Single-cell DNA methylation and 3D genome architecture in the human brain

IINTRODUCTION The intricate gene-regulatory mechanisms governing the diverse cell types within the brain are paramount to comprehending its functions in both health and disease. The recent surge in high-throughput epigenomic profiling has heralded groundbreaking revelations into these gene-regulatory frameworks. Particularly, DNA methylation, in conjunction with the three-dimensional (3D) chromatin formations, underpins the fundamentals of gene regulation. This study comprehensively analyzed DNA methylation and chromatin conformation in adult human brain cells spanning multiple regions.RATIONALE Gene expression in brain cells is modulated by DNA methylation and chromatin conformation, and a profound correlation exists between these processes. We can better understand the human brain's gene-regulatory intricacies by deeply probing these epigenomic characteristics in single cells. This study set out to meticulously chart the DNA methylation landscapes and chromatin structures in adult human brain cells.RESULTS The study revealed epigenome-based brain cell-type classifications, elucidating diverse categorizations grounded on their epigenomic imprints. Discernible differences in the chromatin contact distances between neurons and non-neurons were discovered. Insight into the 3D genome organization of brain cells was gleaned from compartments, domains, and loops and their relationship with chromatin accessibility and gene expression. Further, there emerged a distinctive cell-type specificity in the 3D genome features. The study also unearthed patterns of cell-specific DNA methylation and its overarching implications on the gene-regulatory networks. Regional disparities in cortices and basal ganglia were uncovered. A comparative exploration underscored the conservation of brain cell types and DMRs between humans and mice. Finally, the inception of single-cell methylation barcodes (scMCodes) showcased immense promise in precisely identifying human brain cell types.CONCLUSION This comprehensive investigation presents a single-cell DNA methylation and 3D genome structure atlas of the human brain. It illuminates the cell-type specificity and diverse epigenetic architectures of cells across the brain. This epigenomic atlas promises to be a valuable resource, fueling further discoveries in brain cell diversity, gene regulation mechanisms, and the genesis of new genetic tools. DNA methylation and chromatin conformation profiling in the human brain. DNA methylation and chromatin conformation were probed at single-cell resolution in 517 thousand cells from 46 regions of three adult human brains. The comprehensive investigation allowed in-depth analysis of cell-type complexity, epigenetic diversity for gene regulation, comparison between human and mouse brains, and construction of brain cell-type methylation barcodes.