Distinct nuclear compartment-associated genome architecture in the developing mammalian brain

Nuclear compartments are thought to play a role in 3-dimensional (3D) genome organization and gene expression. In mammalian brain, the architecture and dynamics of nuclear compartment-associated genome organization is not known. Here we develop Genome Organization using CUT and RUN Technology (GO-CaRT) to map genomic interactions with two nuclear compartments – the nuclear lamina and nuclear speckles – from different regions of the developing mouse, macaque and human brain. Lamina-associated domain (LAD) architecture in cells in vivo is distinct from that of cultured cells, including major differences in LADs previously considered cell-type invariant. In the mouse and human forebrain, dorsal and ventral neural precursor cells (NPCs) have differences in LAD architecture that correspond to their regional identity. LADs in the human and mouse cortex contain transcriptionally highly active sub-domains characterized by broad depletion of histone-3-lysine-9 di-methylation (H3K9me2). Evolutionarily conserved LADs in human, macaque and mouse brain are enriched for transcriptionally active neural genes associated with synapse function. By integrating GO-CaRT maps with genome-wide association study (GWAS) data, we find speckle-associated domains (SPADs) to be enriched for schizophrenia risk loci, indicating a physical relationship between these disease-associated genetic variants and a specific nuclear structure. Our work lays a framework for understanding the relationship between distinct nuclear compartments and genome function in brain development and disease.