang,
- Ran Duan,
- and Shihua Zhang
Genome Res. March 2023 33: 386-400; Published in Advance March 9, 2023, doi:10.1101/gr.277187.122
...al. 2006; Lieberman-Aiden et al. 2009; Rao et al. 2014) provide unprecedented opportunities to decipher the mysteries of three-dimensional (3D) genomic organizations in the nucleus of eukaryotes. The folds into a hierarchical configuration consisting of multiscale chromatin structures...
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Research: Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization
- Kazuaki Yamaguchi,
- Yoshinobu Uno,
- Mitsutaka Kadota,
- Osamu Nishimura,
- Ryo Nozu,
- Kiyomi Murakumo,
- Rui Matsumoto,
- Keiichi Sato,
- and Shigehiro Kuraku
Genome Res. September 2023 33: 1527-1540; Published in Advance August 17, 2023, doi:10.1101/gr.276840.122
...Center for Biosystems Dynamics Research (BDR), 650-0047, Kobe, Japan; 2Okinawa Churashima Research Center, Okinawa Churashima Foundation, 905-0206, Okinawa, Japan; 3Okinawa Churaumi Aquarium, 905-0206, Okinawa, Japan; 4Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology...
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