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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
...and Amon 2011). Disorders like Down syndrome, caused by the triplication of Chromosome 21, and Cri du chat syndrome, caused by the deletion of a region of Chromosome 5p, affect the expression of hundreds of genes and perturb normal development. 8p syndrome, caused by rearrangements affecting the p arm...
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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
.... Genes that control the characteristic color traits could be genetically mapped on the X and Y Chromosomes (Winge 1922; Khoo et al. 1999; Lindholm and Breden 2002; Tripathi et al. 2009a). A genetic map based on EST- and BAC-derived markers was generated, and LG12 was identified as the sex chromosome...
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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
.... 2008) was run to further improve the gene structure annotation.X Chromosome identification via coverage in malesTo identify the X Chromosome, a male migratory locust was sequenced to nearly 30× coverage. The Illumina reads were aligned to our assembly with BWA-MEM (Li and Durbin 2009), and SAMtools (Li...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...map of pseudobulk gene expression for each DEG group across ages. Right: Top significant GO and KEGG enrichments for genes in each DEG group in oligodendrocytes subclass. Early-up, early upregulated DEGs in aging; Late-up, late upregulated DEGs in aging; Early-down, early downregulated DEGs in aging...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...regulation. By critically examining both established tools and emerging techniques such as editing, synthetic chromosomes, and high-resolution imaging, we provide a practical framework for investigators seeking to uncover direct regulators of specific genes. Our goal is to guide the design of experiments...
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Research: AGAP duplicons associate with structural diversity at Chromosome 10q11.22
- Stefania Fornezza,
- Vincenza Simona Delvecchio,
- William T. Harvey,
- Philip C. Dishuck,
- Evan E. Eichler,
- and Giuliana Giannuzzi
Genome Res. October 2024 34: 1487-1499; Published in Advance September 25, 2024, doi:10.1101/gr.279454.124
...by duplication at the pericentromeric region of ancestral Chromosome 10. Evolutionary genomic rearrangements, assembly gaps in ape references, and interlocus gene conversion hamper the identification of ancestral Chromosome 10 copies, 1:1 orthology relationships between ape s, and lineage-specific more recent...
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Method: BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries
- Yangyang Liu,
- Bingqiang Liu,
- and Juntao Liu
Genome Res. May 2025 35: 1194-1208; Published in Advance March 17, 2025, doi:10.1101/gr.279647.124
...2016; Norton et al. 2018; Chang et al. 2020). Taken together, precise and robust identification of TADs, hierarchical TADs, and partially overlapping TADs using Hi-C data are essential for a deeper understanding of 3D-folding mechanisms and their epigenetic and gene regulatory functions.In recent years...
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Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
- Taylor Anglen,
- Irene M. Kaplow,
- Baekgyu Choi,
- Enya Dewars,
- Robin M. Perelli,
- Kevin T. Hagy,
- Duc Tran,
- Megan E. Ramaker,
- Svati H. Shah,
- Inkyung Jung,
- Andrew P. Landstrom,
- Ravi Karra,
- Yarui Diao,
- and Charles A. Gersbach
Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
..., USA ↵10 Present address: Department of Biological Sciences and Ray and Stephanie Lane Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA Corresponding author: charles.gersbach@duke.eduAbstractA hallmark of heart disease is gene dysregulation and reactivation...
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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
...families based on their functions, including maltose transporter (MALT), enzymes that break down maltose (MALS), and genes that regulate the expression of the pathway (MALR). These genes are often organized into clusters and located near the ends of chromosomes (subtelomeric). To elucidate the origins...
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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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