Joint profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations in single cells of the human brain

Abstract

AbstractThe dynamically organized chromatin complexes often involve multiplex chromatin interactions and sometimes chromatin-associated RNA. Here, we introduce theMulti-Nucleic Acid Interaction Mapping inSingleCell (MUSIC) technique to enable simultaneous profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations within a single nucleus. We applied MUSIC to profile >9,000 single nuclei in the human frontal cortex. MUSIC-derived single-nucleus transcriptomes provide a comprehensive categorization of cortical cell types, subtypes, and cellular states. The genomic sequences of highly expressed genes frequently co-complex with their flanking genomic regions, forming Gene-Expression-Associated Stripes (GEAS), which exemplify the intricate coordination between transcription and chromatin architecture at the single-cell level. Additionally, we observed significant heterogeneity among female cortical cells in the association between the XIST long non-coding RNA (lncRNA) and the X chromosome (XIST-chrX association, quantified as XAL). Cells with high XAL demonstrated a greater difference in spatial organization between the XIST-associated (Xi) and non-associated (Xa) X chromosomes compared to XAL-low cells. Notably, excitatory neurons displayed enrichment in XAL-high cells and exhibited a more pronounced disparity in spatial organization between Xi and Xa compared to other cell types. The MUSIC technique offers a powerful tool for future investigations into chromatin architecture and transcription at a cellular resolution within complex tissues.