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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: Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
- Amy R. Vandiver,
- Allen Herbst,
- Paul Stothard,
- and Jonathan Wanagat
Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124
...Chimeric mitochondrial RNA transcripts predict mitochondrial deletion mutations in mitochondrial genetic diseases and aging Amy R. Vandiver1,2, Allen Herbst3,5, Paul Stothard3 and Jonathan Wanagat2,4 1Department of Medicine, Division of Dermatology, University of California, Los Angeles, Los...
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Resource: Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization
- Cory Gardner,
- Junhao Chen,
- Christina Hadfield,
- Zhaolian Lu,
- David Debruin,
- Yu Zhan,
- Maureen J. Donlin,
- Tae-Hyuk Ahn,
- and Zhenguo Lin
Genome Res. November 2024 34: 2133-2146; Published in Advance September 17, 2024, doi:10.1101/gr.279364.124
...chromosome length, Chr VIIb is similar to Chr VIIa (1,042,311 vs. 1,055,917), so the assembly of Chr VIIb can be considered as complete (Supplemental Table S2).Our assembly generated a circular mitochondrial with a size of 65 kb. To determine the origin of the CBS380 mitochondrial , we first mapped our raw...
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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
...equally to this work. Corresponding authors: spinter@uchc.edu, jason.sheltzer@yale.eduAbstractChromosomal rearrangements on the short arm of Chromosome 8 cause 8p syndrome, a rare developmental disorder characterized by neurodevelopmental delays, epilepsy, and cardiac abnormalities. Although significant...
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Research: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly
- Kang Du,
- Oliver Deusch,
- Ilja Bezrukov,
- Christa Lanz,
- Yann Guiguen,
- Margarete Hoffmann,
- Anette Habring,
- Detlef Weigel,
- Manfred Schartl,
- and Christine Dreyer
Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
...degeneration has not progressed to a measurable degree.Sex chromosomes evolve differently from the rest of the owing to reduced recombination. This process generates on Y Chromosomes a male-specific region (MSY) that is diverging in sequence and structural organization from the homologous region on the X...
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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
...to a restricted region (360–670 Mb) (Fig. 3B), suggests that this Fast-X region may represent a recent addition to the X Chromosome.Complete dosage compensationComplete sex chromosome dosage compensation has evolved many times (Mank 2009, 2013) through a variety of mechanisms (Gu and Walters 2017) in both...
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Research: Hybridization drives mitochondrial DNA degeneration and metabolic shift in a species with biparental mitochondrial inheritance
- Mathieu Hénault,
- Souhir Marsit,
- Guillaume Charron,
- and Christian R. Landry
Genome Res. November/December 2022 32: 2043-2056; Published in Advance November 9, 2022, doi:10.1101/gr.276885.122
...undomesticated isolates of Saccharomyces paradoxus and Saccharomyces cerevisiae. Each cross was independently replicated 48 to 96 times, and the resulting 864 hybrids were evolved under relaxed selection for mitochondrial function. Genome sequencing of 446 MA lines revealed extensive mtDNA recombination...
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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
...age of the sex chromosomes in model systems makes it difficult to study how the complex regulatory mechanisms underlying chromosome-wide dosage compensation can evolve. The sex chromosomes of Poecilia picta have undergone recent and rapid divergence, resulting in widespread gene loss on the male Y...
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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
...Hadar Medini and Dan Mishmar Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel Corresponding author: dmishmar@bgu.ac.ilAbstractInteractions between mitochondrial and nuclear factors are essential to life. Nevertheless, the importance of coordinated...
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Resource: A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state
- Jack F. Cazet,
- Stefan Siebert,
- Hannah Morris Little,
- Philip Bertemes,
- Abby S. Primack,
- Peter Ladurner,
- Matthias Achrainer,
- Mark T. Fredriksen,
- R. Travis Moreland,
- Sumeeta Singh,
- Suiyuan Zhang,
- Tyra G. Wolfsberg,
- Christine E. Schnitzler,
- Andreas D. Baxevanis,
- Oleg Simakov,
- Bert Hobmayer,
- and Celina E. Juliano
Genome Res. February 2023 33: 283-298; Published in Advance January 13, 2023, doi:10.1101/gr.277040.122
...A chromosome-scale epigenetic map of the Hydra reveals conserved regulators of cell state Jack F. Cazet1, Stefan Siebert1,2, Hannah Morris Little1, Philip Bertemes3, Abby S. Primack1, Peter Ladurner3, Matthias Achrainer3, Mark T. Fredriksen4, R. Travis Moreland4, Sumeeta Singh4, Suiyuan Zhang4...

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