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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: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
...and models will continue as long as data generation schemas are expensive and experimentally challenging. Quagga is an important, rapid, and cost-effective solution for identifying architectural stripes at the scale when lacking ChIP-seq or other sequencing data for which only Hi-C or another 3C family data...
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Method: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
- Yuwei Cao,
- Lauren Patel,
- Lauren Alcoser,
- Eric Mendenhall,
- Christopher Benner,
- Sven Heinz,
- and Alon Goren
Genome Res. January 2026 36: 129-141; Published in Advance December 12, 2025, doi:10.1101/gr.281320.125
...localization signals are sensitive to changing the antibody–to–cell-number ratio, whereas the stronger signals remain unaffected. This finding underscores the importance of maintaining consistent antibody–to–cell-number ratio for comparative studies, such as treatment responses or chromatin-QTL mapping...
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Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
- Jingwei Zhou,
- Yuhong Huang,
- Huan Ma,
- Yiqian Chen,
- Chuanye Chen,
- Fangpu Han,
- and Handong Su
Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
...retain essential functions, their chromatin organization may differ from canonical centromeres.Concerted local open chromatin and transcriptional dynamics contribute to genomic stabilization following centromere misdivisionTo investigate how gene expression and chromatin structure respond to centromere...
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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
..., modeling 3D chromatin organization, and predicting gene expression (Thibodeau et al. 2021; Karbalayghareh et al. 2022; Tan et al. 2023; Zhang et al. 2023; Grover et al. 2024). Although experimental assays such as FAIRE-seq (Giresi et al. 2007), DNase-seq (Song and Crawford 2010), and ATAC-seq (Buenrostro...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...of the complex relationship between chromatin organization and transcription.Every eukaryotic encodes the information necessary for cellular viability and growth. Although the underlying instructions embedded in the DNA are identical among the cells of an organism, complex regulatory mechanisms transform...
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Method: Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie
- Krzysztof H. Banecki,
- Haoxi Chai,
- Yijun Ruan,
- and Dariusz Plewczynski
Genome Res. April 8, 2026 ; Published in Advance April 8, 2026, doi:10.1101/gr.280985.125
...of advanced techniques that provide deeper insight into chromatin organization. Methods for analyzing 3D organization can be broadly categorized into microscopic imaging–based approaches, sequencing-based techniques, and their accompanying computational models (Jerkovic and Cavalli 2021). Although microscopic...
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Research: The chromatin landscape of the histone-possessing Bacteriovorax bacteria
- Georgi K. Marinov,
- Benjamin Doughty,
- Anshul Kundaje,
- and William J. Greenleaf
Genome Res. January 2025 35: 109-123; Published in Advance November 21, 2024, doi:10.1101/gr.279418.124
...), and others. For each of these proteins, especially the heat shock ones, it is plausible that polymerase pausing is a regulatory mechanism specifically designed to enable their very rapid activation, in a manner analogous to heat shock genes in Drosophila in which the phenomenon was originally described...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...levels decrease (Fig. 3D; Supplemental Table S4). This observation aligns with the known association between strongly positioned nucleosomes and chromatin organization at active genes, underscoring the role of nucleosome positioning in regulating gene expression and further validating our experimental...
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Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
...of Michigan, Ann Arbor, Michigan 48109, USA; 9Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA Corresponding author: mohlke@med.unc.eduAbstractChromatin accessibility quantitative trait locus (caQTL) studies have identified regulatory...

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