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Proc Natl Acad Sci U S A. 2014 Oct 21;111(42):E4468-77. doi: 10.1073/pnas.1405266111. Epub 2014 Oct 7.

CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors.

Author information

1
Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114; Departments of Neurology and.
2
Molecular Neurogenetics Unit and Departments of Neurology and.
3
Center for Human Disease Modeling and.
4
Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114;
5
Molecular Neurogenetics Unit and.
6
Departments of Pediatrics, Medical Genetics, and Pathology, The Thompson Center for Autism and Neurodevelopmental Disorders, University of Missouri Hospitals and Clinics, Columbia, MO 65201;
7
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139; and Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142.
8
Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114; Departments of Neurology and Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142.
9
Center for Human Disease Modeling and Department of Cell Biology, Duke University, Durham, NC 27710;
10
Molecular Neurogenetics Unit and Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142 Genetics, Harvard Medical School, Boston, MA 02115;
11
Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114; Departments of Neurology and Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142 talkowski@chgr.mgh.harvard.edu.

Abstract

Truncating mutations of chromodomain helicase DNA-binding protein 8 (CHD8), and of many other genes with diverse functions, are strong-effect risk factors for autism spectrum disorder (ASD), suggesting multiple mechanisms of pathogenesis. We explored the transcriptional networks that CHD8 regulates in neural progenitor cells (NPCs) by reducing its expression and then integrating transcriptome sequencing (RNA sequencing) with genome-wide CHD8 binding (ChIP sequencing). Suppressing CHD8 to levels comparable with the loss of a single allele caused altered expression of 1,756 genes, 64.9% of which were up-regulated. CHD8 showed widespread binding to chromatin, with 7,324 replicated sites that marked 5,658 genes. Integration of these data suggests that a limited array of direct regulatory effects of CHD8 produced a much larger network of secondary expression changes. Genes indirectly down-regulated (i.e., without CHD8-binding sites) reflect pathways involved in brain development, including synapse formation, neuron differentiation, cell adhesion, and axon guidance, whereas CHD8-bound genes are strongly associated with chromatin modification and transcriptional regulation. Genes associated with ASD were strongly enriched among indirectly down-regulated loci (P < 10(-8)) and CHD8-bound genes (P = 0.0043), which align with previously identified coexpression modules during fetal development. We also find an intriguing enrichment of cancer-related gene sets among CHD8-bound genes (P < 10(-10)). In vivo suppression of chd8 in zebrafish produced macrocephaly comparable to that of humans with inactivating mutations. These data indicate that heterozygous disruption of CHD8 precipitates a network of gene-expression changes involved in neurodevelopmental pathways in which many ASD-associated genes may converge on shared mechanisms of pathogenesis.

KEYWORDS:

CHD8; ChIP-seq; NPCs; RNA-seq; autism

PMID:
25294932
PMCID:
PMC4210312
DOI:
10.1073/pnas.1405266111
[Indexed for MEDLINE]
Free PMC Article

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