Searching journal content for articles similar to Cohen-Zinder et al. 15 (7): 936.

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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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Method: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
...-defining pattern in Simmental cattle where most of or all the head is depigmented against a pigmented body with white legs and underside, in addition to varying amounts and extent of white body spots as seen in other breeds such as Holstein and Montbéliarde. A typical Hereford animal is characterized by a white...
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Resource: Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle
- Alexander S. Leonard,
- Xena M. Mapel,
- and Hubert Pausch
Genome Res. February 2024 34: 300-309; Published in Advance February 14, 2024, doi:10.1101/gr.278267.123
...with this comprehensive variant set in a subset of 117 cattle that have testis transcriptome data, and find 92 structural variants as causal candidates for eQTL and 73 for sQTL. We find that roughly half of the top associated structural variants affecting expression or splicing are transposable elements, such as SV-eQTL...
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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
...functional diversification during evolution. In this study, we seek to identify the diversification and potential gene neofunctionalization of lung tumors in the TRACERx cohort. We develop a novel computational protocol to identify preduplication and postduplication mutations predicted to affect protein...
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Method: Highly efficient and scarless genome editing via essential gene-coupled homology-directed repair
- Joo Hye Yeo,
- Hyongbum Henry Kim,
- Sang Ho Oh,
- and Jinu Lee
Genome Res. April 15, 2026 gr.281194.125; Published in Advance April 15, 2026, doi:10.1101/gr.281194.125
...for HDR at the target 174 site, (4) sgRNA targeting an essential gene, and (5) donor DNA template for the 175 essential gene that contains synonymous mutations (Fig. 2A). These synonymous 176 mutations were incorporated to disrupt the protospacer adjacent motif (PAM) sequence 177 for preventing sg...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...of mutation rates in germline and soma. Genetics 207: 255–267. doi:10.1534/genetics.117.1114 ↵Choux C, Binquet C, Carmignac V, Bruno C, Chapusot C, Barberet J, Lamotte M, Sagot P, Bourc'his D, Fauque P. 2018. The epigenetic control of transposable elements and imprinted genes in newborns is affected...
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Resource: An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants
- Can Yuan,
- Lijing Tang,
- Thomas Lopdell,
- Vyacheslav A. Petrov,
- Claire Oget-Ebrad,
- Gabriel Costa Monteiro Moreira,
- José Luis Gualdrón Duarte,
- Arnaud Sartelet,
- Zhangrui Cheng,
- Mazdak Salavati,
- D. Claire Wathes,
- Mark A. Crowe,
- GplusE Consortium,
- Wouter Coppieters,
- Mathew Littlejohn,
- Carole Charlier,
- Tom Druet,
- Michel Georges,
- and Haruko Takeda
Genome Res. October 2023 33: 1848-1864; Published in Advance September 26, 2023, doi:10.1101/gr.277947.123
...expressed genes, 14,289 genes were retained for eQTL analyses in blood and 15,458 in liver. All samples were genotyped with a high-density SNV array interrogating 777,962 variants and imputed to whole using Minimac4 (Das et al. 2016) and the 264 sequenced Holstein animals as reference. This yielded usable...
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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
..., but these die as embryos, likely owing to a recessive lethal-effect mutation on the Maculatus Y. In XY males, this mutation is complemented by a gene on the X. The lethal-effect mutation on the Maculatus Y can also be complemented by alleles on Y Chromosomes from other populations (Winge 1922, 1938). Thus...
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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
...unit variance, yielding RT Z-scores. We then categorized the into 12 chromosomal domains with their mean RT Z-scores: two major autosomal arms and their pericentromeric regions, the 4th, X, and Y Chromosomes, and a gene consensus for the ribosomal DNA (rDNA) locus (Fig. 5B). This allowed us...
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Research: Ruminant-specific retrotransposons shape regulatory evolution of bovine immunity
- Conor J. Kelly,
- Carol G. Chitko-McKown,
- and Edward B. Chuong
Genome Res. August 2022 32: 1474-1486; Published in Advance August 10, 2022, doi:10.1101/gr.276241.121
...are a major source of cis-regulatory elements and have been repeatedly co-opted to regulate the expression of host genes (Chuong et al. 2016; Fuentes et al. 2018; Ye et al. 2020). The cattle harbors numerous ruminant-specific retrotransposons including bovine endogenous retroviruses (ERVs) and the Bov...

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