Spatial 3D genome organization controls the activity of bivalent chromatin during human neurogenesis

Subnuclear compartments including the nuclear lamina and speckles organize the genome in three-dimensional (3D) space and regulate gene expression. By studying the neurogenic cell lineage isolated directly from the human brain, we show that lamina association plays a dominant role in maintaining the lowly expressed, poised state of key developmental genes bivalent for H3K27me3 and H3K4me3. During neurogenesis, large regions of the genome relocate from the lamina to speckles, corresponding to enhanced resolution of bivalent chromatin to monovalent H3K4me3 and a ~7-fold increase in transcription. Using cell culture models of human neurogenesis, we confirm the bivalent state of lamina-associated genes and provide further evidence that lamina association contributes strongly to the low expression of bivalent genes independent of H3K27me3. These data support a model in which spatial location of genomic regions in relation to subnuclear structures plays a dominant role in regulating the activity of chromatin state and lineage-specific gene expression. Overall design: LaminB1 GO-CaRT followed by sequential ChIP (LaminB1 GO-CaRT.ChIP-reChIP) and H3K27me3/H3K4me3 CUT&RUN of iPSC-derived NPCs; LaminB1 CUT&Tag, H3K27me3/H3K4me3 CUT&Tag of iPSC-derived NPCs and iPSC-derived neurons (iN); LaminB1 GO-CaRT and H3K27me3/H3K4me3 CUT&RUN of ESC-derived NPCs treated with DMSO or EZH2 inhibitor, EPZ-6438; H3K27me3 CUT&RUN and LaminB1 GO-CaRT of HEK293T cells with or without Fab blocking