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Research: Autism spectrum disorder risk genes have convergent effects on transcription and neuronal firing patterns in primary neurons
- Alekh Paranjapye,
- Rili Ahmad,
- Steven Su,
- Abraham J. Waldman,
- Jennifer E. Phillips-Cremins,
- Shuo Zhang,
- and Erica Korb
Genome Res. November 2025 35: 2433-2444; Published in Advance October 20, 2025, doi:10.1101/gr.280698.125
...spiking and bursting patterns. This suggests that specific neuronal gene sets are particularly sensitive to multiple types of epigenetic manipulations and that disruption of these genes causes robust functional changes in neuronal firing.Both the analyses overlapping individual depletion DEGs...
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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
...–increased expression or decreased accessibility–decreased expression. (F) The enrichment (odds ratio) of the top-ranked genes (based on promoter differential accessibility) in the group of genes with CpG island promoters or in highly coexpressed epigenetic machinery genes. The enrichment is calculated by comparing...
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Research: Neurons show distinctive DNA methylation profile and higher interindividual variations compared with non-neurons
- Kazuya Iwamoto,
- Miki Bundo,
- Junko Ueda,
- Michael C. Oldham,
- Wataru Ukai,
- Eri Hashimoto,
- Toshikazu Saito,
- Daniel H. Geschwind,
- and Tadafumi Kato
Genome Res. May 2011 21: 688-696; Published in Advance April 5, 2011, doi:10.1101/gr.112755.110
...-neuronal cells, and neurons show a unique DNA methylation pattern that cannot be assessed using bulk cortex. We also found that the epigenetic signature in theprefrontal cortex appeared to be highly conserved between two species (Fig. 3C), although there were some exceptions (Supplemental Fig. 2B; Supplemental...
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Research: Methylomic trajectories across human fetal brain development
- Helen Spiers,
- Eilis Hannon,
- Leonard C. Schalkwyk,
- Rebecca Smith,
- Chloe C.Y. Wong,
- Michael C. O’Donovan,
- Nicholas J. Bray,
- and Jonathan Mill
Genome Res. March 2015 25: 338-352; Published in Advance February 3, 2015, doi:10.1101/gr.180273.114
...1995; Geschwind and Levitt 2007; Fatemi and Folsom 2009). Understanding the epigenomic changes occurring during fetal brain development could therefore provide useful insight about the molecular etiology of these conditions, especially given recent evidence for disease-associated epigenetic dysfunction...
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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
...ubiquitous gDMRs/ICRs throughout mouse development. In addition to these, so-called transient gDMRs can also resist preimplantation reprogramming but lose their allele-specific methylation either upon implantation or, more rarely, in a tissue-specific manner.In mammals, epigenetic patterns undergo...
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Resource: Single-nucleus transcriptomic mapping uncovers targets for traumatic brain injury
- Qiuyun Yang,
- Lingxuan Zhang,
- Manrui Li,
- Yang Xu,
- Xiaogang Chen,
- Ruixuan Yuan,
- Xiaofeng Ou,
- Min He,
- Miao Liao,
- Lin Zhang,
- Hao Dai,
- Meili Lv,
- Xiaoqi Xie,
- Weibo Liang,
- and Xiameng Chen
Genome Res. October 2023 33: 1818-1832; Published in Advance September 20, 2023, doi:10.1101/gr.277881.123
...TBI) is the most common type of traumatic brain injury (Silverberg et al. 2020). A single mTBI can trigger pathophysiological changes in the brain, resulting in acute neurological dysfunction and a range of subsequent postacute or chronic sequelae (Mychasiuk et al. 2014; Collins-Praino et al. 2018). Nevertheless...
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Research: Mosaic loss of Chromosome Y in aged human microglia
- Michael C. Vermeulen,
- Richard Pearse,
- Tracy Young-Pearse,
- and Sara Mostafavi
Genome Res. October 2022 32: 1795-1807; Published in Advance August 30, 2022, doi:10.1101/gr.276409.121
...Michael C. Vermeulen1, Richard Pearse2, Tracy Young-Pearse2 and Sara Mostafavi1,3 1Center for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada; 2Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA; 3Paul G...
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Research: Blood-derived mitochondrial DNA copy number is associated with gene expression across multiple tissues and is predictive for incident neurodegenerative disease
- Stephanie Y. Yang,
- Christina A. Castellani,
- Ryan J. Longchamps,
- Vamsee K. Pillalamarri,
- Brian O'Rourke,
- Eliseo Guallar,
- and Dan E. Arking
Genome Res. March 2021 31: 349-358; Published in Advance January 13, 2021, doi:10.1101/gr.269381.120
...energy demand cell types typically possessing higher levels of mtDNA-CN (Chabi et al. 2003; Miller et al. 2003; Clay Montier et al. 2009; Kelly et al. 2012). Due to the importance of mitochondria in metabolism and energy production, mitochondrial dysfunction plays a role in the etiology of many human...
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Research: Suppressor mutations in Mecp2-null mice implicate the DNA damage response in Rett syndrome pathology
- Adebola Enikanolaiye,
- Julie Ruston,
- Rong Zeng,
- Christine Taylor,
- Marijke Schrock,
- Christie M. Buchovecky,
- Jay Shendure,
- Elif Acar,
- and Monica J. Justice
Genome Res. April 2020 30: 540-552; Published in Advance April 21, 2020, doi:10.1101/gr.258400.119
...screen would be beneficial and representative for other diseases. RTT is a nearly monogenic disorder with >95% of patients carrying mutations in methyl-CpG-binding protein 2 (MECP2), a gene not present in invertebrates. MECP2 is central to neurological function and is associated with other diseases...
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