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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. April 2026 36: 849-864; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...of mouse substantia nigra across ageTo investigate cell type–specific transcriptomic and epigenetic changes associated with aging in the substantia nigra, we profiled this brain region in mice at four different age stages: 2 months (adolescent), 6 months (mature adult), 12 months (middle-aged), and 18...
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Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
- Sarah M. Leichter,
- Kami Ahmad,
- and Steven Henikoff
Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
...at lysine 27 (H3K27me3) (Emerson and Lee 2023). For example, global gains in H3K27me3 and widespread heterochromatinization have been observed in the livers of aged mice (Yang et al. 2023) and in the muscles of aging Drosophila (Ma et al. 2018), leading to transcriptional silencing. Forcing aged mouse liver...
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Research: Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells
- Parijat Senapati,
- Masaru Miyano,
- Rosalyn W. Sayaman,
- Mudaser Basam,
- Amy Leung,
- Mark A. LaBarge,
- and Dustin E. Schones
Genome Res. August 2023 33: 1229-1241; Published in Advance July 18, 2023, doi:10.1101/gr.277511.122
...in mammalian s is to repress transposable elements (TEs). The widespread methylation loss that is commonly observed in cancer cells results in the loss of epigenetic repression of TEs. The aging process is similarly characterized by changes to the methylome. However, the impact of these epigenomic alterations...
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Research: Massive reshaping of genome–nuclear lamina interactions during oncogene-induced senescence
- Christelle Lenain,
- Carolyn A. de Graaf,
- Ludo Pagie,
- Nils L. Visser,
- Marcel de Haas,
- Sandra S. de Vries,
- Daniel Peric-Hupkes,
- Bas van Steensel,
- and Daniel S. Peeper
Genome Res. October 2017 27: 1634-1644; Published in Advance September 15, 2017, doi:10.1101/gr.225763.117
...cells (Shah et al. 2013). In another study, FAIRE-seq analysis revealed a widespread change in the distribution of open and closed chromatin (De Cecco et al. 2013). Also, bisulfite-sequencing analysis identified large domains of hypomethylation and focal hypermethylation events in senescent cells, which...
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Research: Hydroxycarbamide effects on DNA methylation and gene expression in myeloproliferative neoplasms
- Stephania Contreras Castillo,
- Bertille Montibus,
- Azucena Rocha,
- Will Duke,
- Ferdinand von Meyenn,
- Donal McLornan,
- Claire Harrison,
- Ann Mullally,
- Reiner Schulz,
- and Rebecca J. Oakey
Genome Res. August 2021 31: 1381-1394; Published in Advance July 9, 2021, doi:10.1101/gr.270066.120
...for the first time two clinically relevant cell types from an epigenomic and transcriptomic point of view using an established MPN mouse model and MPN patients’ samples from a longitudinal study.In mouse LSK cells, HC restores expression of a subset of genes abnormally expressed in the Jak2VF mutant mouse model...
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Research: L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis
- Stephanie N. Schauer,
- Patricia E. Carreira,
- Ruchi Shukla,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Francisco J. Sanchez-Luque,
- Paola Nicoli,
- Michaela Kindlova,
- Serena Ghisletti,
- Alexandre Dos Santos,
- Delphine Rapoud,
- Didier Samuel,
- Jamila Faivre,
- Adam D. Ewing,
- Sandra R. Richardson,
- and Geoffrey J. Faulkner
Genome Res. May 2018 28: 639-653; Published in Advance April 11, 2018, doi:10.1101/gr.226993.117
..., inflammatory cholangitis, pre-neoplastic lesions and, ultimately, metastatic liver cancer (Smit et al. 1993; Mauad et al. 1994). We isolated 12 HCC tumor nodules and matching tail tissue from 10 Mdr2−/− mice at age 15 mo (Supplemental Table S1) and performed mouse retrotransposon capture sequencing (m...
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