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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...is characterized by permissive marks, including H3K4me2/me3 (Fournier et al. 2002; McEwen and Ferguson-Smith 2010). Accordingly, at the -wide level, ICRs are discrete regions with a four-mark signature comprising partial DNA methylation, H3K4me3, H3K9me3, and H4K20me3 in somatic cells.With the exception...
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Research: H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells
- Agustín F. Fernández,
- Gustavo F. Bayón,
- Rocío G. Urdinguio,
- Estela G. Toraño,
- María G. García,
- Antonella Carella,
- Sandra Petrus-Reurer,
- Cecilia Ferrero,
- Pablo Martinez-Camblor,
- Isabel Cubillo,
- Javier García-Castro,
- Jesús Delgado-Calle,
- Flor M. Pérez-Campo,
- José A. Riancho,
- Clara Bueno,
- Pablo Menéndez,
- Anouk Mentink,
- Katia Mareschi,
- Fabian Claire,
- Corrado Fagnani,
- Emanuela Medda,
- Virgilia Toccaceli,
- Sonia Brescianini,
- Sebastián Moran,
- Manel Esteller,
- Alexandra Stolzing,
- Jan de Boer,
- Lorenza Nisticò,
- Maria A. Stazi,
- and Mario F. Fraga
Genome Res. January 2015 25: 27-40; Published in Advance September 30, 2014, doi:10.1101/gr.169011.113
...strongly enriched in the active chromatin mark H3K4me1 in stem and differentiated cells, suggesting this is a cell type–independent chromatin signature of DNA hypomethylation during aging. Analysis of scedasticity showed that interindividual variability of DNA methylation increased during aging in MSCs...
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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
...Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells Jennifer A. Urban1, Daniel Ringwalt1, John M. Urban2,3, Wingel Xue1,5, Ryan Gleason1, Keji Zhao4 and Xin Chen1,2 1Department of Biology, The Johns Hopkins University...
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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
...cells to re-enter the cell cycle partially restores a youthful H3K27me3 landscape, suggesting that DNA replication may rejuvenate chromatin structure (Yang et al. 2023). However, even mitotically active somatic stem cells display age-related increases in Polycomb repression: Aged Drosophila intestinal...
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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
...19 20 21 2 Abstract 22 Parkinson’s disease (PD) is a prevalent neurodegenerative disorder predominantly affecting 23 individuals over 60. Its motor symptoms stem from the deterioration of dopaminergic neurons 24 within the substantia nigra. Despite aging being a significant risk factor, the specific...
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Research: Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations
- Xiu Fan,
- Qili Qian,
- Wenran Li,
- Tianzi Liu,
- Changqing Zeng,
- Peilin Jia,
- Huandong Lin,
- Xin Gao,
- Li Jin,
- Mingfeng Xia,
- Sijia Wang,
- and Fan Liu
Genome Res. October 2025 35: 2173-2188; Published in Advance August 1, 2025, doi:10.1101/gr.280155.124
...and stochastic accumulation of epigenetic changes, such as DNA methylation variability, with advancing age. Although increasingly recognized for its potential role in aging biology, its extent, biological significance, and population specificity remain insufficiently characterized. Here, we present the first...
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Research: Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
- Marcel Tarbier,
- Sebastian D. Mackowiak,
- Vaishnovi Sekar,
- Franziska Bonath,
- Etka Yapar,
- Bastian Fromm,
- Omid R. Faridani,
- Inna Biryukova,
- and Marc R. Friedländer
Genome Res. February 2026 36: 291-302; Published in Advance January 12, 2026, doi:10.1101/gr.279914.124
...resuspended in 2i media (about 106 cells/mL), DNA-stained with 10 µg/mL Hoechst-33342 (Sigma-Aldrich 14533) for 15 min at 37°C, and then stained with 1 µg/mL propidium iodide (Sigma-Aldrich P4864) to reveal cell viability. Single cells were sorted in G2/M using a BD Influx (BD Bioscience) into 96-well plates...
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Research: Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice
- Leandros Boukas,
- Teresa Romeo Luperchio,
- Afrooz Razi,
- Kasper D. Hansen,
- and Hans T. Bjornsson
Genome Res. May 2024 34: 696-710; Published in Advance May 3, 2024, doi:10.1101/gr.278416.123
..., answering this question is important for understanding the potential of DNA methylation–based episignatures (Aref-Eshghi et al. 2021; Levy et al. 2022a) to shed light on the pathogenesis of the disorders. Although these episignatures are almost exclusively derived from whole blood, there is increasing...
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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...of candidate selection. (C) The experimental workflow. Sheared genomic DNA was hybridized to probes specific for the candidate enhancer regions. These regions were then cloned into the STARR-seq plasmid and transfected into phNPCs. (D,E) The fold change correlation between the two technical replicates...
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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...expression. Coordinates were rearranged so that the start/end of COL11A2, the extended class II gene adjacent in s to class II, is given coordinate 0. Pseudogenes are marked with asterisks. Upper right: MHC-I/MHC-like (if any) genes located outside the main MHC region. Lower part: The zoomed in “core” MHC...

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