Chromatin Looping Defects in Neurodevelopmental Disorders Linked to CHD8 Mutations

Abstract

CHD8 is among the highest-confidence risk genes for autism spectrum disorder, yet how heterozygous
loss-of-function mutations in this ATP-dependent chromatin remodeler translate into altered three-dimensional
genome architecture during human neurodevelopment remains poorly resolved. Here we generated isogenic
CHD8+/- human induced pluripotent stem cell lines by CRISPR-Cas9 editing and differentiated them alongside
isogenic wild-type controls into dorsal forebrain cortical organoids, profiling chromatin looping by in situ Hi-C, CHD8
and CTCF occupancy by chromatin immunoprecipitation sequencing (ChIP-seq), and chromatin accessibility by
ATAC-seq across three differentiation time points spanning progenitor expansion and early neurogenesis. CHD8
occupancy overlapped extensively with CTCF and cohesin subunit RAD21 at loop anchors genome-wide, and
CHD8 haploinsufficiency caused measurable weakening of a defined subset of these anchors, disproportionately
concentrated at loops flanking genes previously implicated in synaptic development and neuronal differentiation.
Loop weakening at these anchors was accompanied by reduced insulation across the corresponding domain
boundaries and altered expression of genes within the affected domains, including several additional
autism-associated loci not directly bound by CHD8, consistent with indirect dysregulation through local architectural
change rather than direct promoter occupancy alone. ATAC-seq revealed a parallel, partial loss of accessibility at
CHD8-dependent anchors that preceded detectable expression changes during early differentiation, suggesting
that architectural weakening is an early event relative to downstream transcriptional dysregulation. These findings
connect CHD8 haploinsufficiency to a discrete, anchor-specific pattern of chromatin looping defects during human
corticogenesis and provide a mechanistic bridge between a leading autism risk gene and altered three-dimensional
regulation of neurodevelopmental gene expression programs.