Deciphering Regulatory Networks of Autism Risk Genes: High Resolution Networks Using Ex Vivo and In Vivo Models of Neurodevelopment.

Background:

Recent gene discovery efforts in autism spectrum disorder (ASD) have identified regulatory genes such as the chromatin remodeler CHD8 to be important new contributors to ASD etiology. These and other ASD risk-associated genes are enriched in co-expression networks built from studies of gene expression in human midfetal cortex, suggesting that ASD pathogenesis may result from perturbation of member genes of these regulatory networks. Recently, we demonstrated that CHD8 regulates other ASD risk genes in human brain and human neural stem cells (hNSCs). Strikingly, CHD8 target genes are enriched for ASD risk genes that regulate gene expression, such as POGZ and CHD2, and this targeting is also detectable in mouse cortex.

Objectives:

To investigate ASD risk associated regulatory networks with high temporal and spatial resolution, we have undertaken studies to globally map regulatory targets of ASD risk-associated chromatin modifiers at an early stage of human neurodevelopment, and in specific cell types and brain regions during mouse embryonic cortical development.

Methods:

We are mapping the binding sites of CHD8, POGZ, and CHD2 in hNSCs using ChIP-seq. To facilitate uniform ChIP-seq methods, we have incorporated epitope tags using genome editing. To characterize global CHD8 targets in the developing mouse brain, we have generated a mouse line with a cre-activated epitope tag to allow purification of CHD8 complexes from specific cell types using cre driver lines.

Results:

Genome editing in hNSCs integrates epitope tags into the endogenous loci of selected ASD risk genes consistently and robustly. ChIP-seq performed with antibodies directed to the epitope tag in CHD8-tagged cells verifies ChIP-seq performed with native antibodies, and identifies additional ASD risk genes as CHD8 targets. Genome editing in mouse embryos has generated a similar epitope-tagged Chd8 gene in mice, and we are engaged in on-going efforts to characterize the Chd8 binding sites in specific cell-types using ChIP-seq.

Conclusions:

Correlation of ASD risk gene target maps with each other, and with maps of specific active and/or repressive histone modifications, will identify genes and regulatory elements commonly targeted by other ASD risk genes that are impacted by the CHD8 regulatory network.