Common CHD8 Genomic Targets Contrast With Model-Specific Transcriptional Impacts of CHD8 Haploinsufficiency.

A Ayanna Wade,Kenneth Lim,Alex S Nord,Rinaldo Catta-Preta

doi:10.3389/fnmol.2018.00481

Abstract

The packaging of DNA into chromatin determines the transcriptional potential of cells and is central to eukaryotic gene regulation. Case sequencing studies have revealed mutations to proteins that regulate chromatin state, known as chromatin remodeling factors, with causal roles in neurodevelopmental disorders. Chromodomain helicase DNA binding protein 8 (CHD8) encodes a chromatin remodeling factor with among the highest de novo loss-of-function mutation rates in patients with autism spectrum disorder (ASD). However, mechanisms associated with CHD8 pathology have yet to be elucidated. We analyzed published transcriptomic data across CHD8 in vitro and in vivo knockdown and knockout models and CHD8 binding across published ChIP-seq datasets to identify convergent mechanisms of gene regulation by CHD8. Differentially expressed genes (DEGs) across models varied, but overlap was observed between downregulated genes involved in neuronal development and function, cell cycle, chromatin dynamics, and RNA processing, and between upregulated genes involved in metabolism and immune response. Considering the variability in transcriptional changes and the cells and tissues represented across ChIP-seq analysis, we found a surprisingly consistent set of high-affinity CHD8 genomic interactions. CHD8 was enriched near promoters of genes involved in basic cell functions and gene regulation. Overlap between high-affinity CHD8 targets and DEGs shows that reduced dosage of CHD8 directly relates to decreased expression of cell cycle, chromatin organization, and RNA processing genes, but only in a subset of studies. This meta-analysis verifies CHD8 as a master regulator of gene expression and reveals a consistent set of high-affinity CHD8 targets across human, mouse, and rat in vivo and in vitro studies. These conserved regulatory targets include many genes that are also implicated in ASD. Our findings suggest a model where perturbation to dosage-sensitive CHD8 genomic interactions with a highly-conserved set of regulatory targets leads to model-specific downstream transcriptional impacts.

Highlights

Genetic studies have found that heterozygous loss-of-function mutations to chromatin remodeling genes significantly contribute to autism spectrum disorder (ASD) neurobiology, presumably through disruptions to transcriptional regulation in the developing and mature brain (O’Roak et al, 2012a,b; Parikshak et al, 2013; De Rubeis et al, 2014; Iossifov et al, 2014; Sanders et al, 2015; Vissers et al, 2016)
We tested the similarity between Differentially expressed genes (DEGs) across studies, finding significant overlap across some studies, with the strongest overlap among datasets testing the impact of heterozygous Chd8 mutation on mouse embryonic and postnatal brain (Figure 1F)
Simons Foundation Autism Research Initiative (SFARI) ASD genes associated with neurogenesis, axonogenesis, and synaptic signaling showed much lower representation in the high-affinity target sets. This meta-analysis of published genomic datasets from in vitro and in vivo mouse, human, and rat studies revealed both consistent and study-specific effects of chromodomain helicase DNA binding protein 8 (CHD8) haploinsufficiency on gene expression and largely concordant high-affinity CHD8 genomic interaction loci. Our results illustrate both the power and limitation of comparing genomic datasets and challenge previous assumptions regarding the regulatory mechanisms and transcriptional pathology associated with CHD8 haploinsufficiency

Summary

Introduction

Genetic studies have found that heterozygous loss-of-function mutations to chromatin remodeling genes significantly contribute to autism spectrum disorder (ASD) neurobiology, presumably through disruptions to transcriptional regulation in the developing and mature brain (O’Roak et al, 2012a,b; Parikshak et al, 2013; De Rubeis et al, 2014; Iossifov et al, 2014; Sanders et al, 2015; Vissers et al, 2016). As some CHD proteins demonstrate chromatin remodeling activity (Tong et al, 1998; Hall and Georgel, 2007; McKnight et al, 2011), CHD8 has been speculated to drive pathological changes in neurodevelopmental gene expression by targeting and remodeling chromatin at specific promoters and enhancers (Sugathan et al, 2014; Ceballos-Chávez et al, 2015; Cotney et al, 2015). This is supported by evidence that CHD8 can reposition nucleosomes in vitro and in mammalian cell culture (Thompson et al, 2008)

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Results

Conclusion