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Davis KN, Qu PP, Ma S, Lin L, Plastini M, Dahl N, Plazzi G, Pizza F, O’Hara R, Wong WH, Hallmayer J, Mignot E, Zhang X, Urban AE. Mutations in human DNA methyltransferase DNMT1 induce specific genome-wide epigenomic and transcriptomic changes in neurodevelopment. Hum Mol Genet 2023; 32:3105-3120. [PMID: 37584462 PMCID: PMC10586194 DOI: 10.1093/hmg/ddad123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 08/17/2023] Open
Abstract
DNA methyltransferase type 1 (DNMT1) is a major enzyme involved in maintaining the methylation pattern after DNA replication. Mutations in DNMT1 have been associated with autosomal dominant cerebellar ataxia, deafness and narcolepsy (ADCA-DN). We used fibroblasts, induced pluripotent stem cells (iPSCs) and induced neurons (iNs) generated from patients with ADCA-DN and controls, to explore the epigenomic and transcriptomic effects of mutations in DNMT1. We show cell type-specific changes in gene expression and DNA methylation patterns. DNA methylation and gene expression changes were negatively correlated in iPSCs and iNs. In addition, we identified a group of genes associated with clinical phenotypes of ADCA-DN, including PDGFB and PRDM8 for cerebellar ataxia, psychosis and dementia and NR2F1 for deafness and optic atrophy. Furthermore, ZFP57, which is required to maintain gene imprinting through DNA methylation during early development, was hypomethylated in promoters and exhibited upregulated expression in patients with ADCA-DN in both iPSC and iNs. Our results provide insight into the functions of DNMT1 and the molecular changes associated with ADCA-DN, with potential implications for genes associated with related phenotypes.
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Affiliation(s)
- Kasey N Davis
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto CA 94304, USA
| | - Ping-Ping Qu
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto CA 94304, USA
| | - Shining Ma
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Ling Lin
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Center for Narcolepsy, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Melanie Plastini
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto CA 94304, USA
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology Sciences for Life Laboratory, Uppsala University BMC, Uppsala 75122, Sweden
| | - Giuseppe Plazzi
- IRCCS—Istituto delle Scienze Neurologiche di Bologna, Bologna 40139, Italy
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Fabio Pizza
- IRCCS—Istituto delle Scienze Neurologiche di Bologna, Bologna 40139, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40126, Italy
| | - Ruth O’Hara
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Wing Hung Wong
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Joachim Hallmayer
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Emmanuel Mignot
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Center for Narcolepsy, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Xianglong Zhang
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto CA 94304, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto CA 94304, USA
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