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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
..., as no individual dosage-sensitive gene within this region has been demonstrated to drive pathological development, and individuals with this disorder exhibit significant variability in the size and location of the chromosomal rearrangements (Lo Bianco et al. 2020; Okur et al. 2021; Vibert et al. 2022).A number...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...”) number and subsequent divergence of function (Hahn 2009).Approximately 75% of lung cancers have WGD events during their evolutionary history (Jamal-Hanjani et al. 2017). Furthermore, changes in gene copy number owing to aneuploidy, in which chromosomes or chromosomal regions are gained or lost, represent...
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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
.... Shown are the location and identification of regions that are replicating earlier in the indicated comparison. (E) The sum total genomic size of pairwise comparisons that are replicating earlier in the specified cell comparison for the left and right arms of Chromosome 2. Statistical significance...
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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
...(Tripathi et al. 2009a,b). Several markers including the most distal genetic marker M_229 (located in the cyclin I gene) (Tripathi et al. 2009a,b) differentiating X and Y were located by molecular cytogenetic analysis on the homologous chromosomes of different guppy populations and the two sister species...
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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
...1. Host/nested gene pair identification. Schematic of the pipeline used to generate the list of host/nested gene pairs.Hosts harbor nested genes preferentially inside a long intron and show no strong orientation biasTo identify any preferences of host/nested gene structure and location, we performed...
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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
...AGAP4 genomic sequence as query, we identified the location of Chromosome 10 AGAP genes in the chimpanzee (panTro6), gorilla (gorGor6), and orangutan (ponAbe3) s. In chimpanzee, we identified AGAP sequences at five locations on Chromosome 10, as well as complete or partial alignments in four...
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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 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
..., Opalin, Septin4, Il33, Ccp110 gene loci (Fig. 4E, Supplemental Fig. S9A). Apod, a 259 member of the lipocalin family, is elevated in brains of aging and neurodegenerative disorders, 260 and its increased levels in glial cells surrounding dopaminergic neurons in the brains of PD 261 might be linked...
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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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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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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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