Local and global chromatin interactions are altered by large genomic deletions associated with human brain development

Xianglong Zhang, Ying Zhang, Xiaowei Zhu, Carolin Purmann, Michael S. Haney, Thomas Ward, Arineh Khechaduri, Jie Yao, Sherman M. Weissman and Alexander E. Urban ()
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Xianglong Zhang: Stanford University School of Medicine
Ying Zhang: Yale University
Xiaowei Zhu: Stanford University School of Medicine
Carolin Purmann: Stanford University School of Medicine
Michael S. Haney: Stanford University School of Medicine
Thomas Ward: Stanford University School of Medicine
Arineh Khechaduri: Stanford University School of Medicine
Jie Yao: Yale University School of Medicine
Sherman M. Weissman: Yale University
Alexander E. Urban: Stanford University School of Medicine

Nature Communications, 2018, vol. 9, issue 1, 1-15

Abstract: Abstract Large copy number variants (CNVs) in the human genome are strongly associated with common neurodevelopmental, neuropsychiatric disorders such as schizophrenia and autism. Here we report on the epigenomic effects of the prominent large deletion CNVs on chromosome 22q11.2 and on chromosome 1q21.1. We use Hi-C analysis of long-range chromosome interactions, including haplotype-specific Hi-C analysis, ChIP-Seq analysis of regulatory histone marks, and RNA-Seq analysis of gene expression patterns. We observe changes on all the levels of analysis, within the deletion boundaries, in the deletion flanking regions, along chromosome 22q, and genome wide. We detect gene expression changes as well as pronounced and multilayered effects on chromatin states, chromosome folding and on the topological domains of the chromatin, that emanate from the large CNV locus. These findings suggest basic principles of how such large genomic deletions can alter nuclear organization and affect genomic molecular activity.

Date: 2018
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DOI: 10.1038/s41467-018-07766-x

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