Researchers sequenced nearly 85,000 regulatory regions of the genome in 600 individuals with autism (200 parent-child trios) who had no detectable coding mutations. Using deep learning and single-cell RNA sequencing from both post-mortem ASD brains and cortical organoids, they found that many rare non-coding variants disrupt CTCF chromatin boundary elements and alter gene regulation in a cell-type-specific way. Notably, genes targeted by de novo regulatory variants — including POGZ, a known White-Sutton syndrome gene — showed dynamic, stage-specific expression in developing brain cell types such as outer radial glia and oligodendrocytes. The findings suggest that non-coding mutations contribute meaningfully to ASD risk and often affect the same genes disrupted by coding mutations identified in large-scale sequencing studies.