Epigenetic dysregulation of SHANK3 in brain tissues from individuals with autism spectrum disorders
Open accessAbstract
The molecular basis for the majority of cases of autism spectrum disorders (ASD) remains unknown. We tested the hypothesis that ASD have an epigenetic cause by performing DNA methylation profiling of five CpG islands (CGI-1 to CGI-5) in the SHANK3 gene in postmortem brain tissues from 54 ASD patients and 43 controls. We found significantly increased overall DNA methylation (epimutation) in three intragenic CGIs (CGI-2, CGI-3 and CGI-4). The increased methylation was clustered in the CGI-2 and CGI-4 in ∼15% of ASD brain tissues. SHANK3 has an extensive array of mRNA splice variants resulting from combinations of five intragenic promoters and alternative splicing of coding exons. Altered expression and alternative splicing of SHANK3 isoforms were observed in brain tissues with increased methylation of SHANK3 CGIs in ASD brain tissues. A DNA methylation inhibitor modified the methylation of CGIs and altered the isoform-specific expression of SHANK3 in cultured cells. This study is the first to find altered methylation patterns in SHANK3 in ASD brain samples. Our finding provides evidence to support an alternative approach to investigating the molecular basis of ASD. The ability to alter the epigenetic modification and expression of SHANK3 by environmental factors suggests that SHANK3 may be a valuable biomarker for dissecting the role of gene and environment interaction in the etiology of ASD.
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Increased levels of SHANK3 DNA methylation, corresponding to decreased isoform-specific expression of SHANK3, have been observed in postmortem brain tissues of ASD patients compared with neurotypical control tissues.
“and increased levels of SHANK3 DNA methylation, corresponding to decreased isoform-specific expression of SHANK3, have been observed in postmortem brain tissues of ASD patients compared with neurotypical control tissues [ 162 ].”
From DNA methylation: a mechanism linking environmental chemical exposures to risk of autism spectrum disorders? (2016) · cites this paper as [162]
SHANK3 expression in brain and other tissues is regulated by DNA methylation.
“SHANK3 expression in brain and other tissues is regulated by DNA methylation [ 161 , 162 ], and increased levels of SHANK3 DNA methylation, corresponding to decreased isoform-specific expression of SHANK3, have been observed in postmortem brain tissues of ASD patients compared with neurotypical control tissues [ 162 ].”
From DNA methylation: a mechanism linking environmental chemical exposures to risk of autism spectrum disorders? (2016) · cites this paper as [162]
Recent reports have linked individual microexons with neurodevelopmental disorders, including ASD, schizophrenia, and epilepsy.
“recent reports have begun to link individual microexons with neurodevelopmental disorders, including ASD (Zhu et al., 2014), schizophrenia (Ovadia and Shifman, 2011) and epilepsy (Rusconi et al., 2014)”
From A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains (2014) · cites this paper as Zhu et al., 2014
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- Authors
- Zhu, L., Wang, X., Li, X.-L., Towers, A., Cao, X., Wang, P., Bowman, R., Yang, H., Goldstein, J., Li, Y.-J., & Jiang, Y.-H.
- Affiliations
- Duke University (US)
- Corresponding author
- Jiang, Yong-Hui
- Venue
- Human Molecular Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-11-01
- Volume
- 23
- Issue
- 6
- Pages
- 1563-1578
- ISSN
- 0964-6906 (ISSN-L)
- 1460-2083
- PMC
- PMC3929093
- OpenAlex
- W2146527331
- Cited by
- 147
- References
- 71
- Citations by year
- 2026: 8 · 2025: 8 · 2024: 10 · 2023: 16 · 2022: 10 · 2021: 16 · 2020: 11 · 2019: 11 · 2018: 7 · 2017: 8 · 2016: 17 · 2015: 16 · 2014: 9
- FWCI
- 7.68
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Human Molecular Genetics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Autism Speaks
- National Institute of Mental Health (R01MH098114)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (K12HD043494)
- Topics
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- autism spectrum disorder, SHANK3, DNA methylation, epigenetic dysregulation, CpG islands, postmortem brain, alternative splicing, splice variants, DNA methylation inhibitors, biomarkers, gene-environment interaction, ASD etiology
- MeSH terms
- Brain, Child Development Disorders, Pervasive, Exons, Gene Expression Regulation, Humans, Nerve Tissue Proteins, Promoter Regions, Genetic, Alternative Splicing, CpG Islands, DNA Methylation, Protein Isoforms, Epigenesis, Genetic, Cell Line, Tumor, HEK293 Cells, Gene-Environment Interaction
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