Functional organization of the human 4D Nucleome

The 4D organization of the interphase nucleus, or the 4D Nucleome (4DN), reflects a dynamical interaction between 3D genome structure and function and its relationship to phenotype. We present initial analyses of the human 4DN, capturing genome-wide structure using chromosome conformation capture and 3D imaging, and function using RNA-sequencing. We introduce a quantitative index that measures underlying topological stability of a genomic region. Our results show that structural features of genomic regions correlate with function with surprising persistence over time. Furthermore, constructing genome-wide gene-level contact maps aided in identifying gene pairs with high potential for coregulation and colocalization in a manner consistent with expression via transcription factories. We additionally use 2D phase planes to visualize patterns in 4DN data. Finally, we evaluated gene pairs within a circadian gene module using 3D imaging, and found periodicity in the movement of clock circadian regulator and period circadian clock 2 relative to each other that followed a circadian rhythm and entrained with their expression. Significance We explored the human genome as a dynamical system. Using a data-guided mathematical framework and genome-wide assays, we interrogated the dynamical relationship between genome architecture (structure) and gene expression (function) and its impact on phenotype, which defines the 4D Nucleome. Structure and function entrained with remarkable persistence in genes that underlie wound healing processes and circadian rhythms. Using genome-wide intragene and intergene contact maps, we identified gene networks with high potential for coregulation and colocalization, consistent with expression via transcription factories. In an intriguing example, we found periodic movements of circadian genes in three dimensions that entrained with expression. This work can be broadly applied to identifying genomic signatures that define critical cell states during differentiation, reprogramming, and cancer.