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Allele-specific open chromatin in human iPSC neurons elucidates functional disease variants
Open accessAbstract
Effects of allele-specific open chromatin: Genetic variants in noncoding regions of the genome may underlie the development of disease. However, we are just beginning to tease apart the function of such variants associated with neuropsychiatric disease. Using five types of neural progenitor cells derived from 20 human induced pluripotent stem cell lines, Zhang et al. looked at allele-specific open chromatin (ASoC) variants. Many ASoC variants overlapped with genomic elements, such as transcription factor binding sites, and loci identified in genome-wide association studies for neurological traits. From the experimental and computational analyses, they identified single-nucleotide polymorphisms and illuminate how one schizophrenia-associated variant affects neurodevelopment. Science , this issue p. 561
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“eSNP-karyotyping was performed for all cell lines used to eliminate potential chromosomal abnormalities, as previously described20,21.”
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Metadata
- Authors
- Zhang, S., Zhang, H., Zhou, Y., Qiao, M., Zhao, S., Kozlova, A., Shi, J., Sanders, A. R., Wang, G., Luo, K., Sengupta, S., West, S., Qian, S., Streit, M., Avramopoulos, D., Cowan, C. A., Chen, M., Pang, Z. P., Gejman, P. V., He, X., & Duan, J.
- Affiliations
- Endeavor Health (US)
- University of Chicago (US)
- National Cancer Institute (US)
- Johns Hopkins University (US)
- Harvard University (US)
- Rutgers, The State University of New Jersey (US)
- Corresponding author
- Zhang, Siwei
- Zhang, Hanwen
- Zhou, Yifan
- Qiao, Min
- Zhao, Siming
- He, Xin
- Duan, Jubao
- ORCID
- Venue
- Science
- Published
- 2020-07-31
- Volume
- 369
- Issue
- 6503
- Pages
- 561-565
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC7773145
- OpenAlex
- W3046891017
- Cited by
- 127
- References
- 88
- Citations by year
- 2026: 13 · 2025: 14 · 2024: 17 · 2023: 25 · 2022: 30 · 2021: 20 · 2020: 8
- FWCI
- 6.81
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- NIH Office of the Director (R01MH106575, R01MH116281, R01AG063175, R01MH110531, R01AA023797, R01MH113215)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- non-coding variants, chromatin accessibility, iPSC-derived neurons, brain development, transcription factor binding, enhancers, expression quantitative trait loci, chromatin interactions
- MeSH terms
- Alleles, Brain, Chromatin, Enhancer Elements, Genetic, Humans, Risk, Schizophrenia, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Induced Pluripotent Stem Cells
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