Single-Cell Atlas of Transcription and Chromatin States Reveals Regulatory Programs in the Human Brain

SUMMARY Directly measuring chromatin states alongside transcription is essential for understanding how cell-type-specific regulatory programs are established and maintained in the adult human brain. We present a large-scale single-cell multimodal atlas generated by jointly profiling transcriptome with active (H3K27ac) and repressive (H3K27me3) histone modifications across 18 brain regions. We profile >750,000 nuclei spanning 160 cell types and integrate these data with chromatin accessibility, DNA methylation, 3D genome architecture, and spatial transcriptome. This framework annotates >500,000 regulatory elements and resolves cell-type-specific chromatin states. We link enhancers to target genes, infer gene regulatory networks, and classify chromatin interactions, revealing neuron-enriched long-range Polycomb repression of developmental genes. Integrating these maps with GWAS data and sequence-based model prioritizes noncoding variants, effector genes, and vulnerable cell types for neuropsychiatric disorders. Finally, cross-species comparisons show conserved activation but more divergent repression. Together, this study provides a functional reference for interpreting noncoding variants, epigenetic memory, and brain organization. HIGHLIGHTS Joint single-cell profiling of transcriptomes with active or repressive histone modification in >750,000 nuclei across adult human brain. Chromatin state annotation of >500,000 candidate cis-regulatory elements distinguishes active enhancers from accessible and Polycomb-repressed regions. Cell-type-resolved regulatory networks and sequence-based deep learning model prioritize functional neuropsychiatric risk variants. Spatial epigenomic imputation reveals laminar layer-specific Polycomb repression programs. Integration with 3D genome architecture reveals neuron-specific super long-range chromatin loops silencing early developmental genes. Evolutionary analysis uncovers conserved active regulatory grammar but divergent repressive landscape. Competing Interest Statement B.R. is a consultant of and has equity interests in Arima Genomics, Inc. B.R. is a cofounder of Epigenome Technologies Inc. J.R.E. is a scientific adviser for Zymo Research Inc. and Ionis Pharmaceuticals. The remaining authors declare no competing interests.