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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
...size ranging from three to 11 shown for each of the three breast cancer stages. Asterisks indicate significant differences (see Supplemental Table S10). Inset illustrates how “TAD cliques” are identified from the statistically significant Hi-C interactions between TADs. (B) Example region on Chromosome...
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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
..., Davoli and colleagues published a new system for targeted chromosome missegregation (Bosco et al. 2023). In this approach, called KaryoCreate, catalytically inactive dCas9 is used to target a checkpoint-deficient kinetochore protein to a specific mammalian centromere (Fig. 3A). The mutant kinetochore...
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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
...Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells Jennifer A. Urban1, Daniel Ringwalt1, John M. Urban2,3, Wingel Xue1,5, Ryan Gleason1, Keji Zhao4 and Xin Chen1,2 1Department of Biology, The Johns Hopkins University...
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Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
- Yanis Zekri,
- Sebastian Gregoricchio,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Tunç Morova,
- Umut Berkay Altıntaş,
- Gozde Korkmaz,
- Nathan A. Lack,
- and Wilbert Zwart
Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
...et al. 2018).Constitutively active ERBS exhibited higher chromatin accessibility in breast tumors than both induced and inactive ERBS (Supplemental Fig. S2A). Chromatin at induced ERBS was largely inaccessible in ESR1-negative tumors and became accessible only in ESR1-positive tumors. In contrast...
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Research: Alternative splicing generates HER2 isoform diversity underlying antibody–drug conjugate resistance in breast cancer
- Gabriela D.A. Guardia,
- Carlos H. dos Anjos,
- Aline Rangel-Pozzo,
- Filipe F. dos Santos,
- Alexander Birbrair,
- Paula F. Asprino,
- Anamaria A. Camargo,
- and Pedro A.F. Galante
Genome Res. September 2025 35: 1942-1958; Published in Advance July 15, 2025, doi:10.1101/gr.280304.124
...and guided the development of HER2-targeted therapies (Sørlie et al. 2001; Prat et al. 2017).HER2-positive breast cancers, accounting for ∼20% of all breast cancers, are characterized by the overexpression or amplification of the HER2 gene (Wolff et al. 2013). Located on Chromosome 17q12, the HER2...
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Method: Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing
- Sena A. Gocuk,
- James Lancaster,
- Shian Su,
- Jasleen K. Jolly,
- Thomas L. Edwards,
- Doron G. Hickey,
- Matthew E. Ritchie,
- Marnie E. Blewitt,
- Lauren N. Ayton,
- and Quentin Gouil
Genome Res. November 2024 34: 1954-1965; Published in Advance September 16, 2024, doi:10.1101/gr.279396.124
...inactivation (XCI) is a dosage-compensation mechanism equalizing the expression of the majority of X-linked genes between males and females (Van den Veyver 2001). In 46, XX females, one X Chromosome is chosen stochastically as the inactive X (Xi) in a small number of cells early in embryonic development...
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Research: Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions
- Stacey E.P. Joosten,
- Sebastian Gregoricchio,
- Suzan Stelloo,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Kerim Yavuz,
- Maria Donaldson Collier,
- Tunç Morova,
- Umut Berkay Altintaş,
- Yongsoo Kim,
- Sander Canisius,
- Cathy B. Moelans,
- Paul J. van Diest,
- Gozde Korkmaz,
- Nathan A. Lack,
- Michiel Vermeulen,
- Sabine C. Linn,
- and Wilbert Zwart
Genome Res. April 2024 34: 539-555; Published in Advance May 6, 2024, doi:10.1101/gr.278680.123
...binding, which is associated with affected expression of the genes they control.DiscussionBreast cancer is a heterogenous disease, with clearly distinct inter-tumor differences on subtype, aggressiveness, and, ultimately, patient prognostication. Here, we show that on epigenetic scale, substantial inter...
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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
.... 2011. The ecoresponsive of Daphnia pulex. Science 331: 555–561. doi:10.1126/science.1197761 ↵Conrad T, Akhtar A. 2012. Dosage compensation in Drosophila melanogaster: epigenetic fine-tuning of chromosome-wide transcription. Nat Rev Genet 13: 123–134. doi:10.1038/nrg3124 ↵Crow EW, Crow JF. 2002. 100...
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Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
- David C.H. Metzger,
- Imogen Porter,
- Brendan Mobley,
- Benjamin A. Sandkam,
- Lydia J.M. Fong,
- Andrew P. Anderson,
- and Judith E. Mank
Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
...X Chromosome silencing in mammals (Do Kim et al. 2006; Donohoe et al. 2007; Jeon and Lee 2011; Makhlouf et al. 2014; Chen et al. 2016). In the context of mammalian X inactivation, YY1 binding is regulated by the differences in the epigenetic landscape between the active and inactive X in females...
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Research: Random replication of the inactive X chromosome
- Amnon Koren and
- Steven A. McCarroll
Genome Res. January 2014 24: 64-69; Published in Advance September 24, 2013, doi:10.1101/gr.161828.113
...is a dosage compensation mechanism in which one of the two X chromosome copies in females is transcriptionally inactivated ( Lyon 1961 ). The inactive chromosome is randomly chosen and subsequently clonally maintained through an epigenetic mechanism that involves coating of the chromosome by the noncoding RNA...

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