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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
...mutation rate across vertebrates. Nature 615: 285–291. doi:10.1038/s41586-023-05752-y ↵Bonduelle M. 2002. Prenatal testing in ICSI pregnancies: incidence of chromosomal anomalies in 1586 karyotypes and relation to sperm parameters. Hum Reprod 17: 2600–2614. doi:10.1093/humrep/17.10.2600 ↵Bristow RG, Hill...
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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
...was below the threshold (see Methods).FIE genes showed signals of positive selection, assessed using dN/dS (Fig. 2A; Supplemental Note 4), indicating significant enrichment in missense, nonsense, splice, and truncating mutations compared with synonymous variants. Pancancer FIEs showed positive cancer effect...
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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
...a separate MER41_BT element located 19 kb upstream of the gene IFNAR2 (MER41_BT.IFNAR2), which encodes a membrane-bound receptor mediating type I interferon signaling. Bovine IFNAR2 shows IFNG-inducible expression in leukocytes, MDBK cells, and BL3.1 cells (Fig. 4A). IFNAR2 expression is also induced...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...DNA regions (such as gene spacer regions) to achieve spatiotemporal-specific epigenetic encoding (Suzuki and Bird 2008). Furthermore, k-mers frequently found in eukaryotic negative samples (e.g., “CCC,” “GGG,” “GCC,” etc.) potentially act as an “antimethylation” signal, analogous to the methylation...
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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
...introduce new elements, such as exogenous proteins, activating mutations, plasmids, artificial chromosomes, or knock-in modifications. Conversely, loss-of-function approaches remove specific factors using mutations, siRNA silencing, or gene-editing techniques. These modifications can be applied to either...
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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
...-specific long-range control element (a silencer) that causes ectopic expression of a 327-kb cluster of imprinted genes in postnatal skeletal muscle. ATAC-seq peaks overlapping the mutation site were called only in testis and tongue samples but not in skeletal muscle. (C) Bovine PLAG1 promoter region...
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Research: Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
- Benjamin D. Umans and
- Yoav Gilad
Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
...'s correlation > 0.6), five were identified as significant eGenes using our pseudobulk approach, with effects exclusively in cortical hem or radial glial cells. For example, among the top 12 eGenes is the cholesterol transporter ABCA1 (Pearson's correlation 0.77), which showed modest eQTL effects in our...
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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
...are largely unknown. Here, we profile -wide changes to gene expression and chromatin structure in cardiomyocytes derived from human pluripotent stem cells. We identify and characterize a gene regulatory element essential for regulating MYH6 expression, which encodes human fetal myosin. Using chromatin...
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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
...). qPCR of CLN8, UNC5D, and four other genes encoded within the rearranged region on 8p confirmed the changes in expression expected based on the copy number of these loci (Fig. 4D).Interestingly, we observed that a majority of differentially expressed genes were located outside of Chromosome 8p (Fig...
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Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
...of the Austrian Academy of Sciences, 1090 Vienna, Austria; 11Eric and Wendy Schmidt Center, The Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA Corresponding author: valentina.boeva@inf.ethz.chAbstractGene signature scoring is integral to single-cell RNA sequencing (scRNA-seq) data analysis...
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